Pierre Lindenbaum
2011-04-15
"Bioinformatics"[JOUR] or "Comput Appl Biosci"[JOUR]
7685
10000
Year
Count
OK
%
18
1
5
1995
1
0
0
1996
9
3
33
1997
13
3
23
1998
86
19
22
1999
70
17
24
2000
83
25
30
2001
110
64
58
2002
121
78
64
2003
284
170
59
2004
402
257
63
2005
495
359
72
2006
374
297
79
2007
448
381
85
2008
466
415
89
2009
507
462
91
2010
605
566
93
2011
283
268
94
http://-compare.org/
java.net.UnknownHostException : -compare.org
http://123d.ncifcrf.gov/
java.net.UnknownHostException : 123d.ncifcrf.gov
http://134.99.88.55/aio/
java.net.SocketTimeoutException : connect timed out
http://140.116.99.138/
200
http://144.16.71.146/cap/
java.net.NoRouteToHostException : No route to host
http://144.16.93.115/hb_page/index.html
java.net.NoRouteToHostException : No route to host
http://152.2.15.114/
java.net.SocketTimeoutException : connect timed out
http://166.111.201.7/help.html
java.net.SocketTimeoutException : connect timed out
http://166.111.201.7/MethCGI.html
java.net.SocketTimeoutException : connect timed out
http://166.111.24.5/webtools/TSSub/index.html
java.net.SocketTimeoutException : connect timed out
http://166.111.30.65/hying/fuzzy_loc.htm
java.net.SocketTimeoutException : connect timed out
http://202.120.37.186/bioinf/fold/PFP-Pred.htm
java.net.NoRouteToHostException : No route to host
http://202.127.30.184:8080/software.html
200
http://202.41.85.117/htmfiles/faculty/tsr/tsr.html
java.io.FileNotFoundException : http://202.41.85.117/htmfiles/faculty/tsr/tsr.html
http://203.195.151.46/copsv2/index.html
java.net.SocketException : Network is unreachable
http://203.197.254.154/IMEX/
java.net.SocketTimeoutException : connect timed out
http://203.90.127.70/copsv2/index.html
java.net.NoRouteToHostException : No route to host
http://2struc.cryst.bbk.ac.uk
200
http://59.79.168.90/piRNA/index.php
200
http://66.170.16.154/EuSplice
java.net.SocketTimeoutException : connect timed out
http://abacas.sourceforge.net
200
http://abagyan.scripps.edu/lab/web/sad/show.cgi
java.net.UnknownHostException : abagyan.scripps.edu
http://abagyan.ucsd.edu/SimiCon
200
http://abc-sysbio.sourceforge.net
200
http://abcgrid.cbi.pku.edu.cn
200
http://abmapper.sourceforge.net/
200
http://absalpha.dcrt.nih.gov:8008/
java.net.UnknownHostException : absalpha.dcrt.nih.gov
http://abwgc.jnu.ac.in/_sarba
java.io.FileNotFoundException : http://abwgc.jnu.ac.in/_sarba
http://acephpx.cropdb.org/blogo/
java.net.SocketTimeoutException : Read timed out
http://acgh.afcri.upenn.edu
java.net.SocketTimeoutException : connect timed out
http://acgt.cs.tau.ac.il/matisse
200
http://aclame.ulb.ac.be/prophinder
200
http://acrmwww.biochem.ucl.ac.uk/saap/
200
http://act.gersteinlab.org
200
http://actin.pharm.mssm.edu/AVIS2
200
http://adan-embl.ibmc.umh.es/
200
http://adan.crg.es/
200
http://adegenet.r-forge.r-project.org/
200
http://adios.tau.ac.il/regmotifs
200
http://admis.tongji.edu.cn/Projects/pnnp.aspx
200
http://affycomp.biostat.jhsph.edu
200
http://agave.health.unm.edu/iphace/
200
http://agave.wustl.edu/yeast/
java.net.SocketTimeoutException : connect timed out
http://agem.cnb.csic.es
200
http://agknapp.chemie.fu-berlin.de/agknapp/index.php?menu=software&page=PeptideClassifier
200
http://agra.fzv.uni-mb.si/
200
http://ai.cau.ac.kr/sicago.html
200
http://aiia.iis.sinica.edu.tw/
200
http://aiia.iis.sinica.edu.tw/biocreative2.htm
200
http://aimed11.unipv.it/TimeClust
200
http://aims.cps.msu.edu/hiclas/
java.net.UnknownHostException : aims.cps.msu.edu
http://akt.ucsf.edu/EGAN/
200
http://albuquerque.bioinformatics.uottawa.ca/pathgroup/Quartet.html
java.io.FileNotFoundException : http://albuquerque.bioinformatics.uottawa.ca/pathgroup/Quartet.html
http://alchemy.sourceforge.net/
200
http://algo.inria.fr/nicodeme/proteomes/proteocomp.html
200
http://algorithmics.molgen.mpg.de/mixture
200
http://algorithmics.molgen.mpg.de/probetrees
200
http://algorithmics.molgen.mpg.de/Supplements/InfDif/
200
http://alibaba.informatik.hu-berlin.de/
200
http://align.bmr.kyushu-u.ac.jp/mafft/software/
java.net.SocketTimeoutException : Read timed out
http://alla.cs.gsu.edu/
200
http://alla.cs.gsu.edu:8080/MinePW/pages/gmapping/GMMain.html
200
http://alpha.dmi.unict.it/
java.net.SocketTimeoutException : connect timed out
http://alse.cs.hku.hk
200
http://altair.sci.hokudai.ac.jp/g6/Research/POCASA_e.html
200
http://alterna.cbrc.jp/
200
http://aluru-sun.ece.iastate.edu/doku.php?id=software
200
http://amiga.cbmeg.unicamp.br
200
http://amos.sourceforge.net/Figaro
200
http://amp.pharm.mssm.edu/lib/chea.jsp
200
http://amp.pharm.mssm.edu/lib/kea.jsp
200
http://amp.pharm.mssm.edu/maayan-lab/gate.htm
200
http://anais.versailles.inra.fr
200
http://ancestors.bioinfo.uqam.ca/ancestorWeb/
200
http://anchor.enzim.hu
200
http://andromeda.botany.gu.se/galaxiewelcome.html
java.io.FileNotFoundException : http://andromeda.botany.gu.se/galaxiewelcome.html
http://angel.elte.hu/clustering
200
http://anolis.oeb.harvard.edu/
200
http://antares.protres.ru/fold-amyloid/
200
http://anti.lab.nig.ac.jp/4ddb/
java.net.SocketTimeoutException : connect timed out
http://anti.lab.nig.ac.jp/spi/
java.net.SocketTimeoutException : connect timed out
http://antimony.sourceforge.net/
200
http://ape.mpl.ird.fr/pegas/
200
http://apollo.berkeleybop.org
200
http://apollo11.isto.unibo.it/software/
200
http://appliedbioinformatics.wur.nl/GC-MS
200
http://appserver.biotec.tu-dresden.de/MSPocket/
200
http://aqua.unife.it
200
http://aqua.unife.it/GAMES
200
http://arcadiapathways.sourceforge.net/
200
http://archaea.u-psud.fr/bin/baget.dll
200
http://archimedes.cheme.cmu.edu/biosoftware.html
200
http://arep.med.harvard.edu/enhancer
java.io.FileNotFoundException : http://arep.med.harvard.edu/enhancer
http://argon.cshl.org/
200
http://arianna.bio.uniroma1.it/pigs
200
http://array.kobic.re.kr/ADGO
java.net.SocketTimeoutException : connect timed out
http://array.sdsc.edu
java.net.UnknownHostException : array.sdsc.edu
http://arrayanalysis.mbni.med.umich.edu/arrayanalysis.html
200
http://arrowsmith.psych.uic.edu
200
http://asap.ahabs.wisc.edu/gril
200
http://ashtoret.tau.ac.il/
200
http://asiago.stanford.edu/SmashCell
java.net.UnknownHostException : asiago.stanford.edu
http://aspendb.uga.edu/downloads
200
http://asqa.iis.sinica.edu.tw/fXaWeb/
200
http://astro.temple.edu/
200
http://atgc.lirmm.fr/star
java.net.SocketTimeoutException : connect timed out
http://athena.bioc.uvic.ca/genomes/
java.io.FileNotFoundException : http://athena.bioc.uvic.ca/genomes/
http://athena.bioc.uvic.ca/genomes/index.html
java.io.FileNotFoundException : http://athena.bioc.uvic.ca/genomes/index.html
http://athena.bioc.uvic.ca/pbr/jdotter/
java.io.FileNotFoundException : http://athena.bioc.uvic.ca/pbr/jdotter/
http://atted.jp
200
http://aug.csres.utexas.edu/msa/
200
http://aug.csres.utexas.edu/msnet
200
http://augustus.gobics.de
200
http://autogo.biopathway.org
200
http://automation.inha.ac.kr/khan
java.net.UnknownHostException : automation.inha.ac.kr
http://automotif.bioinfo.pl/
200
http://avis.princeton.edu/contextPIXIE/
200
http://babel.ucmp.umu.se/ond-crf/
200
http://babylone.ulb.ac.be/autoosc/
200
http://babylone.ulb.ac.be/popmusic
200
http://babylone.ulb.ac.be/Prelude_and_Fugue
200
http://baderlab.org/Data/PDZAffinity
200
http://baderlab.org/Software/NetMatch
200
http://balabio.dcs.gla.ac.uk/mallika/WebTOPS/topsplus.html
200
http://balabio.dcs.gla.ac.uk/tops
200
http://baliga.systemsbiology.net/medichi
200
http://bamics2.cmbi.ru.nl/websoftware/pancgh/
200
http://bamview.sourceforge.net/
200
http://barleybase.org
200
http://barton.ebi.ac.uk
java.net.UnknownHostException : barton.ebi.ac.uk
http://barton.ebi.ac.uk/servers/3Dee.html
java.net.UnknownHostException : barton.ebi.ac.uk
http://barton.ebi.ac.uk/servers/jpred.h
java.net.UnknownHostException : barton.ebi.ac.uk
http://barton.ebi.ac.uk/servers/protest.html
java.net.UnknownHostException : barton.ebi.ac.uk
http://bat.ina.certh.gr/tools/circoletto/
200
http://bat.ina.certh.gr/tools/masive/
200
http://bayesweb.wadsworth.org/gibbs/gibbs.html
200
http://bbm1.ucm.es/torralba/funder/down/
java.io.FileNotFoundException : http://bbm1.ucm.es/torralba/funder/down/
http://bcb.cs.tufts.edu/hubcomps
200
http://bcb.cs.tufts.edu/pairwise/
200
http://bcf.isb-sib.ch/mamot
200
http://bch.msu.edu/
java.net.UnknownHostException : bch.msu.edu
http://bcl.med.harvard.edu/proteomics/proj/APBA/
200
http://bcms.bioinfo.cnio.es
200
http://bdval.campagnelab.org
200
http://beagle-lib.googlecode.com/
200
http://bear.fhcrc.org/
200
http://beast.bio.ed.ac.uk/
200
http://bental.tau.ac.il/ConQuass/
200
http://best.utmb.edu/BEST/
java.net.UnknownHostException : best.utmb.edu
http://bgee.unil.ch/
200
http://bgx.org.uk/software/ESS.html
200
http://bibiserv.cebitec.uni-bielefeld.de/rnashapes
200
http://bibiserv.techfak
java.net.UnknownHostException : bibiserv.techfak
http://BiBiServ.TechFak.Uni-Bielefeld
java.net.UnknownHostException : BiBiServ.TechFak.Uni-Bielefeld
http://bibiserv.techfak.uni-bielefeld.de/agt-sdp/
200
http://bibiserv.techfak.uni-bielefeld.de/altavist/
200
http://bibiserv.techfak.uni-bielefeld.de/chroma
200
http://bibiserv.TechFak.Uni-Bielefeld.DE/dca/
200
http://bibiserv.techfak.uni-bielefeld.de/decomp/
200
http://bibiserv.TechFak.Uni-Bielefeld.DE/dial
java.io.FileNotFoundException : http://bibiserv.TechFak.Uni-Bielefeld.DE/dial
http://bibiserv.techfak.uni-bielefeld.de/dialign/
200
http://bibiserv.techfak.uni-bielefeld.de/guugle
200
http://bibiserv.techfak.uni-bielefeld.de/locomotif
200
http://bibiserv.techfak.uni-bielefeld.de/mcope/
java.io.FileNotFoundException : http://bibiserv.techfak.uni-bielefeld.de/mcope/
http://bibiserv.techfak.uni-bielefeld.de/parnass
200
http://bibiserv.techfak.uni-bielefeld.de/possumsearch2/
200
http://bibiserv.techfak.uni-bielefeld.de/rep
java.io.FileNotFoundException : http://bibiserv.techfak.uni-bielefeld.de/rep
http://bibiserv.techfak.uni-bielefeld.de/rnacast/supplementary.html
200
http://bibiserv.TechFak.Uni-Bielefeld.DE/rose/
200
http://bibs.snu.ac.kr/software/arrayQCplot
200
http://bidd.nus.edu.sg/group/trmp/sm.pdf
200
http://bidd.nus.edu.sg/group/trmp/trmp.asp
200
http://big.crg.cat/services/selenoprofiles
200
http://bigarea.area.ba.cnr.it:8000/EmbIT/Pats
java.net.UnknownHostException : bigarea.area.ba.cnr.it
http://bighost.ba.itb.cnr.it:8080/Framework
java.net.ConnectException : Connection refused
http://biit.cs.ut.ee/KEGGanim/
200
http://bio-ai.myeweb.net/box_widget.html
200
http://bio-bwa.sourceforge.net
200
http://bio.chip.org/doc/start/START-supplementary.pdf
200
http://bio.chip.org/start/
200
http://bio.cigb.edu.cu
200
http://bio.cse.ohio-state.edu/Vorometric
200
http://bio.dlg.cn
200
http://bio.gsc.riken.jp/ProteoMix/
java.net.SocketTimeoutException : connect timed out
http://bio.ifom-ieo-campus.it/galaxy
200
http://bio.informatics.indiana.edu/projects/arcs
200
http://bio.informatics.indiana.edu/projects/compam/
200
http://bio.informatik.uni-jena.de/software/
200
http://bio.kuas.edu.tw/PPO/
java.net.SocketTimeoutException : Read timed out
http://bio.math.berkeley.edu/amap/
200
http://bio.math.berkeley.edu/TangleSolve/
200
http://bio301.iis.sinica.edu.tw/
200
http://bioag.byu
java.net.UnknownHostException : bioag.byu
http://bioalgo.iit.cnr.it/rehap
200
http://bioalgorithm.life.nctu.edu.tw/HPKNOTTER/
200
http://bioanalysis.genomics.mcg.edu/parasam
200
http://biochem.otago.ac.nz/double.html
java.io.FileNotFoundException : http://biochem.otago.ac.nz/double.html
http://biocom1.ssu.ac.kr/FKNNacc/
java.net.SocketTimeoutException : connect timed out
http://biocomp.bioen.uiuc.edu/nacep
200
http://biocomp.chem.uw.edu.pl/BioShell
200
http://biocomp.chem.uw.edu.pl/services/tpile
200
http://biocomputer.bio.cuhk.edu.hk/softwares/BPBAac
200
http://bioconductor.org
200
http://bioconductor.org/packages/2.0/bioc
200
http://bioconductor.org/packages/2.3/bioc/html/affyContam.html
200
http://bioconductor.org/packages/2.3/bioc/html/arrayMvout.html
200
http://bioconductor.org/packages/2.3/bioc/html/rHVDM.html
200
http://bioconductor.org/packages/2.6/bioc/html/GOSemSim.html
200
http://bioconductor.org/packages/release/bioc/html/BayesPeak.html
200
http://bioconductor.org/packages/release/Software.html
200
http://biocontrasts.biopathway.org
200
http://biocontrasts.i2r.a-star.edu.sg
java.net.SocketTimeoutException : connect timed out
http://biocyc.org
200
http://biodbnet.abcc.ncifcrf.gov
200
http://biodcv.fbk.eu/listspy.html
301
http://biodev.extra.cea.fr/docs/irma
200
http://biodev.extra.cea.fr/interoporc/
200
http://biodiversity.colorado.edu
200
http://bioeditor.sdsc.edu
200
http://biogibbs.stanford.edu/
java.net.SocketTimeoutException : connect timed out
http://bioguide-project.net/gv
200
http://bioinf.boku.ac.at/alexp/robmca.html
200
http://bioinf.charite.de/superdrug
200
http://bioinf.cs.ucl.ac.uk/disopred/
200
http://bioinf.cs.ucl.ac.uk/GTD
java.net.SocketTimeoutException : connect timed out
http://bioinf.cs.ucl.ac.uk/memsat
java.io.FileNotFoundException : http://bioinf.cs.ucl.ac.uk/memsat/
http://bioinf.cs.ucl.ac.uk/psipred/
200
http://bioinf.eva.mpg.de/patman
200
http://bioinf.gen.tcd.ie/
200
http://bioinf.man.ac.uk/rapid
java.io.FileNotFoundException : http://www.bioinf.manchester.ac.uk/rapid
http://bioinf.may.ie/software/clann
200
http://bioinf.mii.lu.lv/epsrc_project/struct_ev.html
200
http://bioinf.ncl.ac.uk/gnapn
200
http://bioinf.nuigalway.ie
200
http://bioinf.nuigalway.ie/sombrero
200
http://bioinf.scri.ac.uk/flapjack
200
http://bioinf.scri.ac.uk/lp/programs.html
200
http://bioinf.scri.ac.uk/strudel/
200
http://bioinf.scri.ac.uk/tablet
200
http://bioinf.umbc.edu/dmdm
200
http://bioinf.umbc.edu/EMU/ftp
200
http://bioinf.uta.fi/Rank.htm
200
http://bioinf.uta.fi/wml/welcome.wml
200
http://bioinf.wehi.edu.au/affylmGUI
200
http://bioinf.wehi.edu.au/folders/immunol
200
http://bioinf.wehi.edu.au/limmaGUI
200
http://bioinf.wehi.edu.au/resources/
200
http://bioinf.wehi.edu.au/resources/webReferences.html
200
http://bioinf.wehi.edu.au/software/linkdatagen/
200
http://bioinf.xmu.edu.cn/databases/ADR/index.html
200
http://bioinf.xmu.edu.cn/databases/TiSGeD/index.html
200
http://bioinfo
java.net.UnknownHostException : bioinfo
http://bioinfo-igbmc.u-strasbourg.fr/BioInfo/RASCAL/paper/rascal_supp.html
java.net.UnknownHostException : bioinfo-igbmc.u-strasbourg.fr
http://bioinfo-out.curie.fr/projects/freec/
200
http://bioinfo-pharma.u-strasbg.fr/scPDB
200
http://bioinfo.amu.edu.pl/agos/
200
http://bioinfo.au.tsinghua.edu.cn/alignpi/
200
http://bioinfo.au.tsinghua.edu.cn/atie/
200
http://bioinfo.au.tsinghua.edu.cn/member/xwwang/mircisreg
200
http://bioinfo.au.tsinghua.edu.cn/member/ylwang/Matlabfiles_CNI.zip
200
http://bioinfo.au.tsinghua.edu.cn/miralign
200
http://bioinfo.au.tsinghua.edu.cn/oscar
200
http://bioinfo.au.tsinghua.edu.cn/software/degseq
200
http://bioinfo.ceng.metu.edu.tr/Pub/LFMPro
java.net.SocketTimeoutException : connect timed out
http://bioinfo.cis.nctu.edu.tw
200
http://bioinfo.cnio.es/sotarray
200
http://bioinfo.cs.rice.edu/phylonet/
200
http://bioinfo.cs.technion.ac.il/haploblock/
200
http://bioinfo.cs.technion.ac.il/IBDmap
200
http://bioinfo.cs.technion.ac.il/people/zohar/MonoClad/software
java.io.FileNotFoundException : http://bioinfo.cs.technion.ac.il/people/zohar/MonoClad/software
http://bioinfo.cs.umn.edu/supplements/binf2009
200
http://bioinfo.curie.fr/projects/binom
200
http://bioinfo.curie.fr/projects/maia
200
http://bioinfo.curie.fr/vamp
200
http://bioinfo.ebc.ee/download/
200
http://bioinfo.ebc.ee/mprimer3/
200
http://bioinfo.ebc.ee/multiplx/
200
http://bioinfo.genopole-toulouse.prd.fr/Alvira
java.io.FileNotFoundException : http://bioinfo.genopole-toulouse.prd.fr/Alvira
http://bioinfo.genopole-toulouse.prd.fr/remora
200
http://bioinfo.hku.hk/cpgieintro
java.io.FileNotFoundException : http://bioinfo.hku.hk/cpgieintro
http://bioinfo.hku.hk/iggweb
200
http://bioinfo.hku.hk/wclustag/
200
http://bioinfo.hrbmu.edu.cn/GsNetCom
java.net.SocketTimeoutException : Read timed out
http://bioinfo.icgeb.res.in/protvirdb
200
http://bioinfo.iconcologia.net/SNPstats
200
http://bioinfo.iq.usp.br/zerg
200
http://bioinfo.knu.ac.kr/research/CARD/
java.io.FileNotFoundException : http://bioinfo.knu.ac.kr/research/CARD/
http://bioinfo.mbb
java.net.UnknownHostException : bioinfo.mbb
http://bioinfo.mbb.yale.edu/expression/echipchip
200
http://bioinfo.mc.vanderbilt.edu/dmGWAS.html
200
http://bioinfo.mc.vanderbilt.edu/SZGR/
200
http://bioinfo.mikrobio.med.uni-giessen.de/augur
200
http://bioinfo.mikrobio.med.uni-giessen.de/geco2/GecoMainServlet
200
http://bioinfo.montp.cnrs.fr/?r=repeatDB
200
http://bioinfo.montp.cnrs.fr/?r=t-reks
200
http://bioinfo.mshri.on.ca/BIND/asn-browser/
java.net.UnknownHostException : bioinfo.mshri.on.ca
http://BioInfo.PL/LiveBench/
200
http://BioInfo.PL/Meta/
java.io.FileNotFoundException : http://BioInfo.PL/Meta/
http://bioinfo.pl/PDB-Preview/
java.io.IOException : Server returned HTTP response code: 500 for URL: http://meta.bioinfo.pl/pdb-preview.pl
http://BioInfo.PL/services.html
200
http://BioInfo.PL/ToolShop/
java.io.FileNotFoundException : http://BioInfo.PL/ToolShop/
http://bioinfo.thep.lu.se/acid.html
200
http://bioinfo.ucc.ie/blastxtract/
200
http://bioinfo.uh.edu/PIQA
200
http://bioinfo.unc.edu/downloads/
java.io.FileNotFoundException : http://bioinfo.unc.edu/downloads/
http://bioinfo.unice.fr/publications/genminer_article/
200
http://bioinfo.ut.ee/multimprimer3/
200
http://bioinfo.vipbg.vcu.edu/SNPNB/
java.net.SocketTimeoutException : connect timed out
http://bioinfo.weizmann.ac.il/protmot/
200
http://bioinfo.wilmer.jhu.edu/morenet/
200
http://bioinfo.wilmer.jhu.edu/PDI/
200
http://bioinfo3d.cs.tau.ac.il/ARTS
200
http://bioinfo3d.cs.tau.ac.il/gossip/
200
http://bioinfobase.umkc.edu/speed/
200
http://bioinfome.cgm.cnrs-gif.fr/
java.net.SocketTimeoutException : connect timed out
http://bioinform.genetika.ru/projects/swan/www/
200
http://bioinform.genetika.ru/SeSiMCMC
200
http://bioinformatics.albany.edu/
200
http://bioinformatics.bc.edu/clotelab/
200
http://bioinformatics.bc.edu/clotelab/RNAbor/
200
http://bioinformatics.biol.rug.nl/standalone/fiva/
200
http://bioinformatics.biol.uoa.gr/ExTopoDB
200
http://bioinformatics.biol.uoa.gr/gpDB
200
http://bioinformatics.biol.uoa.gr/PRED-COUPLE2
200
http://bioinformatics.burnham.org/liwz/vissa
200
http://bioinformatics.cau.edu.cn/ARSER
200
http://bioinformatics.cau.edu.cn/LSPR
200
http://bioinformatics.cau.edu.cn/tCal
200
http://bioinformatics.charite.de/cobweb
200
http://bioinformatics.clemson.edu/G-SESAME
200
http://bioinformatics.clemson.edu/Publication/Supplement/gsp.htm
200
http://bioinformatics.cnmcresearch.org/GOTreePlus/
200
http://bioinformatics.cribi.unipd.it/alphasimp
java.io.FileNotFoundException : http://bioinformatics.cribi.unipd.it/alphasimp
http://bioinformatics.cribi.unipd.it/primex
java.io.FileNotFoundException : http://bioinformatics.cribi.unipd.it/primex
http://bioinformatics.cs.unibo.it/Al-Eigen
200
http://bioinformatics.cs.unibo.it/FT-COMAR
200
http://bioinformatics.emedea.it/geco
200
http://bioinformatics.fccc.edu
200
http://bioinformatics.forsyth.org/mtd
200
http://bioinformatics.hungry.com/clearcut
200
http://bioinformatics.iastate.edu/aat/align/align.html
java.io.FileNotFoundException : http://bioinformatics.iastate.edu/aat/align/align.html
http://bioinformatics.iastate.edu/bioinformatics2go/gs/download.html
200
http://bioinformatics.iastate.edu/bioinformatics2go/mb/MuSeqBox.html
200
http://bioinformatics.iastate.edu/bioinformatics2go/MyGV
java.io.FileNotFoundException : http://bioinformatics.iastate.edu/bioinformatics2go/MyGV
http://bioinformatics.iastate.edu/cgi-bin/gs.cgi
200
http://bioinformatics.iastate.edu/cgi-bin/sp.cgi
200
http://bioinformatics.icmb.utexas.edu/mspire
java.net.SocketTimeoutException : connect timed out
http://bioinformatics.icmb.utexas.edu/plex
java.net.SocketTimeoutException : connect timed out
http://bioinformatics.iis.sinica.edu.tw/HYPROSPII/
java.net.SocketTimeoutException : connect timed out
http://bioinformatics.lcd-ustc.org/css_palm/
java.io.IOException : Server returned HTTP response code: 403 for URL: http://bioinformatics.lcd-ustc.org/css_palm/
http://bioinformatics.leeds.ac.uk/
200
http://bioinformatics.mdanderson.org
200
http://bioinformatics.mdanderson.org/software.html
200
http://bioinformatics.mdanderson.org/supplements.html
200
http://bioinformatics.med.ohio-state.edu/GDVTK
java.net.SocketTimeoutException : connect timed out
http://bioinformatics.med.utah.edu/
200
http://bioinformatics.med.utah.edu/Genie/hapConstructor.html
200
http://bioinformatics.med.yale.edu
200
http://bioinformatics.med.yale.edu/DNACopyNumber
200
http://bioinformatics.med.yale.edu/interaction
200
http://bioinformatics.med.yale.edu/pathway-analysis/rf.htm
200
http://bioinformatics.med.yale.edu/TFcooperativity
200
http://bioinformatics.musc.edu/agmlcentral
java.io.IOException : Server returned HTTP response code: 503 for URL: http://bioinformatics.musc.edu/agmlcentral
http://bioinformatics.musc.edu/bstlab/
java.io.IOException : Server returned HTTP response code: 503 for URL: http://bioinformatics.musc.edu/bstlab/
http://bioinformatics.musc.edu/resources.html
java.io.IOException : Server returned HTTP response code: 503 for URL: http://bioinformatics.musc.edu/resources.html
http://bioinformatics.musc.edu/webmetabol/
java.io.IOException : Server returned HTTP response code: 503 for URL: http://bioinformatics.musc.edu/webmetabol/
http://bioinformatics.musc.edu/wmetric
java.io.IOException : Server returned HTTP response code: 503 for URL: http://bioinformatics.musc.edu/wmetric
http://bioinformatics.myweb.hinet.net/freedom.htm
200
http://bioinformatics.myweb.hinet.net/iptree.htm
200
http://bioinformatics.nki.nl/
200
http://bioinformatics.org.au/mosaic/
200
http://bioinformatics.org.au/stream/
200
http://bioinformatics.org/assemble
200
http://bioinformatics.org/disperse
200
http://bioinformatics.org/metaquant
200
http://bioinformatics.org/pecop
200
http://bioinformatics.org/S2S/
200
http://bioinformatics.oxfordjournals.org
200
http://bioinformatics.picr.man.ac.uk
200
http://bioinformatics.picr.man.ac.uk/adapt
java.io.IOException : Server returned HTTP response code: 403 for URL: http://bioinformatics.picr.man.ac.uk/adapt/Scrape.adapt
http://bioinformatics.psb.ugent.be/
200
http://bioinformatics.psb.ugent.be/software
200
http://bioinformatics.psb.ugent.be/software/details/CyClus3D
200
http://bioinformatics.psb.ugent.be/supplementary_data/
200
http://bioinformatics.psb.ugent.be/webtools/pronet/
200
http://bioinformatics.psb.ugent.be/webtools/tapir
200
http://bioinformatics.rutgers.edu/Software/MVQueries/
200
http://bioinformatics.tudelft.nl
200
http://bioinformatics.uams.edu/mirror/betaturns/
200
http://bioinformatics.uams.edu/mirror/propred1/
200
http://bioinformatics.uams.edu/raghava/haptendb/
200
http://bioinformatics.ubc.ca/genecomber
java.io.FileNotFoundException : http://www.bioinformatics.ubc.ca/genecomber
http://bioinformatics.ucd.ie/shields/software/comparimotif/
200
http://bioinformatics.ust.hk/BOOST.html
200
http://bioinformatics.ust.hk/ReRankPSMwMS1.rar
200
http://bioinformatics.ust.hk/SNPAssociation.zip
200
http://bioinformatics.ust.hk/SNPHarvester.html
200
http://bioinformatics.ust.hk/SNPRuler.zip
200
http://bioinformatics.vub.ac.be
200
http://bioinformatics.weizmann.ac.il/cards/
200
http://bioinformatics.well.ox.ac.uk/GRR
200
http://bioinformatics.zj.cn/pgf/
java.io.FileNotFoundException : http://bioinformatics.zj.cn/pgf/
http://bioinformatics1.smb.wsu.edu/Ceres
200
http://bioinfoserver.rsbs.anu.edu.au/
200
http://bioinfoserver.rsbs.anu.edu.au/downloads/clans/
200
http://bioinfoserver.rsbs.anu.edu.au/downloads/mclip.jar
200
http://bioinfoserver.rsbs.anu.edu.au/utils/mclip/info.php
200
http://bioinfow.dep.usal.es/apid/
200
http://biojava.org/wiki/BioJava
java.io.FileNotFoundException : http://biojava.org/wiki/BioJava
http://biol.dgbm.unina.it:8080/virtlab.html
java.net.ConnectException : Connection refused
http://biolinfo.org/mpid-t2
200
http://biomaj.genouest.org
200
http://biomath.med.uth.gr
200
http://biomed.umit.at/page.cfm?pageid=516
200
http://biomed.umit.at/page.cfm?pageid=526
200
http://biomed.umit.at/upload/lcfx.zip
200
http://BioMedEmpire.org/
java.net.UnknownHostException : BioMedEmpire.org
http://biomine.ece.ualberta.ca/MFDp.html
java.net.SocketException : Network is unreachable
http://biomint.oefai.at/
200
http://bionet.bioapps.biozentrum.uni-wuerzburg.de
200
http://bionlp-uima.sourceforge.net/
200
http://bionlp.sourceforge.net
200
http://bionlp.stanford.edu/gapscore/
java.net.SocketTimeoutException : connect timed out
http://bionlp.utu.fi/
200
http://bioonto.de/pmwiki.php/Main/PheneOntology
200
http://bioonto.gen.cam.ac.uk/el-ont
200
http://bioportal.kobic.re.kr/SNP2NMD
200
http://bioportal.weizmann.ac.il/promate
200
http://bioputer.mimuw.edu.pl/
200
http://bioputer.mimuw.edu.pl/modevo
200
http://bioputer.mimuw.edu.pl/papers/cappi
200
http://biorg.cis.fiu.edu/SNE
200
http://biorg.cis.fiu.edu/vPhyloMM/
200
http://bios.ugr.es/BMapBuilder
200
http://biosearch.berkeley.edu
200
http://biosemantics.org/geneE
200
http://biosemantics.org/jane
200
http://bioserv.cbs.cnrs.fr/VITO/DOC/
java.io.FileNotFoundException : http://bioserv.cbs.cnrs.fr/VITO/DOC/
http://bioserv.mps.ohio-state.edu/HybridPSI
200
http://bioserv.mps.ohio-state.edu/Vienna
java.io.FileNotFoundException : http://bioserv.mps.ohio-state.edu/Vienna
http://bioserv.rpbs.jussieu.fr/swelfe
200
http://bioserver-1.bioacademy.gr/Bioserver/PeptideFinder/
200
http://bioserver-1.bioacademy.gr/Bioserver/UniMaP/
200
http://bioserver.cs.rice.edu/gs2
200
http://bioserver.cs.ucsb.edu/
200
http://bioshell.chem.uw.edu.pl
200
http://biosoft.kaist.ac.kr/
200
http://biostat.jhsph.edu/
200
http://biostat.mc.vanderbilt.edu/GWAsimulator
200
http://biostat.mc.vanderbilt.edu/LilyWang
200
http://biosun1.harvard.edu/complab/dchip/snp/
200
http://biotech.bmi.ac.cn/PerturbationAnalyzer
200
http://biotools.com
java.net.UnknownHostException : biotools.com
http://bioverse.compbio.washington.edu
200
http://bioverse.compbio.washington.edu/viewer
200
http://bioware.ucd.ie/
200
http://bioweb.pasteur.fr/seqanal/difftool
java.io.FileNotFoundException : http://bioweb2.pasteur.fr/difftool
http://bioweb.pasteur.fr/seqanal/interfaces/melting.html
200
http://bioweb.ucr.edu/ChemMineV2/chemminer
200
http://bioweb2.pasteur.fr/projects/mobyle/
302
http://biowiki.org/PhyloComposer
200
http://biowiki.org/PhyloDirector
200
http://biowiki.org/RnaAlignmentViewers
200
http://biowiki.org/StemLocAMA
200
http://bioxsd.org
200
http://biozon.org/tools/domains/
200
http://biplot.usal.es
200
http://biq-analyzer.bioinf.mpi-inf.mpg.de/
200
http://birg.cs.wright.edu/nmr_synthetic_data_sets
java.io.IOException : Server returned HTTP response code: 503 for URL: http://birg.cs.wright.edu/nmr_validation_sets/control_data_sets
http://birg1.fbb.utm.my/birghpc
200
http://biron.usc.edu/
200
http://biskit.pasteur.fr
200
http://biskit.sf.net
200
http://bix.ucsd.edu/projects/rapid
200
http://blackhawk.cs.uni.edu
200
http://blast.wustl.edu
200
http://blast.wustl.edu/exalin
200
http://blm.sis.pitt.edu:8080/axis/services/TMProFetcherService
java.net.SocketTimeoutException : connect timed out
http://blocks.fhcrc.org/
200
http://blog.malde.org/index.php/flowsim/
200
http://blog.naver.com/aggie100
200
http://bmchust.3322.org/Data/Soft/332-DV-Curve2.0.zip
java.net.SocketTimeoutException : connect timed out
http://bmf.colorado.edu/codonexplorer/
200
http://bmi.osu.edu/
200
http://bmm.cancerresearchuk.org/
200
http://bmm.cancerresearchuk.org/servers/pip
200
http://bonaire.lbl.gov/shadower
java.net.UnknownHostException : bonaire.lbl.gov
http://bonsai.ims.u-tokyo.ac.jp/
200
http://bonsai.ims.u-tokyo.ac.jp/mdehoon/software/cluster
java.io.FileNotFoundException : http://bonsai.hgc.jp/mdehoon/software/cluster
http://bosque.udec.cl
200
http://bq.ub.es/bioqint/label_distribution/
200
http://brahms.biology.rochester.edu/software.html
java.net.SocketTimeoutException : connect timed out
http://brainarray.mbni.med.umich.edu/Brainarray/Database/SearchSNP/snpfunc.aspx
200
http://brainarray.mbni.med.umich.edu/brainarray/datamining/MarkerInfoFinder
200
http://brainarray.mbni.med.umich.edu/brainarray/Rgpgpu
200
http://brainarray.mbni.med.umich.edu/glay/
200
http://brainarray.mbni.med.umich.edu/gsearcher/
200
http://brainarray.mhri.med.umich.edu/MARRAY/BC_ASP/brainarray.htm
java.io.FileNotFoundException : http://brainarray.mhri.med.umich.edu/MARRAY/BC_ASP/brainarray.htm
http://brcapp.kribb.re.kr/HPD/
java.net.SocketTimeoutException : connect timed out
http://bsu.ncl.ac.uk/ondexview
200
http://bumble.hgc.jp/
200
http://bws.iis.sinica.edu.tw/PubMed-EX
200
http://bykdb.ibcp.fr
200
http://C-It.mpi-bn.mpg.dehttp
java.net.UnknownHostException : C-It.mpi-bn.mpg.dehttp
http://c13.usal.es
200
http://c2s2.yale.edu/software/LOT/
200
http://cactus.salk.edu/RankProd
java.io.FileNotFoundException : http://cactus.salk.edu/RankProd
http://cafasp4.bioinformatics.buffalo.edu/dp/update.html
java.net.NoRouteToHostException : No route to host
http://cagrid-browser.nci.nih.gov
java.net.UnknownHostException : cagrid-browser.nci.nih.gov
http://camda.duke.edu
200
http://capb.dbi.udel.edu/casa
java.net.UnknownHostException : capb.dbi.udel.edu
http://caps.ncbs.res.in/SMotif/index.html
200
http://carcweb.musc.edu/TextminingProjects/
200
http://carlit.toulouse.inra.fr/MilPaT/MilPat.pl
200
http://cartan.gmd.de/FlexX
java.net.UnknownHostException : cartan.gmd.de
http://cartan.gmd.de/ToPLign.html
java.net.UnknownHostException : cartan.gmd.de
http://casp.rnet.missouri.edu/multicom_3d.html
200
http://cassandra.bio.uniroma1.it/mr-results-casp.html
java.io.FileNotFoundException : http://cassandra.bio.uniroma1.it/mr-results-casp.html
http://cassis.in.tum.de/
200
http://caulobacter.stanford.edu/CellCycle/
java.net.SocketTimeoutException : connect timed out
http://cbbc.murdoch.edu.au/
java.io.FileNotFoundException : http://ccg.murdoch.edu.au/cbbc.shtml
http://cbbc.murdoch.edu.au/projects/masv/
java.io.FileNotFoundException : http://ccg.murdoch.edu.au/cbbc.shtmlprojects/masv/
http://cbc.case.edu/maven
200
http://cbcb.umd.edu/software/glimmer
200
http://cbcb.umd.edu/software/jigsaw
200
http://cbcsrv.watson.ibm.com/
200
http://cbdb.nimh.nih.gov/
200
http://cbi.labri.fr/eng/proviz.htm
200
http://cbi.labri.fr/Genolevures/fam/
200
http://cbi.labri.fr/outils/alias/
200
http://cbi.labri.fr/outils/ippred/
java.io.IOException : Server returned HTTP response code: 403 for URL: http://cbi.labri.fr/outils/ippred/
http://cbio
java.net.UnknownHostException : cbio
http://cbio.ensmp.fr/
200
http://cbio.ensmp.fr/kiss
200
http://cbioc.eas.asu.edu/gnat/
200
http://cbr.jic.ac.uk/dicks/software/
200
http://cbsuapps.tc.cornell.edu/sfscode.aspx
200
http://cc.ucsf.edu/jain/public
java.io.FileNotFoundException : http://cancer.ucsf.edu//jain/public
http://ccgb.umn.edu/software/java/apps/TableView/
java.net.UnknownHostException : ccgb.umn.edu
http://ccst.jlu.edu.cn/CSBG/PIVS/index.htm
200
http://cd-hit.org
200
http://cdb.ics.uci.edu
200
http://ceb.scs.fsu.edu/awty
200
http://cebc.unc.edu/fastmap86.html
200
http://cebc.unc.edu/software/
200
http://cebs.niehs.nih.gov
200
http://cebs.niehs.nih.gov/cebsdownloads
200
http://cebs.niehs.nih.gov/SysBioOM/
200
http://cedar.genetics.soton.ac.uk/public_html/primer2.html
200
http://cegg.unige.ch/newick_utils
200
http://cellcircuits.org/VERA
200
http://cellpublisher.gobics.de/
200
http://cellsignaling.lanl.gov/FateMaps/
200
http://cellsignaling.lanl.gov/Reactivity/
200
http://celmia.bigr.nl/
200
http://centrallab.hosp.ncku.edu.tw/imz
200
http://centre.bioinformatics.zj.cn/proTF
200
http://centrifuge.unil.ch/
java.io.FileNotFoundException : http://centrifuge.unil.ch/
http://cetus.cs.memphis.edu/motif
java.io.FileNotFoundException : http://cetus.cs.memphis.edu/motif
http://cg1.iis.sinica.edu.tw/
200
http://cgal.inria.fr/abs/Intervor
200
http://cgas.ist.hokudai.ac.jp/
java.net.SocketTimeoutException : connect timed out
http://cgcv.cgb.indiana.edu/cgi-bin/index.cgi
java.net.SocketTimeoutException : Read timed out
http://cggc.agtec.uga.edu/Data/download.asp
200
http://cgi.uc.edu/cgi-bin/kzhang/haploBlockFinder.cgi
java.net.SocketTimeoutException : connect timed out
http://cgl.imim.es/fcp
200
http://cgl.imim.es/iphace/
200
http://cgs.csail.mit.edu/gps
200
http://cgsigma.cshl.org/jian
java.io.FileNotFoundException : http://cgsigma.cshl.org/jian
http://chah.ucc.ie/MIAH
java.net.UnknownHostException : chah.ucc.ie
http://chembench.mml.unc.edu
200
http://chgr.mc.vanderbilt.edu/ritchielab/pMDR
200
http://chianti.ucsd.edu/cyto_web/plugins/
200
http://chianti.ucsd.edu/cyto_web/plugins/index.php
200
http://chipcodis.dacya.ucm.es
200
http://chipdb.wi.mit.edu/
200
http://chirimoyo.ac.uma.es/bitlab/services/index.htm
200
http://choyce.ismb.lon.ac.uk/
200
http://chrg.inf.ethz.ch
java.net.UnknownHostException : chrg.inf.ethz.ch
http://ci.vbi.vt.edu/cammer/schism2.html
200
http://cib.cf.ocha.ac.jp/DACSIS/
200
http://cibex.nig.ac.jp/
200
http://cil.pharmaceuticalbioinformatics.de
java.net.UnknownHostException : cil.pharmaceuticalbioinformatics.de
http://cilab.cs.ccu.edu.tw/service_dl.html
200
http://cityscape.inf.cs.cmu.edu/phylogeny/
200
http://cleaver.sourceforge.net/
200
http://clinicalproteomics.steem.com
java.net.UnknownHostException : clinicalproteomics.steem.com
http://cloudburst-bio.sourceforge.net/
200
http://ClusterAnalysis.org/
200
http://cmb.bnu.edu.cn/pdart/
200
http://cmb.genomics.sinica.edu.tw
java.net.SocketTimeoutException : connect timed out
http://cmb.gis.a-star.edu.sg/ChIPSeq/tools.htm
200
http://cmbi.bjmu.edu.cn/misim
200
http://cmdd.csie.ntu.edu.tw/
200
http://cmgm.stanford.edu/pbrown/sporulation
java.net.SocketTimeoutException : Read timed out
http://cmotifs.tchlab.org
200
http://cmpg.unibe.ch/software/simcoal2/
200
http://CNVVdb.genomics.sinica.edu.tw
200
http://code.google.com/p/annotare/
200
http://code.google.com/p/bedtools
200
http://code.google.com/p/biclustering/
200
http://code.google.com/p/crop-tingchenlab/
200
http://code.google.com/p/datapflex
200
http://code.google.com/p/fishfinder/downloads/list
200
http://code.google.com/p/fugetoolkit
200
http://code.google.com/p/hooke
200
http://code.google.com/p/midia
200
http://code.google.com/p/mu2a/
200
http://code.google.com/p/perm/
200
http://code.google.com/p/phylo-puma
200
http://code.google.com/p/phyutility
200
http://code.google.com/p/poisson-multigraph/
200
http://code.google.com/p/pubchemdb
200
http://code.google.com/p/quantproreloaded/
200
http://code.google.com/p/refolding
200
http://code.google.com/p/robinviz/
200
http://code.google.com/p/sbpipeline/
200
http://code.google.com/p/simultaneous-pin/
200
http://code.google.com/p/treesimj
200
http://code.google.com/p/wcdest
200
http://coding.plantpath.ksu.edu/qgene
200
http://coepra.org
200
http://coevolution.gersteinlab.org
200
http://columba.ebi.ac
java.net.UnknownHostException : columba.ebi.ac
http://comonca.org.cn/fdca/resources/softwares/deg.zip
200
http://comp.chem.nottingham.ac.uk/dichrocalc
200
http://comp.chem.nottingham.ac.uk/parsepdb
200
http://compare.ibdml.univ-mrs.fr
200
http://compbio.bccrc.ca
200
http://compbio.berkeley.edu/
200
http://compbio.berkeley.edu/proj/andy
200
http://compbio.berkeley.edu/proj/writher/
200
http://compbio.charite.de/index.php/ibd2.html
200
http://compbio.charite.de/ontologizer
200
http://compbio.cs.huji.ac.il/CIS/
200
http://compbio.cs.huji.ac.il/GIAnalysis
200
http://compbio.cs.princeton.edu/ancestralaa
200
http://compbio.cs.princeton.edu/bindsites
200
http://compbio.cs.princeton.edu/conservation/
200
http://compbio.cs.princeton.edu/function
200
http://compbio.cs.princeton.edu/mems
200
http://compbio.cs.princeton.edu/specificity/
200
http://compbio.cs.princeton.edu/spici
200
http://compbio.cs.princeton.edu/zf/
200
http://compbio.cs.sfu.ca/
200
http://compbio.cs.sfu.ca/strvar.htm
200
http://compbio.cs.sfu.ca/taverna/pirna/
200
http://compbio.cs.toronto.edu/cryoem/
200
http://compbio.cs.toronto.edu/psmdb
200
http://compbio.cs.toronto.edu/savant
200
http://compbio.cs.toronto.edu/shrimp/
200
http://compbio.cs.toronto.edu/structvar/
200
http://compbio.cs.umn.edu/Feature_Class
200
http://compbio.cs.umn.edu/HyperPrior
200
http://compbio.cs.utoronto.ca/varid
200
http://compbio.dcs.gla.ac.uk/fabien/abinitio/abinitio.html
200
http://compbio.dfci.harvard.edu/pubs/attract_1.0.1.zip
200
http://compbio.med.harvard.edu/CGHweb
200
http://compbio.med.harvard.edu/nuScore
200
http://compbio.ornl.gov/mira/index.html
200
http://compbio.ornl.gov/proteinpipeline/
java.io.FileNotFoundException : http://compbio.ornl.gov/proteinpipeline/
http://compbio.sookmyung.ac.kr/
200
http://compbio.tgen.org/paper_supp/ROC/roc.html
200
http://compbio.uchsc.edu/Hunter_lab/Bada/nonalignments_2008_03_06.html
java.net.UnknownHostException : compbio.uchsc.edu
http://compbio.utmem.edu/snp/dataset/
java.net.UnknownHostException : compbio.utmem.edu
http://compdiag.molgen.mpg.de/software
200
http://compdiag.molgen.mpg.de/supplements/lottaz05
java.io.FileNotFoundException : http://compdiag.molgen.mpg.de/supplements/lottaz05
http://compdiag.uni-regensburg.de/software/transApproxs.shtml
200
http://compevol.auckland.ac.nz/software/DensiTree/
200
http://compgen.rutgers.edu/mapomat/
200
http://compgen.unc.edu/software
java.io.FileNotFoundException : http://compgen.unc.edu/software
http://compsysbio.org/phylopro/
200
http://compsysbio.org/subseqer/
200
http://compubiotic.sysdiag.cnrs.fr/
200
http://computableplant.ics.uci.edu/bti1036
200
http://computing.unn.ac.uk/staff/CGJF1/tpp/bioinf.html
java.io.FileNotFoundException : http://computing.unn.ac.uk/staff/CGJF1/tpp/bioinf.html
http://condor.urbb.jussieu.fr/CS-PSeq-Gen.html
java.net.UnknownHostException : condor.urbb.jussieu.fr
http://condor.urbb.jussieu.fr/PredAccCfg.html
java.net.UnknownHostException : condor.urbb.jussieu.fr
http://connect.apple.com
302
http://conseq.bioinfo.tau.ac.il/
200
http://consurf.tau.ac.il
200
http://contra.stanford.edu/contrafold/
200
http://contraintes.inria.fr/biocham
200
http://conveyor.cebitec.uni-bielefeld.de
301
http://cooke.gsf.de
java.net.UnknownHostException : cooke.gsf.de
http://copan.bioz.unibas.ch/software/
java.net.UnknownHostException : copan.bioz.unibas.ch
http://corba.ebi.ac.uk/EST/jesam/jesam
java.net.UnknownHostException : corba.ebi.ac.uk
http://corba.ebi.ac.uk/models/
java.net.UnknownHostException : corba.ebi.ac.uk
http://corba.ebi.ac.uk/RHdb/EUCORBA/IOR
java.net.UnknownHostException : corba.ebi.ac.uk
http://corg.molgen.mpg.de/cellcycle
java.io.FileNotFoundException : http://corg.molgen.mpg.de/cellcycle
http://corg.molgen.mpg.de/software
java.io.FileNotFoundException : http://corg.molgen.mpg.de/software
http://corna.sf.net
200
http://correio.cc.fc.ul.pt/
java.net.SocketTimeoutException : connect timed out
http://cowry.agri.huji.ac.il
200
http://cpdb.molgen.mpg.de
200
http://cpfp.sourceforge.net/
200
http://cpr.stanford.edu/cpr/index.html
200
http://cpsp.informatik.uni-freiburg.de
200
http://cran.r-project.org
200
http://cran.r-project.org/mirrors.html
200
http://CRAN.R-project.org/package
java.io.FileNotFoundException : http://CRAN.R-project.org/package
http://cran.r-project.org/src/contrib/Descriptions/WilcoxCV.html
java.io.FileNotFoundException : http://cran.r-project.org/src/contrib/Descriptions/WilcoxCV.html
http://cran.r-project.org/src/contrib/PACKAGES.html
java.io.FileNotFoundException : http://cran.r-project.org/src/contrib/PACKAGES.html
http://cran.r-project.org/web/packages
200
http://cran.r-project.org/web/packages/COSINE/index.html
200
http://cran.r-project.org/web/packages/digeR/index.html
200
http://cran.r-project.org/web/packages/DIME/
200
http://cran.r-project.org/web/packages/gputools
200
http://cran.r-project.org/web/packages/maticce
200
http://cran.r-project.org/web/packages/partDSA/index.html
200
http://cran.r-project.org/web/packages/pegas/index.html
200
http://cran.r-project.org/web/packages/phangorn/index.html
200
http://cran.r-project.org/web/packages/QuACN/
200
http://cran.r-project.org/web/packages/simone/
200
http://cran.r-project.org/web/packages/st/
200
http://cran.us.r-project.org
200
http://crisceb.area.na.cnr.it/angelo/
java.net.UnknownHostException : crisceb.area.na.cnr.it
http://crispi.genouest.org
200
http://cs.bgu.ac.il/
java.net.ConnectException : Connection refused
http://cs.brown.edu/people/braphael/software.html
200
http://cs.ru.nl/gori/software/MTR.tar.gz
java.io.FileNotFoundException : http://cs.ru.nl/gori/software/MTR.tar.gz
http://cs.tau.ac.il/
200
http://csb.gsc.riken.jp/yshira/software/clusterNetwork.zip
200
http://csb.stanford.edu/nbatada/VCN.html
java.io.FileNotFoundException : http://csb.stanford.edu/nbatada/VCN.html
http://csbdb.mpimp-golm.mpg.de/
200
http://csbdb.mpimp-golm.mpg.de/gmd.html
200
http://csbg.cnb.csic.es/mbrole
200
http://csbg.cnb.csic.es/mtserver
200
http://csbi.ltdk.helsinki.fi/CNAmet
200
http://csbi.ltdk.helsinki.fi/moksiskaan/
200
http://csbl.bmb.uga.edu/
200
http://csbl.bmb.uga.edu/publications/materials/tran/
200
http://csbl1.bmb.uga.edu/cgi-bin/Secretion/secretion.cgi
200
http://csbl1.bmb.uga.edu/GolgiP/
200
http://csg.sph.umich.edu/locuszoom
200
http://csrl.ee.nthu.edu.tw/bioinf/
java.io.FileNotFoundException : http://csrl.ee.nthu.edu.tw/bioinf/
http://cssb.biology.gatech.edu/iAlign
200
http://csweb.haifa.ac.il/library/
java.net.SocketTimeoutException : connect timed out
http://ctb.pku.edu.cn/main/SheGroup/MED_Start.htm
200
http://cts.fiehnlab.ucdavis.edu
200
http://ctwc.weizmann.ac.il
200
http://ctwc.weizmann.ac.il.
200
http://cubic.bioc.columbia.edu/eva
200
http://cubic.bioc.columbia.edu/genomes/RES/2002_bioinformatics/
200
http://cubic.bioc.columbia.edu/services/disis
200
http://cubic.bioc.columbia.edu/services/nlprot/
200
http://cuda-sim.sourceforge.net/
200
http://curie.utmb.edu/
200
http://cvtree.cbi.pku.edu.cn
200
http://cyrah.e
java.net.UnknownHostException : cyrah.e
http://cyrah.ebi.ac.uk:1111/Proj/Bio/SAT
java.net.UnknownHostException : cyrah.ebi.ac.uk
http://cyrah.ebi.ac.uk:1111/Serv/PDB_ISL/
java.net.UnknownHostException : cyrah.ebi.ac.uk
http://cytoprophet.cse.nd.edu
200
http://cytoscape.org
200
http://cytoscapeweb.cytoscape.org/
200
http://da.csml.org
200
http://dac.molbio.ku.dk/bioinformatics/MUTAGEN/
200
http://daisy.prevmed.northwestern.edu/
java.net.UnknownHostException : daisy.prevmed.northwestern.edu
http://darned.ucc.ie
200
http://darwin.uvigo.es
200
http://darwin.uvigo.es/rdp/rdp.html
200
http://darwin.uvigo.es/software/prottest3
200
http://darwin.zoology.gla.ac.uk/cgi-bin/build.pl
200
http://dasher.sbc.su.se
200
http://data.compbio.washington.edu/misc/downloads/nannotation_data/
200
http://datamining.dongguk.ac.kr/R/glcoxph
200
http://datf.cbi.pku.edu.cn
200
http://davinci.crg.es/estivill_lab/snpassoc
java.io.FileNotFoundException : http://davinci.crg.es/estivill_lab/snpassoc
http://daweb.ism.ac.jp/
200
http://daweb.ism.ac.jpyoshidar/GDA/
java.net.UnknownHostException : daweb.ism.ac.jpyoshidar
http://db.cse.ohio-state.edu/CellTrack
200
http://db.math.macalester.edu/goproject
java.net.SocketTimeoutException : connect timed out
http://db.systemsbiology.net/projects/local/mhc/acgt/
200
http://dbkgroup.org/handl/decoy_sets
200
http://dbkweb.ch.umist.ac.uk/handl/clustervalidation/
java.net.UnknownHostException : dbkweb.ch.umist.ac.uk
http://dbsr.duke.edu/pub/MedlineR
java.net.UnknownHostException : dbsr.duke.edu
http://dddc.ac.cn/adme
200
http://defiant.i2r.a-star.edu.sg/projects/BayesPromoter/
java.io.FileNotFoundException : http://defiant.i2r.a-star.edu.sg/projects/BayesPromoter/
http://dejavu.vbi.vt.edu/dejavu/
200
http://dendrome.ucdavis.edu/adept2/resequencing.html
java.io.IOException : Server returned HTTP response code: 403 for URL: http://dendrome.ucdavis.edu/adept2/resequencing.html
http://dense.sf.net
200
http://design.RNAi.jp
200
http://diana.uthct.edu
java.net.UnknownHostException : diana.uthct.edu
http://dibernado.tigem.it
java.net.UnknownHostException : dibernado.tigem.it
http://dig.ipk-gatersleben.de/SHMMs/ChIPchip/ChIPchip.html
200
http://digbio.missouri.edu/
200
http://digbio.missouri.edu/grninfer/
200
http://digbio.missouri.edu/primegens/
200
http://dip.doe-mbi.ucla.edu
200
http://diprogb.fli-leibniz.de
200
http://dir.niehs.nih.gov/dirbb/gapwm
200
http://dir.niehs.nih.gov/dirbb/lifiles/softlic.htm
200
http://dir.niehs.nih.gov/dirbb/oriogen/index.cfm
200
http://dir.niehs.nih.gov/dirnmr/nvassign
200
http://dir.niehs.nih.gov/microarray/datamining
200
http://discover.nci.nih.gov/affyprobeminer
200
http://discover.nci.nih.gov/OG/supplementaryMaterials.html
200
http://distill.ucd.ie/porter/
200
http://dl.dropbox.com/u/477240/changept.zip
200
http://dm.unife.it/parlea
200
http://dmi.uib.es/people/jairo/bio/ProtDeform
200
http://dmi.uib.es/ProtDeform/
200
http://dmle.org
200
http://dna.ccs.tulane.edu
200
http://dna.cs.byu.edu/gnumap
200
http://dna.cs.byu.edu/pathgen
200
http://dna.cs.gwu.edu
java.net.UnknownHostException : dna.cs.gwu.edu
http://dna.korea.ac.kr/pub/mohca
200
http://dna.leeds.ac.uk/qsv/
200
http://dna.ucdavis.edu/
java.net.SocketTimeoutException : connect timed out
http://dna.uio.no/salsa/
200
http://dnagarden.ims.u-tokyo.ac.jp/afujita/en/doku.php?id=ggranger
200
http://dnmad.bioinfo.cnio.es
200
http://dockground.bioinformatics.ku.edu
200
http://dockground.bioinformatics.ku.edu/UNBOUND/decoy/decoy.php
200
http://domaingraph.bioinf.mpi-inf.mpg.de
200
http://doqcs.ncbs.res.in
200
http://dot.bcm.tmc
java.net.UnknownHostException : dot.bcm.tmc
http://dot.ped.med.umich.edu:2000/pub/assoc_rules/assoc_rules.zip
java.io.FileNotFoundException : http://dot.ped.med.umich.edu:2000/pub/assoc_rules/assoc_rules.zip
http://dot.ped.med.umich.edu:2000/pub/assoc_rules/yeast_results.zip
java.io.FileNotFoundException : http://dot.ped.med.umich.edu:2000/pub/assoc_rules/yeast_results.zip
http://download.savannah.gnu.org/releases/par/par.tgz
200
http://dpdb.uab.es
200
http://dps.plants.ox.ac.uk/sequencing/proseq.htm
200
http://dptf.cbi.pku.edu.cn
200
http://dragon.bio.purdue.edu/3d-surfer
200
http://dragon.bio.purdue.edu/ESG/
200
http://dragon.kaist.ac.kr/gk
java.net.SocketTimeoutException : connect timed out
http://droog.gs.washington.edu/scimmkit
200
http://drtf.cbi.pku.edu.cn
200
http://dsplab.eng.umd.edu/
java.io.IOException : Server returned HTTP response code: 403 for URL: http://dsplab.eng.umd.edu/
http://dtai.cs.kuleuven.be/ml/systems/merci
200
http://dunbrack.fccc.edu/BioDownloader
200
http://dunbrack.fccc.edu/molide/molide.php
200
http://dunbrack.fccc.edu/ProtBuD.php
200
http://dynamics.iam.u-tokyo.ac.jp/DTA/
200
http://e-cell.org/
200
http://EAA.mpi-bn.mpg.de/
200
http://easyfig.sourceforge.net/
200
http://ecocyc.org
200
http://ecocyc.org:1555/HPY/organism-summary?object=HPY
java.net.SocketTimeoutException : connect timed out
http://econport.arizona.edu:8080/NetVis/index.html
java.net.SocketTimeoutException : connect timed out
http://ecrbase.dcode.org
200
http://ee.tamu.edu/
java.net.SocketTimeoutException : connect timed out
http://eecoli.kaist.ac.kr
200
http://egg.umh.es/iwocs/
java.net.SocketTimeoutException : Read timed out
http://egob.biomedicine.gu.se
200
http://eh3.uc.edu/gimm
200
http://ekhidna.biocenter.helsinki.fi/dali_lite/downloads/v3
200
http://ekhidna.biocenter.helsinki.fi/dali_server
200
http://ekhidna.biocenter.helsinki.fi/locp/
200
http://el-vira.googlecode.com
200
http://elm.eu.org/
200
http://embio.yonsei.ac.kr/haplowser
200
http://emu.src.riken.jp/MOCSphaser/MOCSphaser.zip
200
http://engine.euresist.org
200
http://engineering.utsa.edu/
200
http://envgen.nox.ac.uk/biolinux.html
200
http://epa.gov/ncct/dsstox/
200
http://ephpublic.aecom.yu.edu/sites/rkim/Supplementary
302
http://epigenomique.genopole.fr/
200
http://erebus.dokhlab.org
200
http://eresearch.fit.qut.edu.au/downloads
200
http://ergatis.sourceforge.net
200
http://err.bio.nyu.edu/cytoscape/bionetbuilder/
200
http://esbg.gatech.edu/jordan/software/map
200
http://esbtl.sf.net
200
http://EST-PAGE.binf.gmu.edu
200
http://eudoxus.scs.uiuc.edu/r3.html
java.net.UnknownHostException : eudoxus.scs.uiuc.edu
http://eureka.ims.u-tokyo.ac.jp/asian
java.net.UnknownHostException : eureka.ims.u-tokyo.ac.jp
http://everest.bic.nus.edu.sg/p2p/
200
http://evogen.molgen.mpg.de/server/substitution-analysis
200
http://evol.bio.lmu.de/statgen/software/treetime
java.io.FileNotFoundException : http://evol.bio.lmu.de/statgen/software/treetime
http://evol.nhri.org.tw/MamPhEA/
200
http://evolu3.ism.ac.jp/
java.net.SocketTimeoutException : connect timed out
http://evolution.gs.washington.edu/lamarc
200
http://evolution.sysu.edu.cn/mapview/
200
http://evolve.zoo
java.net.UnknownHostException : evolve.zoo
http://evolve.zoo.ox.ac.uk
200
http://evolve.zoo.ox.ac.uk/software/blastalign
200
http://evolver.psc.riken.jp/
200
http://exgen.ma.umist.ac.uk
200
http://exon.niaid.nih.gov/applications.html
200
http://exon.ucsd.edu/ShortFuse
200
http://expression.microslu.washington.edu/expression/kayee/medvedovic2003/medvedovic_bioinf2003.html
java.io.FileNotFoundException : http://expression.microslu.washington.edu/expression/kayee/medvedovic2003/medvedovic_bioinf2003.html
http://exprimer.ibab.ac.in/exprimer_html/exprimer.html
200
http://facs.biotech.kth.se
200
http://faculty.ucr.edu/
200
http://faculty.virginia.edu/wrpearson/fasta/PUBS/gonzalez09a
200
http://famhap.meb.uni-bonn.de
200
http://farrar.michael.googlepages.com/Smith-waterman
java.io.FileNotFoundException : http://sites.google.com/site/farrarmichael/Smith-waterman
http://fatcat.burnham.org/POSA
200
http://fbasimvis.ipk-gatersleben.de/
200
http://fc.isima.fr/
200
http://fcg.tamu.edu/C_Hunter/
200
http://fermi.utmb.edu/SDAP/index.html
200
http://fester.cs.dal.ca/manuel
200
http://ffas.burnham.org/svar/supp.html
200
http://ffas.burnham.org/XtalPred
200
http://fields.scripps.edu/XDIA
java.io.FileNotFoundException : http://fields.scripps.edu/XDIA
http://fields.scripps.edu/yada
200
http://fifi.ibbmc.u-psud.fr/DiMoVo
java.net.SocketTimeoutException : connect timed out
http://filtrest3d.genesilico.pl/
200
http://finder.sourceforge.net
200
http://fleece.ucsd.edu/
java.io.IOException : Server returned HTTP response code: 403 for URL: http://fleece.ucsd.edu/
http://flipper.services.came.sbg.ac.at
302
http://flora.acpfg.com.au/
200
http://fly.mpi-cbg.de/catmaid
200
http://flydev.berkeley.edu/cgi-bin/cld/submit.cgi
java.io.FileNotFoundException : http://flydev.berkeley.edu/cgi-bin/cld/submit.cgi
http://flydev.berkeley.edu/cgi-bin/GTEM/dmap_dm-ag/index_dmap.htm
java.io.FileNotFoundException : http://flydev.berkeley.edu/cgi-bin/GTEM/dmap_dm-ag/index_dmap.htm
http://flyex.ams.sunysb.edu/FlyEx/
java.net.SocketTimeoutException : connect timed out
http://foldalign.ku.dk/
200
http://foldalign.kvl.dk/
200
http://folk.uio.no/gillesg/AscB/
java.io.FileNotFoundException : http://folk.uio.no/gillesg/AscB/
http://folk.uio.no/gillesg/Bioinformatics-HMRF
java.io.FileNotFoundException : http://folk.uio.no/gillesg/Bioinformatics-HMRF
http://folk.uio.no/gillesg/CFM/SuppMat.pdf
java.io.FileNotFoundException : http://folk.uio.no/gillesg/CFM/SuppMat.pdf
http://folk.uio.no/gillesg/Geneland.html
java.io.FileNotFoundException : http://folk.uio.no/gillesg/Geneland.html
http://folk.uio.no/idasch/imp
200
http://folk.uio.no/thoree/FEST
200
http://foo.maths.uq.edu.au/
java.net.SocketTimeoutException : connect timed out
http://forkhead.cgb.ki.se/TFBS/
200
http://fps.sdsc.edu
java.net.SocketException : Network is unreachable
http://franklin.imgen.bcm.tmc.edu/OntologyTraverser/
200
http://fraser.qimr.edu.au/general/daleN/ssSNPer/
java.io.FileNotFoundException : http://fraser.qimr.edu.au/general/daleN/ssSNPer/
http://frl.lptc.u-bordeaux.fr
java.net.UnknownHostException : frl.lptc.u-bordeaux.fr
http://frpred.tuebingen.mpg.de
200
http://ftfd.snu.ac.kr/
java.net.ProtocolException : Server redirected too many times (20)
http://ftmap.bu.edu/
200
http://ftp.cs.wisc.edu/machine-learning/shavlik-group/programs/acmi/
200
http://ftp.maizegdb.org/open_source/locus_lookup/
200
http://func.med.harvard.edu/
200
http://function.cs.princeton.edu/ChARM/
200
http://function.princeton.edu/coalesce
200
http://function.princeton.edu/genesite/
200
http://function.princeton.edu/mitochondria
200
http://function.princeton.edu/sleipnir
200
http://function.princeton.edu/SPELL
200
http://furlonglab.embl.de/methods/tools/coco
200
http://gaia.biotech.vt.edu/goat/
java.net.UnknownHostException : gaia.biotech.vt.edu
http://galaxie.cgb.ki.se
java.net.NoRouteToHostException : No route to host
http://garban.tecnun.es
200
http://gardnerlab.bu.edu/SSEMLasso
200
http://gather.genome.duke.edu/
java.net.SocketTimeoutException : Read timed out
http://gauss.usouthal.edu/publ/logit/
200
http://gbic.biol.rug.nl/supplementary
java.io.FileNotFoundException : http://gbic.biol.rug.nl/supplementary
http://gbic.biol.rug.nl/supplementary/2009/ChromatinProfiles/
java.io.FileNotFoundException : http://gbic.biol.rug.nl/supplementary/2009/ChromatinProfiles/
http://gbnci.abcc.ncifcrf.gov/geo/
200
http://gc.bcm.tmc
java.net.UnknownHostException : gc.bcm.tmc
http://gclust.c.u-tokyo.ac.jp/Gclust_Download.html
java.net.SocketTimeoutException : connect timed out
http://gcrg.ucsd.edu/organisms/ecoli.html
java.io.FileNotFoundException : http://gcrg.ucsd.edu/organisms/ecoli.html
http://gefu.cribi.unipd.it/papers/miRNA-simulation/
200
http://gel.ahabs.wisc.edu/mauve
200
http://genapha.icapture.ubc.ca/PathTutorial
200
http://genapha.icapture.ubc.ca/SLIMS/index.jsp
200
http://gencolors.imb-jena.de
200
http://gene3d.biochem.ucl.ac.uk/Gene3D/
200
http://genebank.rda.go.kr/powercore/
java.io.FileNotFoundException : http://genebank.rda.go.kr/powercore/
http://genecanvas.ecgene.net
200
http://genecards.weizmann.ac.il/geneannot/
200
http://genecards.weizmann.ac.il/genenote/
200
http://genecensus.org/expression/translatome
200
http://genemachine.nhgri.nih.gov
200
http://genenetwork.sbl.bc.sinica.edu.tw/
200
http://genepath.org
200
http://genepro.ccb.sickkids.ca
java.net.UnknownHostException : genepro.ccb.sickkids.ca
http://genes.cse.wustl.edu
200
http://genes.toronto.edu
200
http://genesilico.pl/protmap2d.htm
200
http://genesis.UGent.be/dbtoolkit/
200
http://genetics.ich.ucl.ac.uk/linksearchtool
java.net.SocketTimeoutException : connect timed out
http://genetrack.googlecode.com
200
http://genex.hgu.mrc.ac.uk
200
http://genge.molgen.mpg.de
200
http://genie.Dartmouth.edu/SPACER/
200
http://geno3d-pbil.ibcp.fr
200
http://genomatix.gsf.de/cgi-bin/fastm2/fastm.pl
java.net.UnknownHostException : genomatix.gsf.de
http://genome-www.stanford.edu/cellcycle/
200
http://genome.crg.cat:9000/das/Selenoprofiles_ensembl
200
http://genome.crg.es/software/secisaln/
200
http://genome.cribi.unipd.it
java.net.UnknownHostException : genome.cribi.unipd.it
http://genome.cs.iastate.edu/CBL/DupTree
200
http://genome.cs.iastate.edu/Rainbow/
java.io.FileNotFoundException : http://genome.cs.iastate.edu/Rainbow/
http://genome.dfci.harvard.edu/
java.io.IOException : Server returned HTTP response code: 403 for URL: http://genome.dfci.harvard.edu/
http://genome.dkfz-heidelberg.de/
200
http://genome.fli-leibniz.de/software.html
200
http://genome.gbf.de/bioinformatics/
200
http://genome.gbf.de/wavepaper
200
http://genome.gsc.riken.jp/osc/english/software/
200
http://genome.imb-jena.de/dictyostelium/
200
http://genome.imim.es/cgi-bin/moby/GeneClustering_DataSubmission.cgi
200
http://genome.imim.es/software/gfftools/GFF2APLOT.html
200
http://genome.imim.es/webservices/
200
http://genome.jouy.inra.fr/eugene/cgi-bin/eugene_form.pl
200
http://genome.kbrin.uky.edu/fungi_tel/TruMatch/
java.net.SocketTimeoutException : connect timed out
http://genome.ku.dk/resources/mirclust
200
http://genome.life.nctu.edu.tw/MUSIC
java.net.SocketTimeoutException : connect timed out
http://genome.life.nctu.edu.tw/MUSICME
java.net.SocketTimeoutException : connect timed out
http://genome.nhgri.nih
java.net.UnknownHostException : genome.nhgri.nih
http://genome.nhgri.nih.gov/genemachine
java.io.FileNotFoundException : http://genome.nhgri.nih.gov/genemachine
http://genome.tugraz.at
200
http://genome.tugraz.at/BayesianClustering/
200
http://genome.tugraz.at/lda
200
http://genome.tugraz.at/Software/ClusterControl
200
http://genome.ucsc.edu
200
http://genome.uiowa.edu/pubsoft/software.html
302
http://genomes.urv.es/topd
200
http://genometools.org/annotationsketch.html
200
http://genomics.catholic.ac.kr/arrayCGH/
200
http://genomics.eu.org/
java.net.SocketTimeoutException : connect timed out
http://genomics.eu.org/spip/-Bioinformatics-tools-
java.net.SocketTimeoutException : connect timed out
http://genomics.imim.es/peaks
200
http://genomics.lbl.gov/llda
200
http://genomics.senescence.info/uarrays/signatures.html
200
http://GenomicsPortals.org/
200
http://genomine.org/edge/
200
http://genoplante-info.infobiogen.fr/spads
java.net.UnknownHostException : genoplante-info.infobiogen.fr
http://genoplotr.r-forge.r-project.org/
200
http://genopole.toulouse.inra.fr/ENDscript
java.io.FileNotFoundException : http://genopole.toulouse.inra.fr/ENDscript
http://genoviz.sourceforge.net
200
http://genoweb.univ-rennes1.fr/tom_dog/AutoGRAPH/
200
http://genserv.anat.ox.ac.uk/software
200
http://geocities.com/jg_liao
java.io.FileNotFoundException : http://geocities.com/jg_liao
http://geometry.molmovdb.org
200
http://gepas.bioinfo.cipf.es/tutorial/prophet.html
java.io.FileNotFoundException : http://gepas.bioinfo.cipf.es/tutorial/prophet.html
http://gepasi.dbs.aber.ac.uk/softw/Gepasi
java.net.UnknownHostException : gepasi.dbs.aber.ac.uk
http://germonline.biochem.s.u-tokyo.ac.jp/
java.net.UnknownHostException : germonline.biochem.s.u-tokyo.ac.jp
http://germonline.igh.cnrs.fr/
java.net.UnknownHostException : germonline.igh.cnrs.fr
http://germonline.unibas.ch/
200
http://germonline.yeastgenome.org/
java.net.ConnectException : Connection refused
http://gersteinlab.org/proj/funcsim
200
http://geta.life.uiuc.edu/
java.net.SocketTimeoutException : connect timed out
http://getbonnie.org
200
http://getgalaxy.org
301
http://getutopia.com
200
http://gf.genome.ad.jp/
java.net.UnknownHostException : gf.genome.ad.jp
http://gforge.nci.nih.gov/projects/visda/
200
http://ghmm.org/gql
200
http://gi.cebitec.uni-bielefeld.de/qalign
200
http://gift.cryst.bbk.ac.uk/gift
java.io.IOException : Server returned HTTP response code: 500 for URL: http://gift.cryst.bbk.ac.uk/gift/
http://gin.ncibi.org
200
http://gin.univ-mrs.fr/GINsim/
200
http://gin.univ-mrs.fr/webdistin
200
http://ginger.ucdavis.edu/paloverde/paloverde.html
java.net.SocketTimeoutException : connect timed out
http://ginger.ucdavis.edu/r8s
java.net.SocketTimeoutException : connect timed out
http://gladyshevlab.bwh.harvard.edu/trace_element/
200
http://glinka.bio.neu.edu/SEDB/SEDB.html
java.net.NoRouteToHostException : No route to host
http://globin.bio.warwick.ac.uk/psipred/
java.io.FileNotFoundException : http://globin.bio.warwick.ac.uk/psipred/
http://gloome.tau.ac.il/
200
http://glscompute.gis.a-star.edu.sg/
java.net.UnknownHostException : glscompute.gis.a-star.edu.sg
http://glycobase.ucd.ie
200
http://gmc.mdc-berlin.de/alohomora/
200
http://gmod-dbsf.googlecode.com
200
http://gmod.cvs.sourceforge.net/gmod/apollo
200
http://gmod.org
200
http://go.warwick.ac.uk/majuarez/home/materials
200
http://go.warwick.ac.uk/SimMLST
java.io.FileNotFoundException : http://go.warwick.ac.uk/SimMLST
http://gobics.de/software
200
http://goldengate.case.edu/projects/arcs
java.net.UnknownHostException : goldengate.case.edu
http://golgi.ebi.ac.uk:8080/Spearmint/
java.net.UnknownHostException : golgi.ebi.ac.uk
http://gordion.hpc.eng.ku.edu.tr/prism
200
http://gostat.wehi.edu.au
200
http://gp.fms.saitama-u.ac.jp/
200
http://gpcr.biocomp.unibo.it/cgi/predictors/cchmmprof/pred_cchmmprof.cgi
200
http://gpcr.biocomp.unibo.it/cgi/predictors/K-Fold/K-Fold.cgi
200
http://gpcr.biocomp.unibo.it/cgi/predictors/PhD-SNP/PhD-SNP.cgi
200
http://gpcr.biocomp.unibo.it/predictors/
java.io.IOException : Server returned HTTP response code: 401 for URL: http://gpcr.biocomp.unibo.it/predictors/
http://gpcr2.biocomp.unibo.it/cgi/predictors/I-Mutant2.0/I-Mutant2.0.cgi
200
http://gpi.unibe.ch
200
http://gremlin1.gdcb.iastate.edu/
java.io.IOException : Server returned HTTP response code: 403 for URL: http://gremlin1.gdcb.iastate.edu/
http://gremlin1.zool.iastate.edu/cgi-bin/g
java.io.FileNotFoundException : http://gremlin1.zool.iastate.edu/cgi-bin/g
http://gremlin1.zool.iastate.edu/cgi-bin/s
java.io.FileNotFoundException : http://gremlin1.zool.iastate.edu/cgi-bin/s
http://grid.inb.uni-luebeck.de/
java.net.SocketTimeoutException : connect timed out
http://grimmond.imb.uq.edu.au/RNA-MATE/
200
http://grimmond.imb.uq.edu.au/uniqueome/
200
http://grimmond.imb.uq.edu.au/X-MATE/
200
http://gscan.well.ox.ac.uk/software
200
http://gscope.gsc.riken.go.jp
java.net.UnknownHostException : gscope.gsc.riken.go.jp
http://gsp.tamu.edu/Publications/BNs/bn.htm
200
http://gsp.tamu.edu/Publications/rejectoption/
200
http://gsp.tamu.edu/Publications/supplement.htm
java.io.FileNotFoundException : http://gsp.tamu.edu/Publications/supplement.htm
http://gsp.tamu.edu/Publications/supplementary/ghaffari10a/
200
http://gsp.tamu.edu/Publications/supplementary/yousefi09a/
200
http://gspsnap.tamu.edu/gspweb/zxb/missing_zxb/
java.net.SocketTimeoutException : connect timed out
http://gspsnap.tamu.edu/smallsample/
java.net.SocketTimeoutException : connect timed out
http://gto.kaist.ac.kr/
java.net.UnknownHostException : gto.kaist.ac.kr
http://guanine.evolbio.mpg.de/alfy/
200
http://guanine.evolbio.mpg.de/kr2/
200
http://guinevere.otago.ac.nz/stats.html
200
http://guitar.rockefeller.edu/approximately
java.net.UnknownHostException : guitar.rockefeller.edu
http://guitar.rockefeller.edu/DBAli/
java.net.UnknownHostException : guitar.rockefeller.edu
http://guitar.rockefeller.edu/modview
java.net.UnknownHostException : guitar.rockefeller.edu
http://guppy.mpe.nus.edu.sg/
200
http://gurkan.case.edu/software
200
http://gview.ca
301
http://hammerlab.biosci.arizona.edu/software.html
200
http://haplopainter.sourceforge.net/
200
http://harlequin.jax.org/atpacdb/
200
http://harlequin.jax.org/pacdb/
200
http://harvester.embl.de
java.io.FileNotFoundException : http://harvester.embl.de
http://hatch.cpmc.columbia.edu/highresmrs.html
200
http://hawaii.aist-nara.ac.jp/
200
http://hci.iwr.uni-heidelberg.de/mip/proteomics
200
http://hci.iwr.uni-heidelberg.de/MIP/Software
200
http://hci.iwr.uni-heidelberg.de/software.php
200
http://hcv-db.org
java.net.UnknownHostException : hcv-db.org
http://hcv.lanl.gov
200
http://helab.bioinformatics.med.umich.edu/crcview/
200
http://heliquest.ipmc.cnrs.fr
200
http://helix.ex.ac.uk/metabolism
java.net.UnknownHostException : helix.ex.ac.uk
http://helix.gersteinlab.org
200
http://hercules.tigem.it/TargetFinder.html
java.net.UnknownHostException : hercules.tigem.it
http://hesweb1.med.virginia.edu/bioinformatics
200
http://hex.loria.fr/
200
http://hexserver.loria.fr/
200
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
200
http://hgdownload.cse.ucsc.edu/admin/jksrc.zip
200
http://hgdownload.cse.ucsc.edu/downloads.html
200
http://hhsvm.dlakiclab.org/
200
http://hits.isb-sib.ch
200
http://hiv.lanl.gov/content/sequence/MOSAIC/
200
http://hivdb.stanford.edu
200
http://hivdb.stanford.edu/pages/resources.html
200
http://hkumath.hku.hk/web/link/CLUSTAG/CLUSTAG.html
java.io.FileNotFoundException : http://hkumath.hku.hk/web/link/CLUSTAG/CLUSTAG.html
http://hollywood.bx.psu.edu/TabSearch
200
http://home.gwu.edu/
200
http://home.uchicago.edu/
200
http://home.uchicago.edu/abney/Software.html
java.io.FileNotFoundException : http://home.uchicago.edu/abney/Software.html
http://home.ustc.edu.cn/
200
http://homepages.inf.ed.ac.uk/gsanguin/
200
http://homepages.inf.ed.ac.uk/gsanguin/TFInfer.html
200
http://homepages.inf.ed.ac.uk/s0976841/largeComb/
200
http://homepages.lshtm.ac.uk/tgclark/downloads
200
http://homepages.uc.edu/
200
http://homepages.uni-tuebingen.de/beitz/
java.io.FileNotFoundException : http://homepages.uni-tuebingen.de/beitz/
http://homepages.uni-tuebingen.de/beitz/tse.h
java.io.FileNotFoundException : http://homepages.uni-tuebingen.de/beitz/tse.h
http://homes.dsi.unimi.it/
200
http://homes.esat.kuleuven.be/
200
http://homgl.biologie.hu-berlin.de/
java.net.SocketTimeoutException : connect timed out
http://hornbill.cspp.latrobe.edu.au/
java.net.NoRouteToHostException : No route to host
http://hto-c.usc.edu:8000/msms/suffix/
java.net.UnknownHostException : hto-c.usc.edu
http://hts.rutgers.edu/filter
200
http://humgen.med.uu.nl/publications/vanbakel/pathway/
200
http://humphry.chem.wesleyan.edu:8080/MDDNA
java.net.UnknownHostException : humphry.chem.wesleyan.edu
http://hydrodictyon.eeb.uconn.edu/ncl/
200
http://i-cite.org
200
http://iant.toulouse.inra.fr/FrameDP
200
http://iasi.bu.edu/
200
http://ibb.uab.es/snow/
200
http://ibi.imim.es/
200
http://ibi.imim.es/DisGeNET/DisGeNETweb.html
200
http://ibi.vu.nl/programs/efcwww
200
http://ibi.zju.edu.cn/birdflu/
200
http://ibi.zju.edu.cn/pgl/pip/
200
http://ibi.zju.edu.cn/software/qtlnetwork
200
http://ibis.inrialpes.fr/
200
http://ibis.tau.ac.il/miRNAkey
200
http://ibivu.cs.vu.nl/programs/acewww/
200
http://ibivu.cs.vu.nl/programs/trustwww
200
http://ibivu.cs.vu.nl/programs/yaspinwww/
200
http://icb.med.cornell.edu/services/propertm/start
200
http://icb.mssm.edu/crt/RbDg/index.xml
java.net.SocketTimeoutException : connect timed out
http://icb.usp.br/
java.net.SocketTimeoutException : connect timed out
http://iclab.life.nctu.edu.tw/POPI
200
http://icorn.sourceforge.net
200
http://ict.ewi.tudelft.nl/
200
http://idbps.tau.ac.il/
200
http://idefix.univ-rennes1.fr:8080/Dogs/help_rh-server.html
java.io.FileNotFoundException : http://idefix.univ-rennes1.fr:8080/Dogs/help_rh-server.html
http://idefix.univ-rennes1.fr:8080/Dogs/rh-server.html
java.io.FileNotFoundException : http://idefix.univ-rennes1.fr:8080/Dogs/rh-server.html
http://if.kaist.ac.kr/
java.net.UnknownHostException : if.kaist.ac.kr
http://ifold.dokhlab.org
200
http://iFoldRNA.dokhlab.org
200
http://ifr69.vjf.inserm.fr/lbe
200
http://igb.bioviz.org
200
http://igbmc.u-strasbg.fr/GOAnno/GOAnno.html
200
http://igbmc.u-strasbg.fr/GOAnno/GOAnnoHelp.html
200
http://ignm.ccbb.pitt.edu/oPCA_Online.htm
200
http://ihg.gsf.de/cgi-bin/mueller/webehh.pl
200
http://iir.csie.ncku.edu.tw/
200
http://iisr.cse.yzu.edu.tw:8000/PubMed-EX/
java.net.SocketTimeoutException : connect timed out
http://ijsr32.infj.ulster.ac.uk/
java.net.UnknownHostException : ijsr32.infj.ulster.ac.uk
http://IlluminaGUI.dnsalias.org
java.net.UnknownHostException : IlluminaGUI.dnsalias.org
http://imat.cs.tau.ac.il/
java.net.SocketTimeoutException : Read timed out
http://img.cs.man.ac.uk/tambis
200
http://img.jgi.doe.gov/m
200
http://imgt.cines.fr
200
http://immunax.dfci.harvard.edu/bioinformatics/epimhc/
java.io.FileNotFoundException : http://immunax.dfci.harvard.edu/bioinformatics/epimhc/
http://impact.nihs.go.jp/RDB.html
java.net.SocketTimeoutException : connect timed out
http://imtech.res.in/raghava/betatpred/
200
http://indra.mullins.microbiol.washington.edu/blast/viroblast.php
200
http://industry.ebi.ac.uk/JavaShade
java.net.UnknownHostException : industry.ebi.ac.uk
http://infernal.janelia.org
200
http://info.med.yale.edu/genetics/kkidd/programs.html
200
http://informatics-eskitis.griffith.edu.au/SpecificityServer
200
http://informatics.systemsbiology.net/DSection
200
http://innovation.swmed.edu/IRIDESCENT/GO_relationships.htm
java.net.SocketTimeoutException : Read timed out
http://insilico.ehu.es/DDSL
200
http://insilico.utulsa.edu/snprank
200
http://instancestore.man.ac.uk
java.io.IOException : Server returned HTTP response code: 500 for URL: http://instancestore.man.ac.uk
http://integromics.kobic.re.kr/GAzer/
200
http://intelligent.eic.osaka-sandai.ac.jp
java.net.SocketTimeoutException : connect timed out
http://intelligent.eic.osaka-sandai.ac.jp/chenen/software/MNAligner
java.net.SocketTimeoutException : connect timed out
http://interactomics.org
200
http://interdom.lit.org.sg
java.net.UnknownHostException : interdom.lit.org.sg
http://intersnp.meb.uni-bonn.de
200
http://intron.bic.nus.edu.sg/midb/midb.html
java.net.SocketTimeoutException : connect timed out
http://intron.bic.nus.edu.sg/seg/
java.net.SocketTimeoutException : connect timed out
http://invention.swmed.edu/
java.net.SocketTimeoutException : Read timed out
http://iossifovlab.cshl.edu/figurome/
200
http://ipep.moffitt.org
200
http://ipfam.sanger.ac.uk/graph
200
http://ipht.cea.fr/protein.php
200
http://ipubmed.ics.uci.edu/
200
http://isga.cgb.indiana.edu/
200
http://isiosf.isi.it/
200
http://ismp.csie.ncku.edu.tw/
200
http://isorank.csail.mit.edu/
200
http://itb.biologie.hu-berlin.de/
200
http://itol.embl.de
200
http://itsa.ucsf.edu/
java.net.UnknownHostException : itsa.ucsf.edu
http://ittc.ku.edu/
200
http://iubio.bio.indiana.edu/soft/molbio/align/
200
http://iubio.bio.indiana.edu/soft/molbio/pattern/cpg_islands/
200
http://ixa2.si.ehu.es/ukb/
200
http://ixdb.mpimg-berlin-dahlem.mpg.de
java.net.UnknownHostException : ixdb.mpimg-berlin-dahlem.mpg.de
http://jaguar.genetica.uma.es/anagram.htm
java.net.SocketTimeoutException : connect timed out
http://jakob.genetik.uni-koeln.de/bioinformatik/people/nora/nora.html
200
http://java-ml.sf.net
200
http://java.sun.com
200
http://jay.bioinformatics.ku.edu/download/tracker/
java.net.UnknownHostException : jay.bioinformatics.ku.edu
http://jay.bioinformatics.ku.edu/tracker/index.html
java.net.UnknownHostException : jay.bioinformatics.ku.edu
http://jclust.embl.de/
200
http://jcsmr.anu.edu.au/dmm/humgen
java.io.FileNotFoundException : http://jcsmr.anu.edu.au/dmm/humgen
http://jdrf.neurology.med.umich.edu/SciMiner/
200
http://jerry.cs.uga.edu/
java.net.UnknownHostException : jerry.cs.uga.edu
http://jianglab.ibp.ac.cn/lims/cisrr/cisrr.html
200
http://jic-bioinfo.bbsrc.ac.uk/bioinformatics-research/software/index.html
java.io.FileNotFoundException : http://jic-bioinfo.bbsrc.ac.uk/bioinformatics-research/software/index.html
http://jic-bioinfo.bbsrc.ac.uk/bioinformatics-research/staff/graham_etherington/RAT.htm
java.io.FileNotFoundException : http://jic-bioinfo.bbsrc.ac.uk/bioinformatics-research/staff/graham_etherington/RAT.htm
http://jigcell.biol.vt.edu
200
http://jilab.biostat.jhsph.edu/database/cgi-bin/hmChIP.pl
200
http://jjj.biochem.sun.ac.za/
200
http://jjj.vbi.vt.edu/
java.net.UnknownHostException : jjj.vbi.vt.edu
http://jose.med.kuleuven.be/
200
http://jSquid.sbc.su.se
200
http://kamit.med.u-tokai.ac.jp/
java.net.SocketTimeoutException : connect timed out
http://kanehisa.kuicr.kyoto-u.ac.jp/Paper/kcam/glycanMatrix0.1.txt
java.io.FileNotFoundException : http://www.kanehisa.jp/Paper/kcam/glycanMatrix0.1.txt
http://kapow.dc.uba.ar/patterns/
200
http://keia.i3s.unice.fr/?Implementations:GenMiner
java.io.FileNotFoundException : http://keia.i3s.unice.fr/?Implementations:GenMiner
http://kellogg.umich.edu/madeline
200
http://kgml-ed.ipk-gatersleben.de
200
http://ki-www2.intellektik.informatik.tu-darmstadt.de/
java.net.UnknownHostException : ki-www2.intellektik.informatik.tu-darmstadt.de
http://kiefer.stat.ucla.edu/lap2/download/bti656_supplement.pdf
java.net.UnknownHostException : kiefer.stat.ucla.edu
http://kiefer.stat.ucla.edu/lap2/download/KL_supplement.pdf
java.net.UnknownHostException : kiefer.stat.ucla.edu
http://kinase
java.net.UnknownHostException : kinase
http://kinase.ucsf.edu/ksd
java.net.SocketTimeoutException : connect timed out
http://kirac.case.edu/PROTAN
java.net.UnknownHostException : kirac.case.edu
http://kiwi.cs.dal.ca/
200
http://kiwi.cs.dal.ca/Software/PICA
200
http://kiwi.cs.dal.ca/Software/STAMP
200
http://knowledgemap.mc.vanderbilt.edu/research
200
http://kokki.uku.fi/bioinformatics/mirsom
200
http://korflab.ucdavis.edu/Datasets
200
http://kosik-web.mcdb.ucsb.edu/evolmap/index.htm
200
http://krauthammerlab.med.yale.edu/imagefinder/
200
http://krauthammerlab.med.yale.edu/mu2a
200
http://kulibin.mit.edu/coc/
200
http://kurata21.bio.kyutech.ac.jp/grid/grid_layout.htm
200
http://kweelt.sourceforge.net/
200
http://labs.csb.utoronto.ca/yang/TE_Displayer
200
http://labs.genome.duke.edu/FureyLab/cluster_boost.php
200
http://labs.systemsbiology.net/bolouri/models/galconcept.dizzy
200
http://labs.systemsbiology.net/bolouri/software/Dizzy/
200
http://lagan.stanford.edu
200
http://lagash.dft.unipa.it/IR.html
java.io.FileNotFoundException : http://lagash.dft.unipa.it/IR.html
http://lage.sookmyung.ac.kr
200
http://lamp.icsi.berkeley.edu/lamp
200
http://lcbb.epfl.ch
200
http://lccb.scripps.edu
java.net.UnknownHostException : lccb.scripps.edu
http://lcg.rit.albany.edu/dp-bind
200
http://lcg.rit.albany.edu/ProBias
200
http://leelab.nci.nih.gov/leelab/jsp/IGDM/IGDM.html
200
http://leger2.gbf.de/cgi-bin/vis-o-bac.pl
200
http://legumetfdb.psc.riken.jp/
200
http://lehrach.com/wolfgang/dmf
java.io.FileNotFoundException : http://homepages.inf.ed.ac.uk/s0239540/lehrach/wolfgang/dmf
http://leili-lab.cmb.usc.edu/yeastaging/projects/MARD/
java.net.UnknownHostException : leili-lab.cmb.usc.edu
http://lgb.unige.ch/arlequin/
java.net.SocketTimeoutException : connect timed out
http://lgsun.grc.nia.nih.gov/ANOVA/
200
http://liao.cis.udel.edu/website/servers/modmod
200
http://liao.cis.udel.edu/website/servers/TMMOD/
200
http://lie.fe.uni-lj.si/bestrf
200
http://lief.if.ufrgs.br/pub/biosoftwares/viacomplex
200
http://ligand-depot.rutgers.edu/
200
http://Ligand.Info
200
http://line.imb.ac.ru/ChIPMunk
200
http://line.imb.ac.ru/DMMPMM
200
http://linkage.rockefeller.edu/pawe3d/
200
http://linus.nci.nih.gov/BRB-ArrayTools.html
200
http://linus.nci.nih.gov/brb/TechReport.htm
200
http://linus.nci.nih.gov/Data/LAU203_Peptide.pdf
200
http://linus.nci.nih.gov/Data/YounA/LeTICE.zip
200
http://linus.nci.nih.gov/Data/YounA/software.zip
200
http://linzer.blm.cs.cmu.edu/tmpro/
java.net.UnknownHostException : linzer.blm.cs.cmu.edu
http://lipid.biocomp.unibo.it/
200
http://lipm-bioinfo.toulouse.inra.fr/biomoby/PlayMOBY/
200
http://lipm-bioinfo.toulouse.inra.fr/Mobyle
200
http://lis-upmc.snv.jussieu.fr/lis/?q=en/resources/softwares/xper2
java.io.FileNotFoundException : http://lis-upmc.snv.jussieu.fr/lis/?q=en/resources/softwares/xper2
http://liulab.dfci.harvard.edu/CEAS
200
http://liulab.dfci.harvard.edu/Software/MBR/MBR.htm
200
http://llama.med.harvard.edu/funcassociate
200
http://llama.med.harvard.edu/Software.html
200
http://llama.med.harvard.edu/synergizer/doc
200
http://llama.med.harvard.edu/synergizer/translate
200
http://locus.jouy.inra.fr/soft/cloneit/clonei
java.io.FileNotFoundException : http://locus.jouy.inra.fr/soft/cloneit/clonei
http://lombardi.georgetown.edu/labpage
200
http://lpgws.nci.nih.gov/cgi-bin/GeneViewer.cgi
200
http://ls-snp.icm.jhu.edu/ls-snp-pdb
200
http://ls11-www.cs.tu-dortmund.de/people/marschal/paa_md/
200
http://ls2-www.cs.uni-dortmund.de/
200
http://lussierlab.org/GO-Module
200
http://lutece.rutgers.edu/ss_fold_predictions
java.net.SocketTimeoutException : connect timed out
http://lutece.rutgers.edu/ssas
java.net.SocketTimeoutException : connect timed out
http://luz.uab.es/transcout/
java.net.UnknownHostException : luz.uab.es
http://lyle.smu.edu/IDA/EMMSA/
200
http://m3d.bu.edu
200
http://mafft.cbrc.jp/alignment/software/
java.net.SocketTimeoutException : Read timed out
http://magnet.c2b2.columbia.edu/mutagenesys/
200
http://magnet.systemsbiology.net/hac
200
http://mail.cmu.edu.tw/
java.io.IOException : Server returned HTTP response code: 403 for URL: http://mail.cmu.edu.tw/
http://mail.ustc.edu.cn/
200
http://maine.ebi.ac.uk:8000/services/cogent/
java.net.UnknownHostException : maine.ebi.ac.uk
http://maizegdb.org/cgi-bin/locus_lookup.cgi
200
http://mako.cgl.ucsf
java.net.UnknownHostException : mako.cgl.ucsf
http://malde.org/
200
http://malthus.micro.med.umich.edu/Bioinformatics
200
http://mammag.web.uci.edu/bin/view/Mitowiki/ProjectDNACompression
java.io.FileNotFoundException : http://mammag.web.uci.edu/bin/view/Mitowiki/ProjectDNACompression
http://mammoth.bcm.tmc.edu/
200
http://mammoth.bcm.tmc.edu/eta/
200
http://mammoth.bcm.tmc.edu/traceview/HelpDocs/PyETVHelp/pyInstructions.html
200
http://mammoth.bcm.tmc.edu/traceview/index.html
200
http://mammoth.bii.a-star.edu.sg/gprimer/
java.net.UnknownHostException : mammoth.bii.a-star.edu.sg
http://mammoth.bii.a-star.edu.sg/webservices/htblast/index.html
java.net.UnknownHostException : mammoth.bii.a-star.edu.sg
http://mapgaps.igs.umaryland.edu
200
http://mapsp.ifg.uni-muenster.de/
200
http://maq.sourceforge.net
200
http://mariwork.iq.usp.br/dvar/
java.net.NoRouteToHostException : No route to host
http://mars.kribb.re.kr:8080/tfExplorer/
java.net.SocketTimeoutException : connect timed out
http://masish.uab.cat/
200
http://masqot-gui.sourceforge.net/
200
http://mastr.binf.ku.dk/
200
http://math.berkeley.edu/
200
http://math.univ-toulouse.fr/biostat
200
http://mathbio.nimr.mrc.ac.uk/
200
http://matrise.uio.no/marray/marray.html
java.net.SocketTimeoutException : connect timed out
http://matrixdb.ibcp.fr
200
http://mavisto.ipk-gatersleben.de/
200
http://mbel.kaist.ac.kr/
200
http://mbel.kaist.ac.kr/mfaml/
java.io.FileNotFoundException : http://mbel.kaist.ac.kr/mfaml/
http://mbi.dkfz-heidelberg.de/mbi/research/cellsim/ales
java.io.FileNotFoundException : http://mbi.dkfz-heidelberg.de/mbi/research/cellsim/ales
http://mblab.wustl.edu/software/grendel/
200
http://mblab.wustl.edu/software/pairagon/
200
http://mbs.cbrc.jp/poodle/poodle-l.html
200
http://mbs.cbrc.jp/poodle/poodle-s.html
200
http://mcbc.usm.edu/gofetcher/
java.net.SocketTimeoutException : connect timed out
http://mccammon.ucsd.edu/
200
http://mcg.ustc.edu.cn/rpg/mird/mird.php
200
http://mech.ctb.pku.edu.cn/MetaTISA/
java.net.SocketTimeoutException : connect timed out
http://mech.ctb.pku.edu.cn/protisa/TriTISA
java.net.SocketTimeoutException : connect timed out
http://medblast.sibsnet.org
200
http://medeller.info
200
http://melolab.org/supmat.html
200
http://meltdb.cebitec.uni-bielefeld.de
301
http://membraneproteins.swan.ac.uk/TMLOOP
200
http://meme.nbcr.net
java.net.SocketException : Network is unreachable
http://meme.sdsc.edu
java.net.SocketException : Network is unreachable
http://meme.sdsc.edu/MCAST/paper
java.net.SocketException : Network is unreachable
http://mendel.cs.rhul.ac.uk/
200
http://mendel.gene.cwru.edu/laframboiselab/
200
http://mendel.imp.univie.ac.at/sat/DAS/DAS.html
200
http://mendel.imp.univie.ac.at/taxonomy/
java.io.FileNotFoundException : http://mendel.imp.ac.at/taxonomy/
http://mendel.mc.duke.edu/bioinformatics/
java.net.SocketTimeoutException : connect timed out
http://mendes.vbi.vt.edu/tiki-index.php?page=Software
200
http://mep.bio.psu.edu/adaptivevol.html
java.net.SocketTimeoutException : connect timed out
http://mesord.sourceforge.net
200
http://mesquiteproject.org/ontology/
200
http://meta-dp.bioinformatics.buffalo.edu
java.net.SocketTimeoutException : connect timed out
http://metagenealyse.mpimp-golm.mpg.de/
200
http://metagenomics.atc.tcs.com/binning/SOrt-ITEMS
200
http://metagenomics.atc.tcs.com/SPHINX/
200
http://metagenomics.uv.es/CROC/
200
http://metaldetector.dsi.unifi.it
200
http://metnet.vrac.iastate.edu/MetNet_fcmodeler.htm
200
http://metnetdb.gdcb.iastate.edu/medkit
java.io.FileNotFoundException : http://metnetdb.gdcb.iastate.edu/medkit
http://metpa.metabolomics.ca
java.net.ProtocolException : Server redirected too many times (20)
http://metscape.ncibi.org/tryplugin.html
java.io.FileNotFoundException : http://metscape.ncibi.org/tryplugin.html
http://mged.sourceforge.net/ontologies/index.php
200
http://micro-gen.ouhsc.edu/
200
http://microarray.cnmcresearch.org/pgadatatable.asp
java.io.FileNotFoundException : http://microarray.cnmcresearch.org/pgadatatable.asp
http://microarray.cpmc.columbia.edu/matrix2png
java.net.ConnectException : Connection refused
http://microarray.crump.ucla.edu/focus
java.io.IOException : Server returned HTTP response code: 500 for URL: http://microarray.crump.ucla.edu/focus
http://microarray.georgetown.edu/web/files/bioinf.htm
200
http://microarray.imb.uq.edu.au/golgi/
java.io.FileNotFoundException : http://microarray.imb.uq.edu.au/golgi
http://microarray.omrf.org/publications/2004/knowlton/MDAT.zip
java.net.UnknownHostException : microarray.omrf.org
http://microarray.ym.edu.tw/tools/arrayfusion
200
http://microbial.informatics.indiana.edu/acs
200
http://microrna.gr/mirpath
200
http://mimi.ncibi.org
200
http://mimirna.centenary.org.au
200
http://minnou.cchmc.org
200
http://minorthird.sourceforge.net
200
http://mips.gsf.de/CronosWSService/CronosWS?wsdl
200
http://mips.gsf.de/genre/proj/cronos/index.html
200
http://mips.gsf.de/genre/proj/dima
200
http://mips.gsf.de/proj/bfab
200
http://mips.gsf.de/proj/dics
200
http://mips.gsf.de/proj/est
200
http://mips.gsf.de/proj/funat
200
http://mips.gsf.de/proj/hobitws/services/DocSimapService?wsdl
java.io.FileNotFoundException : http://hobit.sourceforge.net/ws/services/DocSimapService?wsdl
http://mips.gsf.de/proj/hobitws/services/RPCSimapService?wsdl
java.io.FileNotFoundException : http://hobit.sourceforge.net/ws/services/RPCSimapService?wsdl
http://mips.gsf.de/proj/regulomips/credo.htm
java.io.FileNotFoundException : http://mips.helmholtz-muenchen.de/proj/regulomips/credo.htm
http://mips.gsf.de/services/analysis/gepard
200
http://mips.gsf.de/services/analysis/simap/
java.io.FileNotFoundException : http://mips.helmholtz-muenchen.de/services/analysis/simap/
http://mirdb.org
200
http://miron.ibb.waw.pl/elise/
200
http://mirrors.rcsb.org//SMS
java.io.FileNotFoundException : http://mirrors.rcsb.org//SMS
http://mirrors.rcsb.org//SMS/STINGm/consseq/
java.io.FileNotFoundException : http://mirrors.rcsb.org//SMS/STINGm/consseq/
http://mirrors.rcsb.org/SMS
java.io.FileNotFoundException : http://mirrors.rcsb.org/SMS
http://misearch.ncibi.org
200
http://mitopred.sdsc.edu
java.net.UnknownHostException : mitopred.sdsc.edu
http://mllab.sogang.ac.kr/
200
http://mmb.pcb.ub.es/DNAlive/
200
http://mmb.pcb.ub.es/FlexServ
200
http://mmtx.nlm.nih.gov
200
http://mobyle.pasteur.fr
200
http://mobyle.rpbs.univ-paris-diderot.fr
200
http://mocklerlab-tools.cgrb.oregonstate.edu/
200
http://model.nmr.ru/platinum/
200
http://models.cellml.org
200
http://models.physiomeproject.org/
200
http://modem.ucsd.edu/won/eHMM.tar.gz
200
http://molbio.nmsu.edu:81
java.net.SocketTimeoutException : connect timed out
http://molevol.ibmb.csic.es/Ktreedist.html
java.net.UnknownHostException : molevol.ibmb.csic.es
http://mom.csbc.vcu.edu
200
http://mombasa.anthro.utah.edu/wooding/
java.net.SocketTimeoutException : connect timed out
http://mombasa.anthro.utah.edu/wooding/PopHist
java.net.SocketTimeoutException : connect timed out
http://monkey.belozersky.msu.ru/NPIDB/
200
http://monkeysnp.ohsu.edu/snp/
200
http://monkshood.colorado.edu/theseus/
java.net.SocketTimeoutException : connect timed out
http://monod.biomath.nyu.edu/rna
200
http://monte.biochem.wisc.edu/
java.net.UnknownHostException : monte.biochem.wisc.edu
http://moris.csie.ncku.edu.tw/cqs/
java.net.ConnectException : Connection refused
http://morrislab.med.utoronto.ca/sara/SW
java.io.FileNotFoundException : http://morrislab.med.utoronto.ca/sara/SW
http://morrislab.med.utoronto.ca/software
200
http://mosta.molgen.mpg.de
200
http://motif.bmi.ohio-state.edu/ChIPMotifs
200
http://motif.bmi.ohio-state.edu/W-ChIPeaks/
200
http://motif.ics.es.osaka-u.ac.jp/Ncut-KL/
java.net.SocketTimeoutException : connect timed out
http://motif.stanford.edu/3motif/
java.io.FileNotFoundException : http://motif.stanford.edu/3motif/
http://motif.stanford.edu/ematrix
java.io.FileNotFoundException : http://motif.stanford.edu/ematrix
http://moulon/
java.net.UnknownHostException : moulon
http://mozart.bio.neu.edu/friend
java.net.NoRouteToHostException : No route to host
http://mrbayesgpu.sourceforge.net/
java.io.FileNotFoundException : http://mrbayesgpu.sourceforge.net/
http://msaprobs.sourceforge.net
java.io.IOException : Server returned HTTP response code: 403 for URL: http://msaprobs.sourceforge.net
http://msbarker.com/software.htm
200
http://msdn.microsoft.com/netframework/downloads/default.asp
200
http://mspire.rubyforge.org
200
http://msqt.weigelworld.org
200
http://msysbio.com/software/cellsys
200
http://mtreemix.bioinf.mpi-sb.mpg.de
200
http://mu2py.biocomp.unibo.it/memloci
200
http://mudshark.brookes.ac.uk/index.php/Albert_Gevorgyan
java.io.FileNotFoundException : http://mudshark.brookes.ac.uk/index.php/Albert_Gevorgyan
http://mugsy.sf.net
200
http://mulcyber.toulouse.inra.fr/projects/agscan/
200
http://multiparanoid.cgb.ki.se
200
http://murphylab.web.cmu.edu/software
200
http://mutdb.org/
200
http://mutdb.org/mutpred
200
http://myamagu.dent.kyushu-u.ac.jp/bioinformatics/trfma/index.html
java.net.SocketTimeoutException : connect timed out
http://mzmine.sourceforge.net/
200
http://names.ubio.org/rss/
200
http://nashua.case.edu/pathways
200
http://nat2pred.rit.albany.edu
200
http://nava.liacs.nl/kye/TEA-O/
200
http://navicluster.cb.k.u-tokyo.ac.jp/
200
http://nbase.biology.gatech.edu/
200
http://nbc.ece.drexel.edu
200
http://ncbr.chemi.muni.cz/triton/
200
http://nciarray.nci.nih.gov/cgi-bin/me/mouse_design.cgi
200
http://ncicb.nci.nih.gov/core
200
http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do
java.io.FileNotFoundException : http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do
http://nclab.hit.edu.cn/PlantMiRNAPred/
java.net.SocketTimeoutException : connect timed out
http://ncRNAppi.bioinfo.asia.edu.tw/
java.net.SocketTimeoutException : connect timed out
http://ncrnappi.cs.nthu.edu.tw
200
http://ncrr.pnl.gov/software/
200
http://ndbserver.rutgers.edu/mmcif
java.io.FileNotFoundException : http://ndbserver.rutgers.edu/mmcif
http://nemo-cyclone.sourceforge.net
200
http://nemo2.sourceforge.net
200
http://neoref.ils.unc.edu/tamal
200
http://netalign.ustc.edu.cn/temsp/
200
http://networks.gersteinlab.org/tyna
200
http://neural.dsi.unifi.it/cysteines
java.io.FileNotFoundException : http://neural.dsi.unifi.it/cysteines
http://neuron.tau.ac.il/
200
http://newton.tmd.ac.jp/
200
http://ng-dec1.gen.cam
java.net.UnknownHostException : ng-dec1.gen.cam
http://ng-dec1.gen.cam.ac.uk/hmm/Passml.html
java.net.UnknownHostException : ng-dec1.gen.cam.ac.uk
http://ngsview.sourceforge.net
200
http://nlp.comp.nus.edu.sg/software
200
http://nmr.proteomics.ics.uci.edu
200
http://nmrb.cbs.cnrs.fr
200
http://noble.gs
java.net.UnknownHostException : noble.gs
http://noble.gs.washington.edu/prism
java.io.IOException : Server returned HTTP response code: 403 for URL: http://noble.gs.washington.edu/prism
http://noble.gs.washington.edu/proj/3dkernel
200
http://noble.gs.washington.edu/proj/dna-binding
200
http://noble.gs.washington.edu/proj/genomedata/
200
http://noble.gs.washington.edu/proj/hmmseg
200
http://noble.gs.washington.edu/proj/intense/
200
http://noble.gs.washington.edu/proj/qvality
200
http://noble.gs.washington.edu/proj/sdp-svm
200
http://noble.gs.washington.edu/proj/seqstruct
200
http://noble.gs.washington.edu/proj/sppi
200
http://nodmutdb.vbi.vt.edu
200
http://nostoc.stanford.edu/Docs/index.html
200
http://npsa-pbil.ibcp.fr
200
http://ntap.cbi.pku.edu.cn/
java.net.UnknownHostException : ntap.cbi.pku.edu.cn
http://ntumaps.cgm.ntu.edu.tw/aCGH_supplementary
200
http://nucleix.mbu.iisc.ernet.in/prombase/
200
http://nypg.bio.nyu.edu/orthologid/
200
http://o2.db
java.net.UnknownHostException : o2.db
http://oberon.fvms.ugent.be:8080/SPADS/
java.net.UnknownHostException : oberon.fvms.ugent.be
http://octopus.cbr.su.se/
200
http://odin.mdacc.tmc.edu/
200
http://odin.mdacc.tmc.edu/jhu/lysatearray-analysis/
java.io.FileNotFoundException : http://odin.mdacc.tmc.edu/jhu/lysatearray-analysis/
http://okeylabimac.med.utoronto.ca/PUNS
java.net.SocketTimeoutException : connect timed out
http://oligos.molgen.mpg.de
200
http://omabrowser.org
200
http://ome.grc.nia.nih.gov/iicbu2008/celegans
200
http://ome.grc.nia.nih.gov/wnd-charm
200
http://omics.pnl.gov/software/
200
http://omics.pnl.gov/software/STEPP.php
200
http://omics.pnl.gov/software/VIBE.php
200
http://omicspace.riken.jp/
200
http://omicspace.riken.jp/gps/
200
http://omnibus.unifreiburg.de/
java.io.IOException : Server returned HTTP response code: 403 for URL: http://omnibus.unifreiburg.de/
http://onthefly.embl.de
java.io.IOException : Server returned HTTP response code: 503 for URL: http://onthefly.embl.de
http://onto.eva.mpg.de/
200
http://ontology.pseudogene.org
200
http://opal.cs.arizona.edu
200
http://opencobra.sourceforge.net
200
http://openmms.sdsc.edu
200
http://ophid.utoronto.ca
200
http://ophid.utoronto.ca/navigator/
200
http://opm.phar.umich.edu
200
http://opus.bch.ed.ac.uk/stp
200
http://orange.genomecenter.ucdavis.edu/benham/sidd/index.html
java.io.FileNotFoundException : http://orange.genomecenter.ucdavis.edu/benham/sidd/index.html
http://orclinux.creighton.edu/DGM/index.htm
java.net.SocketTimeoutException : connect timed out
http://orclinux.creighton.edu/snpp/
java.net.SocketTimeoutException : connect timed out
http://org.uib.no/prokaryotedb/
200
http://osfinder.dna.bio.keio.ac.jp
200
http://ouray.cudenver.edu/
java.net.UnknownHostException : ouray.cudenver.edu
http://outbreak.ceid.ox.ac.uk/software.htm
200
http://oxfordhla.well.ox.ac.uk
200
http://oxytricha.princeton.edu/GeneUnscrambler.htm
200
http://p-cats.hgc.jp/p-cats
200
http://pacific.mpi-cbg.de
200
http://pacosy.informatik.uni-leipzig.de/crex
200
http://paed.hku.hk/uploadarea/yangwl/html/index.html
200
http://panther.appliedbiosystems.com/pub/tree_quality/index.jsp
200
http://panther.appliedbiosystems.com/pub/tree_quality/trees.jsp
200
http://parasol.tamu.edu/foldingserver/
200
http://pass.cribi.unipd.it
200
http://pathbuilder.sourceforge.net/
200
http://pathport.vbi.vt.edu/YODA
java.io.IOException : Server returned HTTP response code: 403 for URL: http://pathport.vbi.vt.edu/YODA
http://pavsey.mpimp-golm.mpg.de
java.net.UnknownHostException : pavsey.mpimp-golm.mpg.de
http://pbil.ibcp.fr/NPSA
200
http://pbil.ibcp.fr/NPSA/npsa_server.ht
200
http://pbil.kaist.ac.kr
200
http://pbil.univ-lyon1.fr/datasets/charif04/
200
http://pbil.univ-lyon1.fr/members/lobry
200
http://pbil.univ-lyon1.fr/roso
200
http://pbil.univ-lyon1.fr/software/Cassis/
200
http://pbil.univ-lyon1.fr/software/cpgprod.html
200
http://pbil.univ-lyon1.fr/software/HoSeqI/
200
http://pbil.univ-lyon1.fr/software/jadis.html
200
http://pbil.univ-lyon1.fr/software/luna/
200
http://pbil.univ-lyon1.fr/software/mareymap/
200
http://pbil.univ-lyon1.fr/software/rrtree.html
200
http://pbil.univ-lyon1.fr/software/TESD
200
http://pc113.imbg.ku.dk/ps/
200
http://pcarvalho.com/patternlab
200
http://pcons.net/
200
http://pcp.sourceforge.net
200
http://pdb.rutgers.edu/mmcif/
200
http://pdbrs3.sdsc.edu/ConStructMap/viewer_argument_generator/singleArguments
200
http://pearl.cs.pusan.ac.kr/phylodraw/
java.io.FileNotFoundException : http://pearl.cs.pusan.ac.kr/phylodraw/
http://pedant.gsf.de/ARIA/index.htm
200
http://pedant.gsf.de/snapper
java.io.FileNotFoundException : http://pedant.gsf.de/snapper
http://pedro.man.ac.uk/
java.net.NoRouteToHostException : No route to host
http://penglab.janelia.org/proj/principal_skeleton
200
http://penglab.janelia.org/proj/v3d
200
http://people.bu.edu/gupta/software.htm
200
http://people.genome.duke.edu/assess
java.io.FileNotFoundException : http://people.genome.duke.edu/assess
http://people.inf.ethz.ch/befische/proteomics
200
http://people.musc.edu/
200
http://people.pcbi.upenn.edu/
java.io.IOException : Server returned HTTP response code: 403 for URL: http://people.pcbi.upenn.edu/
http://people.sissa.it/
200
http://people.virginia.edu/
200
http://pepitope.tau.ac.il/
200
http://pepr.cnmcresearch.org
200
http://peptibase.cs.biu.ac.il/PepCleave_II/
200
http://perlprimer.sourceforge.net
200
http://pestas.kribb.re.kr/
200
http://pfam.cgb.ki.se/pfamalyzer
java.net.UnknownHostException : pfam.cgb.ki.se
http://pfind.ict.ac.cn/FlexStem/
200
http://pfind.ict.ac.cn/pmatch/
200
http://pfind.jdl.ac.cn/IndexToolkit
200
http://pgtdb.csie.ncu.edu.tw
200
http://pgv19.virol.ucl.ac.uk/download/star_linux.tar
200
http://pgv19.virol.ucl.ac.uk/download/star_supplement
200
http://phenos.bsd.uchicago.edu/ITSS/
200
http://phg.mc.vanderbilt.edu/Software/MDR
java.net.UnknownHostException : phg.mc.vanderbilt.edu
http://phmmts.dna.bio.keio.ac.jp/
200
http://phobius.cgb.ki.se/poly.html
java.io.FileNotFoundException : http://phobius.cgb.ki.se/poly.html
http://phylemon2.bioinfo.cipf.es/
200
http://phylodiversity.net/phylocom/
200
http://phylogenomics.berkeley.edu
200
http://phylogenomics.berkeley.edu/phylofacts
200
http://phylogenomics.berkeley.edu/profilealignment/
200
http://phys.protres.ru/resources/termo_meso_base.html
200
http://physiologie.uni-ulm.de//Seiten/Arbeitsgruppe/Jurkat-Rott/Jurkat-Rott.htm
java.net.SocketTimeoutException : connect timed out
http://picante.r-forge.r-project.org
200
http://pie.giddingslab.org/
200
http://pig-pbil.ibcp.fr/magos
200
http://pig.ag.uq.edu.au/qu-gene/
java.net.UnknownHostException : pig.ag.uq.edu.au
http://pin.mskcc.org
200
http://pine.nmrfam.wisc.edu/PINE-SPARKY
200
http://pinguin.biologie.uni-jena.de/bioinformatik/networks/index.html
200
http://pipe.scs.fsu.edu/meta-ppisp.html
200
http://pipe.scs.fsu.edu/ppisp.html
200
http://pipe.systemsbiology.net
200
http://pir.georgetown.edu/
200
http://pir.georgetown.edu/iprolink/biothesaurus
200
http://piranha.protein.osaka-u.ac.jp
java.net.SocketTimeoutException : connect timed out
http://pisqrd.escience-lab.org
200
http://planet-lisa.net/
200
http://plantgenome.agtec.uga.edu/bioinformatics/dating/
200
http://plantgenomics.biology.yale.edu/nmpp
200
http://platcom.informatics.indiana.edu/platcom
java.net.SocketTimeoutException : connect timed out
http://plaza.ufl.edu/junliu/feature.tar.gz
200
http://pmr.sdsc.edu/go
java.net.UnknownHostException : pmr.sdsc.edu
http://pngu.mgh.harvard.edu/purcell/whap/
200
http://pollacklab.stanford.edu/
200
http://polymorphism.scripps.edu/
200
http://polyview.cchmc.org
200
http://pompous.swmed.edu
java.net.SocketTimeoutException : Read timed out
http://popgen.eu/soft/m4s2
200
http://popgen.eu/soft/ogaraK
200
http://popolvuh.wlu.ca/Orthologs
200
http://portal.stats.ox.ac.uk:8080/rahnuma/
java.io.FileNotFoundException : http://portal.stats.ox.ac.uk:8080/rahnuma/
http://pprospector.sourceforge.net
200
http://pprowler.imb.uq.edu.au/
200
http://pprowler.itee.uq.edu.au/NucImport
200
http://pprowler.itee.uq.edu.au/sspred/
200
http://ppw.kuleuven.be/okp/software/BayesianIUT/
200
http://prabi1.inrialpes.fr/trac/wellreader
200
http://pre-s.protein.osaka-u.ac.jp/
200
http://predictioncenter.org/Services/FragHMMent/
200
http://prequips.sourceforge.net
200
http://pride.szbk.u-szeged.hu
java.net.UnknownHostException : pride.szbk.u-szeged.hu
http://primer.duhs.duke.edu/
200
http://prinseq.sourceforge.net/
200
http://prion.biocomp.unibo.it/rcnpred.html
java.net.UnknownHostException : prion.biocomp.unibo.it
http://prism.ccbb.ku.edu.tr/hotpoint/supplement.doc
200
http://prober.cshl.edu
200
http://probis.cmm.ki.si
200
http://prodata.swmed.edu/CASP8
200
http://prodata.swmed.edu/HangOut/
200
http://prodata.swmed.edu/procain/
200
http://prodata.swmed.edu/promals/
200
http://profdist.bioapps.biozentrum.uni-wuerzburg.de
200
http://profs.sci.univr.it/
200
http://projects.dbbe.musc.edu/gosteiner
java.io.IOException : Server returned HTTP response code: 503 for URL: http://projects.dbbe.musc.edu/gosteiner/
http://projects.villa-bosch.de/bcb/sbml/
200
http://promode.socs.waseda.ac.jp
200
http://promoter.ics.uci.edu/BRNN-PRED/
java.net.UnknownHostException : promoter.ics.uci.edu
http://promoterplot.fmi.ch/cgi-bin/dep.html
200
http://prophet.bioinfo.cipf.es/
java.io.IOException : Server returned HTTP response code: 403 for URL: http://prophet.bioinfo.cipf.es/
http://protchem.hunnu.edu.cn/depd/
200
http://protege.stanford.edu
200
http://protein.bio.puc.cl
200
http://protein.bio.unipd.it/mobi/
200
http://protein.bio.unipd.it/repetita/
200
http://protein.bio.unipd.it/tese/
200
http://protein.cribi.unipd.it/ssea/
200
http://protein.toulouse.inra.fr/prodom.html
java.net.UnknownHostException : protein.toulouse.inra.fr
http://ProteinDBS.rnet.missouri.edu/IPSA.php
java.io.FileNotFoundException : http://ProteinDBS.rnet.missouri.edu/IPSA.php
http://proteins.gmu.edu/automute
200
http://proteinworlddb.org
200
http://proteogenomics.musc.edu/pss/home.php
200
http://proteom.biomed.cas.cz/genexp
200
http://proteome.gs.washington.edu/software/skyline
200
http://proteomics-pbil.ibcp.fr
200
http://proteomics.fhcrc.org
200
http://proteowizard.sourceforge.net
200
http://protevo.eb.tuebingen.mpg.de/download
200
http://protlib.uchicago.edu/dloads.html
200
http://pseudoviewer.inha.ac.kr
java.net.SocketTimeoutException : Read timed out
http://psibase.kaist.ac.kr/
java.net.UnknownHostException : psibase.kaist.ac.kr
http://psifr.cssb.biology.gatech.edu/
200
http://psimap.org
200
http://psychro.bioinformatics.unsw.edu.au/pathogen/index.php
200
http://ptcl.chem.ox.ac.uk/
200
http://pubchem.ncbi.nlm.nih.gov
200
http://pubgeneserver.uio.no/figsearch/
java.io.FileNotFoundException : http://pubgeneserver.uio.no/figsearch/
http://public.kgi.edu/
java.net.SocketTimeoutException : connect timed out
http://public.kgi.edu/wild/index.htm
java.net.SocketTimeoutException : connect timed out
http://public.tgen.org/dynstoc/
200
http://public.tgen.org/sqz
200
http://public.tgen.org/tamu/ofs/
200
http://public.tgen.org/tgen-cb/support/testbed/
200
http://publications.mpi-cbg.de/itemPublication.html?documentId=4082
200
http://purl.org/biotop
200
http://purl.org/stemnet/
200
http://pyml.sourceforge.net
200
http://pynast.sourceforge.net
200
http://pypi.python.org/pypi/CROC/
200
http://pypi.python.org/pypi/DendroPy
200
http://pysces.sourceforge.net
200
http://qtl.pzr.uni-rostock.de/cartographer.php
200
http://qtl.pzr.uni-rostock.de/qtlmix.php
200
http://qupe.cebitec.uni-bielefeld.de
200
http://r-forge.r-project.org
200
http://r-forge.r-project.org/projects/adephylo/
200
http://rafalab.jhsph.edu/cnvcomp/
200
http://rafalab.jhsph.edu/software.html
200
http://rana.lbl.gov/
200
http://range.sourceforge.net
200
http://ranger.uta.edu/
200
http://rankprop.gs.washington.edu
200
http://rat.niob.knaw.nl/GENOTRACE
java.net.UnknownHostException : rat.niob.knaw.nl
http://raven.bioc.cam.ac.uk/
java.net.SocketTimeoutException : connect timed out
http://rbs.kaist.ac.kr
200
http://rc.kfshrc.edu.sa/bssc/staff/MusaAsyali/Downloads.asp
200
http://reccr.chem.rpi.edu/Software/pesdserv/
200
http://recode.genetics.utah.edu/arfa
java.io.FileNotFoundException : http://recode.genetics.utah.edu/arfa
http://refdic.rcai.riken.jp/
200
http://relic.bio.anl.gov
200
http://repitools.r-forge.r-project.org/
200
http://research.i2r.a-star.edu.sg/AllerTool/
java.net.UnknownHostException : research.i2r.a-star.edu.sg
http://research.i2r.a-star.edu.sg/BindingMotifPairs/resources
java.net.UnknownHostException : research.i2r.a-star.edu.sg
http://research.i2r.a-star.edu.sg/DNAFSMiner/
java.net.UnknownHostException : research.i2r.a-star.edu.sg
http://research.i2r.a-star.edu.sg/Templar/DB/snake_neurotoxin
java.net.UnknownHostException : research.i2r.a-star.edu.sg
http://research.janelia.org/davis/allenminer
200
http://research.janelia.org/peng/proj/fly_embryo_annotation/
200
http://research.microsoft.com/cue/phylodet/
200
http://research.ncl.ac.uk/synthetic_biology/downloads.html
200
http://research.stowers-institute.org/bioinfo/
200
http://research1t.imb.uq.edu.au/conoserver/
200
http://research1t.imb.uq.edu.au/ragan/machos
200
http://research2.dfci.harvard.edu/dfci/MS_spike-in_data/
200
http://retina.med.harvard.edu/ACTG/
java.net.SocketTimeoutException : connect timed out
http://rloom.mpimp-golm.mpg.de
200
http://rna.bgsu.edu/R3DAlign
200
http://rna.bgsu.edu/ribostral
200
http://rna.eit.hirosaki-u.ac.jp/cofolga2mo/
200
http://rna.tbi.univie.ac.at/cgi-bin/pmcgi.pl
java.io.FileNotFoundException : http://rna.tbi.univie.ac.at/cgi-bin/pmcgi.pl
http://rna.urmc.rochester.edu
200
http://rocr.bioinf.mpi-sb.mpg.de
200
http://rodeo.med.harvard.edu/tools/roundup
301
http://rosalind.infj.ulst.ac.uk/SimTrek.html
200
http://rosenberglab.bioinformatics.med.umich.edu/adze.html
200
http://rosenberglab.bioinformatics.med.umich.edu/clumpp.html
200
http://rosetta.lcb.uu.se/
200
http://rrna.uia.ac.be/rnaviz/
java.net.UnknownHostException : rrna.uia.ac.be
http://rsat.scmbb.ulb.ac.be/rsat/
200
http://rsat.ulb.ac.be/rsat
200
http://rsat.ulb.ac.be/rsat/info-gibbs
200
http://rsbweb.nih.gov/ij
200
http://rseqtools.gersteinlab.org/
200
http://rth.dk/resources/maxAlike
200
http://rth.dk/resources/petcofold
200
http://rubin2.biomath.nyu.edu
200
http://rulai.cshl.edu/dme
200
http://rulai.cshl.edu/MatCompare
200
http://rulai.cshl.edu/tools/dwe
200
http://sadic.sourceforge.net
200
http://safegene.hms.harvard.edu/aa2nt/
200
http://saint-annotate.sourceforge.net
200
http://sakura.ddbj.nig.ac.jp
200
http://salilab.org/LS-SNP/supp-info.pdf
200
http://salilab.org/modloop
200
http://salilab.org/peptide
200
http://salilab.org/pibase
200
http://samstat.sourceforge.net
200
http://samtools.sourceforge.net
200
http://sapiens.wustl.edu/MaskerAid
java.io.FileNotFoundException : http://sapiens.wustl.edu/MaskerAid
http://sapred.cbi.pku.edu.cn/
java.io.IOException : Server returned HTTP response code: 503 for URL: http://sapred.cbi.pku.edu.cn/
http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/src/Quantitation/Pepc
200
http://satdna.sourceforge.net/
200
http://savannah.gnu.org/projects/mcsim
200
http://sb.cs.cmu.edu/ExpQ/
200
http://sbase.abc.hu/domain
java.net.SocketTimeoutException : connect timed out
http://sbenz.github.com/Paradigm
200
http://sbg.cib.csic.es/Software/ADP_EM
200
http://sbg.cib.csic.es/Software/DFprot
200
http://sbg.cib.csic.es/Software/FRODOCK/
200
http://sbi.imim.es/modlink/
200
http://sbi.imim.es/piana
200
http://sbie.kaist.ac.kr/software
200
http://sbm.postech.ac.kr/pna
200
http://sbml.org/software/cellml2sbml/
200
http://sbml.org/software/libsbml
200
http://sbml.org/software/sbmltoolbox
200
http://sbrg2.gist.ac.kr/hcnet
200
http://sceptrans.org/
200
http://scit.us/dawg/
200
http://scit.us/projects/ngila/
200
http://scratch.proteomics.ics.uci.edu
200
http://sdmc.i2r.a-star.edu.sg/BindingMotifPairs
java.net.SocketTimeoutException : connect timed out
http://sdmc.lit.org.sg/GEDatasets/
java.net.UnknownHostException : sdmc.lit.org.sg
http://search.cpan.org/
200
http://search.cpan.org/dist/GO-TermFinder/
200
http://search.cpan.org/dist/ONTO-PERL/
200
http://seevolution.org
200
http://selecton.bioinfo.tau.ac.il
200
http://seqmap.compbio.iupui.edu/
200
http://seqsim.ncgr.org/vector/
java.net.UnknownHostException : seqsim.ncgr.org
http://server.bioicps.org
200
http://servet.dia.fi.upm.es:8080/pubdnafinder
200
http://service.bioinformatik.uni-saarland.de/mins
java.io.FileNotFoundException : http://service.bioinformatik.uni-saarland.de/mins
http://services.bio.ifi.lmu.de/prothesaurus/
200
http://services.came.sbg.ac.at
200
http://setiathome.berkeley.edu
200
http://sf.net/projects/netmotsa
200
http://sfinx.cgb.ki.se
200
http://sfixem.cgb.ki.se
200
http://sfold.wadsworth.org
200
http://sfscode.sourceforge.net
200
http://sgedg.weizmann.ac.il/csu
200
http://sgedg.weizmann.ac.il/lpc
200
http://sgn.cornell.edu/
200
http://sgu.bioinfo.cipf.es/services/SARA/
200
http://shad.cs.utk.edu/sgo/sgo.html
java.net.UnknownHostException : shad.cs.utk.edu
http://share.gene.com/
200
http://share.gene.com/gmap
200
http://share.gene.com/share/gepis
java.io.FileNotFoundException : http://share.gene.com/share/gepis
http://shotgun.zool.gu.se
200
http://si2.epfl.ch/
java.io.IOException : Server returned HTTP response code: 403 for URL: http://si2.epfl.ch/
http://side.bioinfo.cnio.es
java.net.SocketTimeoutException : Read timed out
http://sienabiografix.com
200
http://sign.hgc.jp/signssm/
200
http://SignaLink.org
200
http://sigpep.services.came.sbg.ac.at/signalblast.html
200
http://sigproc-eng.cam.ac.uk/
java.net.UnknownHostException : sigproc-eng.cam.ac.uk
http://sigwww.cs.tut.fi/TICSP/SpotQuality/
java.net.UnknownHostException : sigwww.cs.tut.fi
http://simbioms.org
200
http://simpath.lionbioscience.com:8080/documents/pathscout11/
java.net.ConnectException : Connection refused
http://simupop.sourceforge.net
200
http://sir.lanl.gov/NMR/APART.htm
java.net.UnknownHostException : sir.lanl.gov
http://sir.lanl.gov/NMR/APART_Manual1.pdf
java.net.UnknownHostException : sir.lanl.gov
http://siRecords.umn.edu/siRecords/
java.net.SocketTimeoutException : connect timed out
http://sisbio.recerca.upc.edu/R/MISS_0.2.tar.gz
200
http://sitehound.sanchezlab.org/download.html
200
http://sitepredict.org/
java.net.SocketTimeoutException : connect timed out
http://sites.google.com/a/bioinformatics.ucr.edu/xinping-cui/home/software
302
http://sites.google.com/site/nextgengenomics/ingap
200
http://sites.google.com/site/rosemarieplaetke/home/s/pedmerge
200
http://sites.google.com/site/sbmlpetmpi/
200
http://sites.google.com/site/xmsfilter/
200
http://skuld.protres.ru/
java.net.NoRouteToHostException : No route to host
http://sli.ics.uci.edu/Code/GPRTimeshift/
200
http://slif.cbi.cmu.edu
200
http://smbl.nus.edu.sg/METDAT2/
200
http://smi.stanford.edu/projects/helix/gokbms/
200
http://smi.stanford.edu/projects/helix/pubs/process-model/
200
http://smithlab.cmb.usc.edu/histone/rseg/
200
http://sms.cbi.cnptia.embrapa.br/SMS
200
http://sms.cbi.cnptia.embrapa.br/SMS/STINGm/consseq/
200
http://snap.cifr.ncsu.edu
200
http://snoopcgh.sourceforge.net/
200
http://snp.agrsci.dk/maviant
java.io.FileNotFoundException : http://snp.agrsci.dk/maviant
http://snp.bumc.bu.edu
200
http://snp.toulouse.inra.fr/
200
http://snpeffect.vib.be
200
http://snpomatic.sourceforge.net
200
http://snpsfinder.lanl.gov/
200
http://soap.genomics.org.cn
java.net.SocketTimeoutException : Read timed out
http://socs.biology.gatech.edu/
200
http://soft.synth-bio.org/desharky.html
200
http://software.steenlab.org/fmf
200
http://software.steenlab.org/libfbi
200
http://solidsoftwaretools.com/gf/project/socs/
200
http://sonnhammer.sbc.su.se/download/software/MSPcrunch
java.io.FileNotFoundException : http://sonnhammer.sbc.su.se/download/software/MSPcrunch
http://sonnhammer.sbc.su.se/download/UniDomInt/
200
http://sonnhammer.sbc.su.se/multipfam2go_source_docs.tar
200
http://sosui.proteome.bio.tuat.ac.jp/sosuiframe0.html
java.net.UnknownHostException : sosui.proteome.bio.tuat.ac.jp
http://source.rcsb.org
200
http://sourceforge.net
200
http://sourceforge.net/projects/ccpn
200
http://sourceforge.net/projects/cellpublisher/
200
http://sourceforge.net/projects/compucell/
200
http://sourceforge.net/projects/cplexa/
200
http://sourceforge.net/projects/epigpu/
200
http://sourceforge.net/projects/evopromoter/
200
http://sourceforge.net/projects/expertomica-eda/
200
http://sourceforge.net/projects/expo/
200
http://sourceforge.net/projects/JAMBLAST/
java.io.FileNotFoundException : http://sourceforge.net/projects/JAMBLAST/
http://sourceforge.net/projects/jdesigner
200
http://sourceforge.net/projects/microsoap/
java.io.FileNotFoundException : http://sourceforge.net/projects/microsoap/
http://sourceforge.net/projects/mirach/
200
http://sourceforge.net/projects/nemo-cyclone
200
http://sourceforge.net/projects/NOBLAST
java.io.FileNotFoundException : http://sourceforge.net/projects/NOBLAST
http://sourceforge.net/projects/noisemaker
200
http://sourceforge.net/projects/perlmat
200
http://sourceforge.net/projects/prepms
200
http://sourceforge.net/projects/pychem
200
http://sourceforge.net/projects/pygr
200
http://sourceforge.net/projects/renco/
200
http://sourceforge.net/projects/text2genome/
200
http://south.genomics.org.cn/software/uniblast/index.html
200
http://spacem3.gforge.inria.fr/
200
http://sparks.informatics.iupui.edu/PINUP/
200
http://sparks.informatics.iupui.edu/spot
200
http://spdc.sdsc.edu
200
http://sphinx.rug.ac.be:8080/biocomp/napav/
java.net.NoRouteToHostException : No route to host
http://spies.cs.tsinghua.edu.cn
java.net.UnknownHostException : spies.cs.tsinghua.edu.cn
http://splicenest.molgen.mpg.de
200
http://spore.swmed.edu/dejavu
java.net.SocketTimeoutException : Read timed out
http://src.moffitt.usf.edu/libaffy
200
http://srna-tools.cmp.uea.ac.uk
200
http://srs.ebi.ac.uk
200
http://srs.ebi.ac.uk:5000/
java.net.SocketTimeoutException : connect timed out
http://srs3d.ebi.ac.uk/
200
http://ssli.ee.washington.edu/bilmes/gmtk
java.io.FileNotFoundException : http://ssli.ee.washington.edu/bilmes/gmtk
http://staden.sourceforge.net
200
http://staff.science.uva.nl/
200
http://staff.ustc.edu.cn/
200
http://staff.vbi.vt.edu/cammer/snapp/download/
200
http://staff.vbi.vt.edu/dyermd/publications/dyer2007a.html
200
http://staff.vbi.vt.edu/volkan/p2sl
java.io.IOException : Server returned HTTP response code: 403 for URL: http://staff.vbi.vt.edu/volkan/p2sl
http://staff.washington.edu/brendano/treesimj
200
http://stars.zhengyuhome.com
java.net.UnknownHostException : stars.zhengyuhome.com
http://stash.mrc-lmb.cam.ac.uk/PDB_ISL/
java.net.SocketTimeoutException : Read timed out
http://stat-db.stat.sfu.ca/stepwise/
200
http://stat.ethz.ch/
200
http://stat.fsu.edu/
200
http://stat.genopole.cnrs.fr/ds/
200
http://stat.osu.edu/
200
http://stat.psu.edu/
200
http://stat.stanford.edu/
200
http://stat.tamu.edu/
200
http://stat.tamu.edu/people/faculty/bmallick.html
java.io.FileNotFoundException : http://www.stat.tamu.edu/people/faculty/bmallick.html
http://stat.umn.edu/
200
http://stat.wharton.upenn.edu/
200
http://stateslab.bioinformatics.med.umich.edu/software.html
java.io.IOException : Server returned HTTP response code: 500 for URL: http://stateslab.bioinformatics.med.umich.edu/software.html
http://stateslab.wustl.edu/pub/helix/StructureList
java.net.UnknownHostException : stateslab.wustl.edu
http://statgen.iop.kcl.ac.uk/gpc/
java.io.FileNotFoundException : http://statgen.iop.kcl.ac.uk/gpc/
http://statgen.psu.edu
200
http://statistics.msi.meduniwien.ac.at/float/cross_platform/
200
http://statistics.msi.meduniwien.ac.at/index.php?page=ao2stage
200
http://statistics.msi.meduniwien.ac.at/index.php?page=pageszfnr
200
http://stein.bioch.dundee.ac.uk/
java.io.IOException : Server returned HTTP response code: 403 for URL: http://stein.bioch.dundee.ac.uk/
http://stl.wustl.edu/software/gibbsmap/
java.net.UnknownHostException : stl.wustl.edu
http://stravinsky.ucsc.edu/josh/gesses/
java.io.FileNotFoundException : http://stravinsky.ucsc.edu/josh/gesses/
http://strbio.sourceforge.net/
200
http://structure.bu.edu
200
http://structure.pitt.edu/software/FastContact
200
http://struster.bioinf.mpi-inf.mpg.de
200
http://students.washington.edu/adabney/clanc
java.io.FileNotFoundException : http://students.washington.edu/adabney/clanc
http://sullivan.bu.edu/
200
http://sumo-pbil.ibcp.fr
200
http://sunflower.kuicr.kyoto-u.ac.jp/
200
http://sunny.ebi.ac.uk/
java.net.UnknownHostException : sunny.ebi.ac.uk
http://supfam.cs.bris.ac.uk/kmer
200
http://supfam.org/PRC
200
http://surface.bio.uniroma2.it/seq2struct/
200
http://surya.bic.nus.edu.sg/mpid
java.net.SocketTimeoutException : connect timed out
http://surya.bic.nus.edu.sg/xdom
java.net.SocketTimeoutException : connect timed out
http://sv.gersteinlab.org/age
200
http://svdetect.sourceforge.net/
200
http://svm.sdsc.edu/cgi-bin/nph-SVMsubmit.cgi
200
http://swift.embl-heidelberg.de/servers/
200
http://swissmodel.expasy.org/qmean
200
http://swissmodel.expasy.org/workspace/
200
http://swisspit.cscs.ch
java.net.UnknownHostException : swisspit.cscs.ch
http://sycamore.eml.org
200
http://syen.ualr.edu/nxbouaynaya/Bioinformatics2010.html
200
http://synbioss.sourceforge.net
200
http://synbiowave.sourceforge.net
200
http://synteny.cnr.berkeley.edu/gobe-app/
200
http://synth-bio.yi.org/genetdes.html
200
http://sys-bio.org/sbwWiki/compare
200
http://sysbio.molgen.mpg.de/SBML-PET/
200
http://sysbio3.fhms.surrey.ac.uk/SurreyFBA.zip
200
http://systemsbiology.northwestern.edu/BNICE
java.io.FileNotFoundException : http://systemsbiology.northwestern.edu/BNICE
http://systemsbiology.rcsi.ie/apopto-cell.html
200
http://systemsbiology.ucsd.edu
200
http://tagc.univ-mrs.fr/mireval
200
http://tagc.univ-mrs.fr/SimCT
200
http://tagcalling.mbgproject.org
200
http://tardis.nibio.go.jp/PSIVER/
200
http://tare.medisin.ntnu.no/priorseditor
200
http://targetdb.pdb.org/
200
http://tartara.csd.auth.gr/
java.net.UnknownHostException : tartara.csd.auth.gr
http://tastier.cs.tsinghua.edu.cn/ipubmed
200
http://taverna.sourceforge.net/
200
http://taxonomy.zoology.gla.ac
java.net.UnknownHostException : taxonomy.zoology.gla.ac
http://taxonomy.zoology.gla.ac.uk/
200
http://taxonomy.zoology.gla.ac.uk/rod/circles/
200
http://taxoweb.mmg.msu.edu/datasets
java.net.SocketTimeoutException : connect timed out
http://telethon.bio.unipd.it/GETProfiles/
200
http://text0.mib.man.ac.uk/software/mldic/
200
http://text2genome.org
200
http://textal.tamu.edu
200
http://textmining.i2r.a-star.edu.sg/NLS/demo.htm
java.net.SocketTimeoutException : connect timed out
http://thea.unice.fr/
200
http://thebiogrid.org/download.php
200
http://theinf1.informatik.uni-jena.de/faspad/
200
http://theinf1.informatik.uni-jena.de/metapat/
200
http://theory.med.buffalo.edu
java.net.SocketTimeoutException : connect timed out
http://theoval.cmp.uea.ac.uk/
200
http://tico.gobics.de/
200
http://tiger.dbs.nus.edu.sg/ATLAS/
200
http://tiling.gersteinlab.org/sequence_effects/
200
http://timpani.genome.ad.jp/
java.net.UnknownHostException : timpani.genome.ad.jp
http://tinyurl.com/ngs-sesame
200
http://titan.biotec.uiuc.edu/COMPASS/
200
http://tito.ucsc.edu/dinamo
java.net.UnknownHostException : tito.ucsc.edu
http://titus.u-strasbg.fr/DbW
200
http://tkm.kiom.re.kr/ontology/TraditionalKoreanMedicine.rdf-xml.owl
200
http://tmbeta-svm.cbrc.jp
java.net.NoRouteToHostException : No route to host
http://tommy.unife.it
java.net.NoRouteToHostException : No route to host
http://toolkit.tuebingen.mpg.de/dataa
200
http://toolkit.tuebingen.mpg.de/hhrepid
200
http://tools.camera.calit2.net/camera/meta_rna
200
http://tools.genome.duke.edu/generegulation/image_analysis/insitu
200
http://tools.proteomecenter.org/msBID.php
200
http://topdom.enzim.hu
200
http://tophat.cbcb.umd.edu
200
http://topnet.gersteinlab.org/clique/
200
http://tops.ebi.ac.uk/tops
java.net.UnknownHostException : tops.ebi.ac.uk
http://transcriptome.ens.fr/doelan/
200
http://transcriptome.ens.fr/lgm_bioinfo/
200
http://translationalmedicine.stanford.edu/Mass-Conductor/FDR.html
200
http://transpath.gbf.de
java.net.UnknownHostException : transpath.gbf.de
http://trantor.bioc.columbia.edu/
200
http://trantor.bioc.columbia.edu/SMS
200
http://trantor.bioc.columbia.edu/SMS/STINGm/consseq/
200
http://trap.molgen.mpg.de
200
http://treebase.org
200
http://trimal.cgenomics.org
200
http://try-gobe.appspot.com/
200
http://tsailab.org/BID/
200
http://ttalynx.bio.lnu.edu.ua
200
http://tubic.tju.edu.cn/doric/
200
http://tyerslab.bio.ed.ac.uk/tools/BioGRID_webgraph.php
200
http://u-compare.org/
200
http://u-compare.org/taverna.html
200
http://ub.cbm.uam.es/mammoth/mult
301
http://udgenome.ags.udel.edu/frm_go.html/
java.net.SocketTimeoutException : connect timed out
http://ueg.ulb.ac.be/oligofaktory/
200
http://umbbd.msi.umn.edu/predict/
200
http://umber.sbs.man.ac.uk/dbbrowser/bioie/
200
http://umber.sbs.man.ac.uk/dbbrowser/metis/
200
http://umber.sbs.man.ac.uk/resources/puma
200
http://ural.wustl.edu/
200
http://ural.wustl.edu/software.html
200
http://ural.wustl.edu/softwares.html
java.io.FileNotFoundException : http://ural.wustl.edu/softwares.html
http://uratim.com/pp.zip
200
http://urchin.spbcas.ru/downloads/step/step.htm
200
http://urchin.spbcas.ru/flyex
200
http://usegalaxy.org
200
http://user.it.uu.se/
200
http://users.aber.ac.uk/nii07/bioinformatics2010
200
http://users.utu.fi/jotatu/GOImpute.html
200
http://utgenome.org/
200
http://vancouvershortr.sourceforge.net
200
http://vanted.ipk-gatersleben.de/addons/sbgn-ed
200
http://variome.net
200
http://varna.lri.fr
200
http://vbc.med.monash.edu.au/
200
http://veda.cs.uiuc.edu/d2z/
200
http://veda.cs.uiuc.edu/indelign/
200
http://vimss.sf.net
200
http://virtualplant-prod.bio.nyu.edu/cgi-bin/sungear/index.cgi
200
http://vis.usal.es/bicoverlapper
200
http://vis.usal.es/treevolution
200
http://visionlab.bio.unc.edu/caesar/
java.net.SocketTimeoutException : connect timed out
http://visionlab.uta.edu/biomarker/bioinfo.htm
200
http://vortex.cs.wayne.edu/kute/index.html
java.io.FileNotFoundException : http://vortex.cs.wayne.edu/kute/index.html
http://vortex.cs.wayne.edu/ontoexpress/
200
http://vortex.cs.wayne.edu/Projects.html
200
http://vrac.iastate.edu/
200
http://w3.rennes.inra.fr/AphidBase
200
http://w3.ualg.pt/
200
http://wanglab.hku.hk/pvalue
200
http://watson.hgen.pitt.edu/register
200
http://web.bii.a-star.edu.sg/
200
http://web.bioinformatics.cicbiogune.es/AM/AnnotationModules.php
200
http://web.biostat.ufl.edu/
java.net.UnknownHostException : web.biostat.ufl.edu
http://web.cgb.ki.se/redit
java.net.NoRouteToHostException : No route to host
http://web.kuicr.kyoto-u.ac.jp/supp/yoshi/drugtarget/
200
http://web.kuicr.kyoto-u.ac.jp/supp/yoshi/glycankernel/
200
http://web.me.com/andreas.raue/profile/software.html
200
http://web.mit.edu/bamel/gemoda
200
http://weballergen.bii.a-star.edu.sg/
java.net.SocketTimeoutException : connect timed out
http://webclu.bio.wzw.tum.de/helixcorr/
200
http://webcoli.org
200
http://webgbrowse.cgb.indiana.edu/
200
http://webs.hogent.be/cocoa
200
http://webs2.kazusa.or.jp/kagiana/cop0911/
200
http://webservice.thebiogrid.org/resources/application.wadl
200
http://webservice.thebiogrid.org/resources/interactions
200
http://websites.ntl.com/
200
http://wehih.wehi.edu.au/mhcpep/
200
http://wgs-assembler.cvs.sourceforge.net/wgs-assembler/
200
http://wgs-assembler.sf.net
200
http://wheat.pw.usda.gov/PhysicalMapping/
200
http://whitetail.bemidji.msus
java.net.UnknownHostException : whitetail.bemidji.msus
http://wigid.cgb.ki.se/index.wml
java.net.NoRouteToHostException : No route to host
http://wiki.github.com/mz2/imotifs
301
http://wiki.thebiogrid.org/doku.php/biogridplugin2
200
http://wiki.thebiogrid.org/doku.php/biogridrest
200
http://wilab.inha.ac.kr/interviewer/
200
http://wilab.inha.ac.kr/protein/
200
http://wishart.biology.ualberta.ca/cgview/
200
http://wodaklab.org/orthonets/
200
http://wolfe.gen.tcd.ie/GenomeVx
200
http://wolfe.gen.tcd.ie/wrapper
200
http://won.hongik.ac.kr/
java.net.NoRouteToHostException : No route to host
http://wood.ims.uwm.edu/full_text_classifier/
java.io.FileNotFoundException : http://wood.ims.uwm.edu/full_text_classifier/
http://wooster.bip.bham.ac.uk/DAS.html
java.net.UnknownHostException : wooster.bip.bham.ac.uk
http://works.bepress.com/veera/1/
200
http://wrightlab.group.shef.ac.uk/people_noirel.htm
200
http://ws4.niai.affrc.go.jp/
java.net.UnknownHostException : ws4.niai.affrc.go.jp
http://wsd.nlm.nih.gov
200
http://ww2.cs.mu.oz.au/
200
http://www
java.net.UnknownHostException : www
http://www and
java.net.UnknownHostException : www and
http://www at
java.net.UnknownHostException : www at
http://www comparative
java.net.UnknownHostException : www comparative
http://www interface
java.net.UnknownHostException : www interface
http://www or
java.net.UnknownHostException : www or
http://www server
java.net.UnknownHostException : www server
http://www-ab.informatik.uni-tuebingen.de/software/copycat
200
http://www-ab.informatik.uni-tuebingen.de/software/megan
200
http://www-ab.informatik.unituebingen.de/software/oslay
200
http://www-based
java.net.UnknownHostException : www-based
http://www-bio3d-igbmc.u-strasbg.fr/
200
http://www-bm.ipk-gatersleben.de/semeda/
java.net.NoRouteToHostException : No route to host
http://www-bs.informatik.uni-tuebingen.de/Services/MetaRoute
200
http://www-bs.informatik.uni-tuebingen.de/Services/MultiLoc/
200
http://www-bs.informatik.uni-tuebingen.de/Services/SherLoc/
200
http://www-bs.informatik.uni-tuebingen.de/Software/FRED
200
http://www-cryst.bioc.cam.ac.uk/
200
http://www-cryst.bioc.cam.ac.uk/bipaSUPPLEMENTARY
java.io.FileNotFoundException : http://www-cryst.bioc.cam.ac.uk/bipaSUPPLEMENTARY
http://www-cryst.bioc.cam.ac.uk/cgi-bin/joy.cgi
java.io.FileNotFoundException : http://www-cryst.bioc.cam.ac.uk/cgi-bin/joy.cgi
http://www-cryst.bioc.cam.ac.uk/fugue/
200
http://www-cryst.bioc.cam.ac.uk/homstrad/
200
http://www-cryst.bioc.cam.ac.uk/ulla
200
http://www-cse.ucsd.edu/groups/bioinformatics/GRIMM
200
http://www-cse.ucsd.edu/groups/bioinformatics/software.html
200
http://www-dssz.informatik.tu-cottbus.de/snoopy.html
200
http://www-en.mpimp-golm.mpg.de/03-research/researchGroups/01-dept1/Root_Metabolism/smp/TagFinder/index.html
200
http://www-gcs.iarc.fr/lims/
200
http://www-gcs.iarc.fr/sms.php
200
http://www-genepi.med.utah.edu/Genie
200
http://www-genepi.med.utah.edu/suppl/SLOPE/index.html
200
http://www-gsd.lbl.gov/phylovista
200
http://www-gsd.lbl.gov/vista
200
http://www-helix.inrialpes.fr/gna
200
http://www-hto.usc.edu/software/sbh/index
java.net.UnknownHostException : www-hto.usc.edu
http://www-ibmc.u-strasbg.fr/arn/sws.html
200
http://www-igbmc
java.net.UnknownHostException : www-igbmc
http://www-igbmc.u-strasbg.fr/fcm/
200
http://www-its.chem.uva.nl/research/pac/Software/pcaw.zip
java.io.FileNotFoundException : http://www-its.chem.uva.nl/research/pac/Software/pcaw.zip
http://www-mig.jouy.inra.fr/bdsi/MuGeN
200
http://www-mig.versailles.inra.fr/bdsi/SPiD
java.io.FileNotFoundException : http://www-mig.versailles.inra.fr/bdsi/SPiD
http://www-mitchell.ch.cam.ac.uk/macie/
java.net.UnknownHostException : www-mitchell.ch.cam.ac.uk
http://www-mitchell.ch.cam.ac.uk/pld/
java.net.UnknownHostException : www-mitchell.ch.cam.ac.uk
http://www-personal.umich.edu/
200
http://www-pr.informatik.uni-tuebingen.de/parseq
java.io.FileNotFoundException : http://www-pr.informatik.uni-tuebingen.de/parseq
http://www-ra.informatik.uni-tuebingen.de/software/JCell
200
http://www-rcf.usc.edu/
200
http://www-service
java.net.UnknownHostException : www-service
http://www-shimizu.ist.osaka-u.ac.jp/shimizu_lab/FHarray/
200
http://www-shimizu.ist.osaka-u.ac.jp/shimizu_lab/MSNS/
200
http://www-structure.llnl.gov/cryspred/
java.net.UnknownHostException : www-structure.llnl.gov
http://www-timc.imag.fr/Nicolas.Thierry-Mieg/
200
http://www-tsujii.is.s.u-tokyo.ac.jp/downloads/downloads.cgi
200
http://www-tsujii.is.s.u-tokyo.ac.jp/GENIA/SharedTask/
200
http://www-version
java.net.UnknownHostException : www-version
http://www.1000genomes.org
200
http://www.4shared.com/file/hTWyndYU/extra.html
200
http://www.4shared.com/file/s0uIYWIg/PAPi_10.html
200
http://www.4shared.com/file/VbQIIDeu/intra.html
200
http://www.aad.gov.au/amplicon
java.io.FileNotFoundException : http://www.aad.gov.au/amplicon
http://www.ab.informatik.uni-tuebingen.de/software/genecontent/welcome_en.html
java.net.UnknownHostException : www.ab.informatik.uni-tuebingen.de
http://www.aber.ac.uk/compsci/Research/bio/dss/EXACT/
200
http://www.aber.ac.uk/compsci/Research/bio/dss/polyfarm
200
http://www.aber.ac.uk/compsci/Research/bio/dss/yeastdataand
java.io.FileNotFoundException : http://www.aber.ac.uk/en/cs/research/cb/dss/yeastdataand
http://www.aber.ac.uk/compsci/Research/bio/robotsci/
200
http://www.accelrys.com
200
http://www.ace.ual.es/
200
http://www.acgt.se/online.html
200
http://www.acgt.se/RAMI/SuppInfo
200
http://www.acse.dept.shef.ac.uk/repository/vbems_lineage_tree/VBEMS.ZIP
200
http://www.affymetrix.com
200
http://www.affymetrix.com/analysis/query/go_analysis.affx
200
http://www.affymetrix.com/support/developer/tools/devnettools.affx
200
http://www.affymetrix.com/support/supplement/WGLRH_program.zip
200
http://www.afodor.net/bioinfosup.html
200
http://www.agklebe.de
200
http://www.agr.kuleuven.ac.be/logt/PHIRE.htm
200
http://www.agr.unipg.it/cardinali/index.html
200
http://www.agron.missouri.edu/cMapDB/cMap.html
java.io.FileNotFoundException : http://www.agron.missouri.edu/cMapDB/cMap.html
http://www.agroparistech.fr/mia/outil_A.html
200
http://www.ai.eecs.uic.edu
200
http://www.ai.uic.edu/software
java.io.FileNotFoundException : http://www.ai.uic.edu/software
http://www.aiai.ed.ac.uk/project/cobra-ct
200
http://www.ailab.si/orange
200
http://www.ailab.si/supp/bi-cancer
200
http://www.ailab.si/supp/bi-visprog
200
http://www.ailab.si/supp/bi-vizrank
200
http://www.albany.edu/gilmr/pubxml/
java.io.FileNotFoundException : http://www.albany.edu/gilmr/pubxml/
http://www.allgenes.org
200
http://www.amdcc.org/bioinformatics/bioinformatics.aspx
java.io.FileNotFoundException : http://www.amdcc.org/bioinformatics/bioinformatics.aspx
http://www.amdcc.org/bioinformatics/software/parasam.aspx
java.io.FileNotFoundException : http://www.amdcc.org/bioinformatics/software/parasam.aspx
http://www.ams.ucsc.edu/
200
http://www.anandam.name/multiperm
200
http://www.anchorgen.com/pro_gen/pro_gen.html
java.net.UnknownHostException : www.anchorgen.com
http://www.anm.f2s.com/research/vizard/
200
http://www.ansorge-group.embl.de/bloader
java.net.SocketTimeoutException : connect timed out
http://www.ApiDB.org/apps/SynView/
java.net.UnknownHostException : www.ApiDB.org
http://www.aporc.org/doc/wiki/PRNA
200
http://www.aps.uoguelph.ca/
200
http://www.ar.embnet.org/SMS
java.net.NoRouteToHostException : No route to host
http://www.ar.embnet.org/SMS/STINGm/consseq/
java.net.NoRouteToHostException : No route to host
http://www.arches.uga.edu/
200
http://www.arexdb.org/
200
http://www.argumentation.org
200
http://www.ariadnegenomics.com/downloads/
200
http://www.aroma-project.org/
200
http://www.astrazeneca-montreal.com/AZRDM_info/supporting_info.pdf
java.net.SocketException : Unexpected end of file from server
http://www.async.ece.utah.edu/iBioSim/
200
http://www.aupossom.com
301
http://www.autoprimer.com
200
http://www.awi.de/en/phylogena
200
http://www.b2gfar.org
200
http://www.babbittlab.ucsf.edu/software/intersect
java.io.FileNotFoundException : http://www.babbittlab.ucsf.edu/software/intersect
http://www.bactregulators.org
200
http://www.baderzone.org
200
http://www.ball-project.org
200
http://www.bamarray.com
java.net.SocketTimeoutException : Read timed out
http://www.basis.ncl.ac.uk/software
java.io.FileNotFoundException : http://www.basis.ncl.ac.uk/software
http://www.bcgsc.ca/bioinfo/software/ssake
200
http://www.bcgsc.ca/platform/bioinfo/software/abyss
200
http://www.bcgsc.ca/platform/bioinfo/software/findpeaks
200
http://www.bdagroup.nl
200
http://www.bgx.org.uk/papers.html
java.io.FileNotFoundException : http://www.bgx.org.uk/papers.html
http://www.bgx.org.uk/software.html
200
http://www.bi.uni-duesseldorf.de/software/sissi/
java.net.ConnectException : Connection refused
http://www.bic.kyoto-u.ac.jp/pathway/kayano/bioinfo_three-way.html
200
http://www.bic.kyoto-u.ac.jp/pathway/timhancock
200
http://www.bif.atcc.org/GENEOrder/index.html
java.net.UnknownHostException : www.bif.atcc.org
http://www.bii.a-star.edu.sg/jiren/download.html
java.io.FileNotFoundException : http://www.bii.a-star.edu.sg/jiren/download.html
http://www.bii.a-star.edu.sg/sbg/cellware
java.io.FileNotFoundException : http://www.bii.a-star.edu.sg/sbg/cellware
http://www.bilkent.edu.tr/
200
http://www.binf.ku.dk/Stinus_covariation
java.io.FileNotFoundException : http://www.binf.ku.dk/Stinus_covariation
http://www.bio
java.net.UnknownHostException : www.bio
http://www.bio.davidson.edu/MAGIC
200
http://www.bio.espci.fr/sol/
java.io.FileNotFoundException : http://www.bio.espci.fr/sol/
http://www.bio.ic.ac.uk/research/belshaw/BlastAlign.tar
java.io.FileNotFoundException : http://www.bio.ic.ac.uk/software.html?id=blastalign
http://www.bio.ifi.lmu.de/
200
http://www.bio.ifi.lmu.de/ALPS
200
http://www.bio.ifi.lmu.de/autoscop
200
http://www.bio.ifi.lmu.de/Complexes/ProCope/
200
http://www.bio.ifi.lmu.de/Complexes/Substructures/
200
http://www.bio.ifi.lmu.de/publications/RelEx/
200
http://www.bio.ifi.lmu.de/software/halo
200
http://www.bio.ifi.lmu.de/SSEP/
200
http://www.bio.ifi.lmu.de/Vorolign
java.io.FileNotFoundException : http://www.bio.ifi.lmu.de/Vorolign
http://www.bio.indiana.edu/
200
http://www.bio.inf.uni-jena.de/Software/SECISDesign/index.html
java.net.ConnectException : Connection refused
http://www.bio.inf.uni-jena.de/tandemms
java.net.ConnectException : Connection refused
http://www.bio.nnov.ru/projects/vsdocker2/
200
http://www.bio.psu.edu/people/faculty/Axtell/AxtellLab/Software.html
302
http://www.bio.ub.es/julio/DnaSP.html
200
http://www.bio.usyd.edu.au/jermiin/programs.htm
java.io.FileNotFoundException : http://sydney.edu.au/science/biology/jermiin/programs.htm
http://www.bio.vu.nl/microb/research/tumor.html
200
http://www.bio21.bas.bg/codonpairs/
java.io.FileNotFoundException : http://www.bio21.bas.bg/codonpairs/
http://www.bioafrica.net
200
http://www.biobase.de
200
http://www.biobase.de/cgi-bin/biobase/cbs2/bin/template.cgi?template=cbscall.html
java.io.FileNotFoundException : http://www.biobase.de/cgi-bin/biobase/cbs2/bin/template.cgi?template=cbscall.html
http://www.bioc.aecom.yu.edu/labs/angellab/as
java.io.FileNotFoundException : http://www.bioc.aecom.yu.edu/labs/angellab/as
http://www.bioc.cam.ac.uk/isd
200
http://www.bioc.cam.ac.uk/UTOs/howe/
java.io.FileNotFoundException : http://www.bioc.cam.ac.uk/UTOs/howe/
http://www.bioc.rice.edu/
200
http://www.biocaster.org
200
http://www.biocentre.rdg.ac.uk/bioinformatics/ModFOLD/
200
http://www.biochem.ucl
java.net.UnknownHostException : www.biochem.ucl
http://www.biochem.ucl.ac.uk/bsm/SIMPLE
200
http://www.biochem.ucl.ac.uk/cgi-bin/cath/Grath.pl
java.io.IOException : Server returned HTTP response code: 403 for URL: http://www.biochem.ucl.ac.uk/cgi-bin/cath/Grath.pl
http://www.biochem.uwo.ca/cgi-bin/CDD/index.cgi
200
http://www.biochemj.org/bj/424/3/
200
http://www.biocomp.unibo.it/
200
http://www.biocomp.unibo.it/bacello/
200
http://www.biocomputing.it/picmi
200
http://www.bioconductor.org
200
http://www.bioconductor.org/help/biocviews/release/bioc/html/SQUADD.html
java.io.FileNotFoundException : http://www.bioconductor.org/help/biocviews/release/bioc/html/SQUADD.html
http://www.bioconductor.org/packages//2.7/bioc/html/xcms.html
200
http://www.bioconductor.org/packages/2.0/bioc/html/oneChannelGUI.html
200
http://www.bioconductor.org/packages/release/bioc/html/EBImage.html
200
http://www.bioconductor.org/packages/release/bioc/html/girafe.html
200
http://www.bioconductor.org/repository/devel/package/html/affypdnn.html
java.io.FileNotFoundException : http://bioconductor.org/packages/bioc/devel/src/contrib/html/affypdnn.html
http://www.biodalliance.org/
200
http://www.bioeng.nus.edu.sg/compbiolab/p2/
200
http://www.bioforscher.de/mptv.htm/
java.io.FileNotFoundException : http://www.bioforscher.de/mptv.htm/
http://www.bioguide-project.net
200
http://www.bioinf.au.dk/rnadbtool/
java.net.UnknownHostException : www.bioinf.au.dk
http://www.bioinf.jku.at/publications/papers/farms/supplementary.ps
200
http://www.bioinf.jku.at/software/fabia/fabia.html
200
http://www.bioinf.jku.at/software/farms/farms.html
200
http://www.bioinf.jku.at/software/LSTM_protein/
200
http://www.bioinf.man.ac.uk/dbbrowser/cinema-mx
200
http://www.bioinf.man.ac.uk/phosphabase
200
http://www.bioinf.man.ac.uk/resources/puma
200
http://www.bioinf.manchester.ac.uk/schwartz/grape
200
http://www.bioinf.mdc-berlin.de/unter2.html
java.net.SocketTimeoutException : connect timed out
http://www.bioinf.org.uk/pdbsws/
200
http://www.bioinf.org.uk/saap/
200
http://www.bioinf.ucd.ie/people/iain/iteration.html
200
http://www.bioinf.uni-freiburg.de
200
http://www.bioinf.uni-freiburg.de/Software
200
http://www.bioinf.uni-leipzig.de/Publications/SUPPLEMENTS/05-008/
200
http://www.bioinf.uni-leipzig.de/Software/FRANz/
200
http://www.bioinf.uni-leipzig.de/Software/PLEXY
200
http://www.bioinf.uni-leipzig.de/Software/rip.html
200
http://www.bioinf.uni-leipzig.de/Software/snoReport
200
http://www.bioinf.uni-leipzig/Software/RNAmicro
java.net.UnknownHostException : www.bioinf.uni-leipzig
http://www.bioinf.wits.ac.za/
200
http://www.bioinfo-hr.org/inca
200
http://www.bioinfo.biocenter.helsinki.fi/gtg
200
http://www.bioinfo.org.cn/SM/sRNAconservation.htm
200
http://www.bioinfo.rpi.edu
200
http://www.bioinfo.rpi.edu/applications/sfold
java.io.FileNotFoundException : http://www.bioinfo.rpi.edu/applications/sfold
http://www.bioinfo.sfc.keio.ac.jp/research/intron
200
http://www.bioinfo.tsinghua.edu.cn/
200
http://www.bioinfo.tsinghua.edu.cn/SubLoc/
200
http://www.bioinfo.tsinghua.edu.cn:8080/
java.net.ConnectException : Connection refused
http://www.bioinfor.com/zoom
200
http://www.bioinformatica.unito.it/bioinformatics/rre/rre.html
200
http://www.bioinformatica.unito.it/bioinformatics/snoRNAs
200
http://www.bioinformatics.buffalo.edu/resources/aft/
java.io.FileNotFoundException : http://www.bioinformatics.buffalo.edu/resources/aft/
http://www.bioinformatics.cs.ncl.ac.uk/sarge/index.html
java.net.UnknownHostException : www.bioinformatics.cs.ncl.ac.uk
http://www.bioinformatics.csiro.au/products.shtml
200
http://www.bioinformatics.leeds.ac.uk/
200
http://www.bioinformatics.leeds.ac.uk/BRS-nonint/
200
http://www.bioinformatics.leeds.ac.uk/pocketfinder
200
http://www.bioinformatics.leeds.ac.uk/ppi-pred/supp-material
200
http://www.bioinformatics.leeds.ac.uk/ppi_pred
200
http://www.bioinformatics.leeds.ac.uk/qsitefinder
200
http://www.bioinformatics.med.uu.nl/shops
200
http://www.bioinformatics.nl/netclust/
200
http://www.bioinformatics.nyu.edu
java.net.SocketTimeoutException : Read timed out
http://www.bioinformatics.org.au/evolsim
200
http://www.bioinformatics.org/blogo/
200
http://www.bioinformatics.org/cmview/
200
http://www.bioinformatics.org/combosa3d/
200
http://www.bioinformatics.org/Genquire
200
http://www.bioinformatics.org/grn/atrea.html
200
http://www.bioinformatics.psb.ugent.be/supplementary_data/
java.net.UnknownHostException : www.bioinformatics.psb.ugent.be
http://www.bioinformatics.rcsi.ie/
200
http://www.bioinformatics.sussex.ac.uk/PIRANHA
200
http://www.bioinformatics.sussex.ac.uk/protorp
200
http://www.bioinformatics.sussex.ac.uk/SHARP2
200
http://www.bioinformatics.ucla.edu/poa
200
http://www.bioinformatics.ucla.edu/QPRIMER/
200
http://www.bioinformatics.uwaterloo.ca/software
200
http://www.bioinformatics.uwaterloo.ca/supplements/05eh/
200
http://www.bioinformatics2.wsu.edu/ChromatinDB
200
http://www.bioinformatics2.wsu.edu/Osiris
200
http://www.bioinformaticslaboratory.nl
200
http://www.bioinformaticssolutions.com
200
http://www.bioinformaticssolutions.com/downloads/ph-academic/
java.net.SocketTimeoutException : Read timed out
http://www.bioinformatik.uni-koeln.de/
java.net.NoRouteToHostException : No route to host
http://www.biointeraction.org
200
http://www.bioit.org.cn/ao/targetfinder.htm
200
http://www.biojava.org
200
http://www.biol.sc.edu/
200
http://www.BiologicalNetworks.org
200
http://www.biologie.ens.fr/yeast-publi.html
200
http://www.biologie.uni-regensburg.de/Biophysik/Kalbitzer/permol/permol.html
200
http://www.biomath.org/dormanks/
200
http://www.biomath.org/mlegp
200
http://www.biomath.ucla.edu/msuchard/bali-phy
200
http://www.biomoby.org/
200
http://www.biomodels.net/
200
http://www.bionet.espci.fr/varan/
java.net.UnknownHostException : www.bionet.espci.fr
http://www.bionet.nsc
java.net.UnknownHostException : www.bionet.nsc
http://www.bioontology.org/tools/portal/bioportal.html
200
http://www.biopython.org
200
http://www.bioquery.org
200
http://www.biorag.org/pathway.html
200
http://www.bioruby.org/
200
http://www.bios.unc.edu/
200
http://www.bios.unc.edu/research/genomic_software/DiNAMIC
200
http://www.biosci.ki.se/groups/tbu/logobar/
200
http://www.biosci.ohio-state.edu/
200
http://www.biosemantics.org/chemlist
200
http://www.biosignet.org
200
http://www.biosolveit.de/ToPNet/
200
http://www.bioss.ac.uk/
200
http://www.bioss.ac.uk/associates/marco/supplement/
200
http://www.bioss.ac.uk/software.html
java.io.FileNotFoundException : http://www.bioss.ac.uk/software.html
http://www.bioss.sari.ac.uk/
200
http://www.bioss.sari.ac.uk/frank/Genetics
java.io.FileNotFoundException : http://www.bioss.ac.uk/frank/Genetics
http://www.bioss.sari.ac.uk/grainne
java.io.FileNotFoundException : http://www.bioss.ac.uk/grainne
http://www.bioss.sari.ac.uk/staff/adriano/research.html
200
http://www.bioss.uni-freiburg.de/cms/sbml-pet-mpi.html
200
http://www.biostat.harvard.edu/
200
http://www.biostat.jhsph.edu/
200
http://www.biostat.pitt.edu/bioinfo/
200
http://www.biostat.umn.edu/
200
http://www.biostat.umn.edu/cgi-bin/rrs?print+2001,2001a,b)
java.io.FileNotFoundException : http://www.biostat.umn.edu/cgi-bin/rrs?print+2001,2001a,b)
http://www.biostat.wisc.edu/
200
http://www.biostat.wisc.edu/gene-regulation
200
http://www.biotec.or.th/ISL/SMOL/
200
http://www.biotech.kth.se/molbio/microarray/
200
http://www.biotechniques.com/softlib/qgene.html
java.io.FileNotFoundException : http://www.biotechniques.com/softlib/qgene.html
http://www.biowaredb.org/
200
http://www.biowebdb.org/garsa/
java.io.FileNotFoundException : http://www.biowebdb.org/garsa/
http://www.bioweka.org
java.io.IOException : Server returned HTTP response code: 500 for URL: http://bioweka.sourceforge.net
http://www.biowiki.org/
200
http://www.biowiki.org/Handel
200
http://www.bioxsd.org/BioXSD-1.0.xsd
200
http://www.bioz.unibas.ch/gocluster
java.io.FileNotFoundException : http://www.biozentrum.unibas.ch/gocluster
http://www.bip.bham.ac.uk/vivo/fumo.html
200
http://www.birc.au.dk/
200
http://www.birc.au.dk/snptools
java.io.FileNotFoundException : http://www.birc.au.dk/snptools/
http://www.birc.dk/Software/evogene
java.io.FileNotFoundException : http://www.birc.dk/Software/evogene
http://www.birc.dk/Software/QDist
200
http://www.birc.dk/Software/RBT
java.io.FileNotFoundException : http://www.birc.dk/Software/RBT
http://www.blast2go.de
200
http://www.blisstool.org/
200
http://www.bme.ucdavis.edu/savageaulab/
200
http://www.bme.virginia.edu/csbl/downloads/
200
http://www.bmi.osu.edu/
200
http://www.bmm.icnet.uk/
java.net.UnknownHostException : www.bmm.icnet.uk
http://www.bmm.icnet.uk/servers/sawted
java.net.UnknownHostException : www.bmm.icnet.uk
http://www.bnplusplus.org/
200
http://www.bork
java.net.UnknownHostException : www.bork
http://www.bork.embl-heidelberg.de/alerting/
java.io.FileNotFoundException : http://www.bork.embl-heidelberg.de/alerting/
http://www.bork.embl-heidelberg.de/Docu/purclust/
200
http://www.bork.embl.de/
200
http://www.bork.embl.de/blast2gene
200
http://www.bork.embl.de/Docu/AQUA
200
http://www.bork.embl.de/Docu/STRING-IE
200
http://www.bork.embl.de/kat
200
http://www.bork.embl.de/LSAT
java.io.FileNotFoundException : http://coot.embl.de/LSAT
http://www.bork.embl.de/Sircah
200
http://www.bork.embl.de/software/smash
200
http://www.bq.ub.es/bioqint/selivanov.htm
200
http://www.brc.riken.jp/lab/bpmp/SDOP/
java.net.SocketTimeoutException : Read timed out
http://www.broad.mit.edu/annotation/argo/
200
http://www.broad.mit.edu/cancer/software
java.io.IOException : Server returned HTTP response code: 403 for URL: http://www.broadinstitute.org/cancer/software/
http://www.broad.mit.edu/genepattern
200
http://www.broad.mit.edu/GSEA
200
http://www.broad.mit.edu/mpg/haploview/
200
http://www.broad.mit.edu/mpg/snap/
200
http://www.broadinstitute.org/perl/seq/specialprojects/primerDesign.cgi
200
http://www.broadinstitute.org/science/programs/genome-biology/spines/
200
http://www.broadinstitute.org/science/software/
200
http://www.bru.ed.ac.uk/
java.net.UnknownHostException : www.bru.ed.ac.uk
http://www.buchnera.org/
200
http://www.burkholderia.com
200
http://www.bussemakerlab.org/
200
http://www.bussemakerlab.org/software/MatrixREDUCE
200
http://www.bx.psu.edu/miller_lab
200
http://www.cac.science.ru.nl
200
http://www.cad.zju.edu.cn/home/humin
200
http://www.cadlive.jp
200
http://www.cage.wbmei.jhu.edu
java.net.SocketTimeoutException : connect timed out
http://www.caleydo.org
200
http://www.calibayes.ncl.ac.uk/Resources/dsmts/
200
http://www.calit2.net/compbio/hap/
200
http://www.came.sbg.ac.at/wilma/
java.io.FileNotFoundException : http://www.came.sbg.ac.at/wilma/
http://www.cancerbiostats.onc.jhmi.edu/cogaps.cfm
200
http://www.casbase.org/casvm/index.html
200
http://www.caspur.it/
200
http://www.caspur.it/ASPicDB
200
http://www.caspur.it/ExpEdit/
200
http://www.cbcb.umd.edu/DiseaseNet
200
http://www.cbcb.umd.edu/software/jellyfish
200
http://www.cbi-platform.net
200
http://www.cbi-tmhs.org/AxonTracker/
200
http://www.cbi.seu.edu.cn/DBindR/DBindR.htm
200
http://www.cbil.ece.vt.edu/caBIG-PUGSVM.htm
200
http://www.cbil.ece.vt.edu/publications.htm
200
http://www.cbil.ece.vt.edu/ResearchOngoingSNP.htm
200
http://www.cbil.ece.vt.edu/software.htm
200
http://www.cbil.upenn.edu/mgs/systems/acti
java.io.FileNotFoundException : http://www.cbil.upenn.edu/mgs/systems/acti
http://www.cbil.upenn.edu/mgs/systems/c
java.io.FileNotFoundException : http://www.cbil.upenn.edu/mgs/systems/c
http://www.cbil.upenn.edu/mgs/systems/r
java.io.FileNotFoundException : http://www.cbil.upenn.edu/mgs/systems/r
http://www.cbil.upenn.edu/RAD
200
http://www.cbio.uct.ac.za/pub_support/bioinf06
200
http://www.cbrc.jp/
200
http://www.cbs
java.net.UnknownHostException : www.cbs
http://www.cbs.dtu
java.net.UnknownHostException : www.cbs.dtu
http://www.cbs.dtu.dk/
200
http://www.cbs.dtu.dk/gorodkin/appl/slogo
java.io.FileNotFoundException : http://www.cbs.dtu.dk/gorodkin/appl/slogo
http://www.cbs.dtu.dk/services/GenomeAtlas/
200
http://www.cbs.dtu.dk/services/InterMap3D/
200
http://www.cbs.dtu.dk/services/NetMHC-3.0
200
http://www.cbs.dtu.dk/services/NetMHCpan-1.1
200
http://www.cbs.dtu.dk/services/NetPhosYeast/
200
http://www.cc.utah.edu/
200
http://www.ccbb.pitt.edu/anm
200
http://www.ccbb.pitt.edu/p2p
200
http://www.ccbi.cam.ac.uk/software/psyk/software.html
200
http://www.ccbm.jhu.edu
200
http://www.ccg.unam.mx/tfmodeller
java.net.UnknownHostException : www.ccg.unam.mx
http://www.ccpn.ac.uk
200
http://www.ccpn.ac.uk/metabolomics/
200
http://www.ccr.buffalo.edu/halfon/spike/index.html
200
http://www.cdfd.org.in/imex
200
http://www.cdisc.org/models/sdtm/index.html
java.io.FileNotFoundException : http://www.cdisc.org/models/sdtm/index.html
http://www.cdisc.org/models/send/v2/index.html
java.io.FileNotFoundException : http://www.cdisc.org/models/send/v2/index.html
http://www.cebitec.uni-bielefeld.de/brf/saruman/saruman.html
200
http://www.cebl.auckland.ac.nz
java.net.SocketTimeoutException : connect timed out
http://www.cellclassifier.ethz.ch
200
http://www.cellmc.org
200
http://www.cellml.org/models
200
http://www.cellml.org/tools/pmr/
200
http://www.cellprofiler.org
200
http://www.cgb.ki.se/OrthoGUI
java.net.NoRouteToHostException : No route to host
http://www.cgl.ucsf.edu/chimera/
200
http://www.cgl.ucsf.edu/Research/genentech/gepis/
200
http://www.cgr.ki.se/cgr/groups/sonnhammer/Blixem.html
java.net.NoRouteToHostException : No route to host
http://www.cgr.ki.se/cgr/MEDUSA
java.net.NoRouteToHostException : No route to host
http://www.cgr.ki.se/Pfam
java.net.NoRouteToHostException : No route to host
http://www.charite.de/bioinf/strap/
200
http://www.charite.de/bioinformatics
200
http://www.che.udel.edu/eXPatGen/
200
http://www.che.udel.edu/systems/people/zak
200
http://www.chem.uky.edu/research/lynn/Nelson.pdf
200
http://www.chem.utoronto.ca/staff/GAW/links.html
java.io.FileNotFoundException : http://www.chem.utoronto.ca/staff/GAW/links.html
http://www.chem.utoronto.ca/staff/MCG/
java.io.IOException : Server returned HTTP response code: 403 for URL: http://www.chem.utoronto.ca/staff/MCG/
http://www.chemi.muni.cz/lbsd/triton.ht
java.io.IOException : Server returned HTTP response code: 403 for URL: http://www.chemi.muni.cz/lbsd/triton.ht
http://www.chems.msu.edu/groups/chan/ssm.zip
200
http://www.chgb.org.cn/lda/lda.htm
java.io.FileNotFoundException : http://www.chgb.org.cn/lda/lda.htm
http://www.chibi.ubc.ca/Gemma
200
http://www.chibi.ubc.ca/GEOMMTX
200
http://www.chip.org/
200
http://www.chokkan.org/research/acromine/
200
http://www.cib.nig.ac.jp/dda/yossuzuk/welcome.html
200
http://www.cibiv.at/software/treesnatcher
200
http://www.ciml.univ-mrs.fr/software/ferrier.htm
200
http://www.cin.ufpe.br/
200
http://www.cin.ufpe.br/approxiamtely
java.io.FileNotFoundException : http://www.cin.ufpe.br/approxiamtely
http://www.cis.hut.fi/projects/mi/software/ismb09
200
http://www.cis.hut.fi/projects/mi/software/multiWayCCA/
200
http://www.cis.hut.fi/projects/mi/software/NetResponse
200
http://www.cis.upenn.edu/biocomp/manuscripts/bioinformatics_bti245/supp-info.html
java.io.FileNotFoundException : http://biocomp.cis.upenn.edu/manuscripts/bioinformatics_bti245/supp-info.html
http://www.cis.upenn.edu/datamining/software_dist/autoterm/
301
http://www.cisban.ac.uk/saint
java.net.SocketTimeoutException : connect timed out
http://www.cise.ufl.edu/
200
http://www.cityofhope.org/Researchers/ChenYuan/NvMap/
java.io.FileNotFoundException : http://www.cityofhope.org/Researchers/ChenYuan/NvMap/
http://www.clab.kwansei.ac.jp/mining/discas/discas.html
200
http://www.clantox.cs.huji.ac.il
200
http://www.cls.zju.edu.cn/binfo/BNArray/
200
http://www.cmb.usc.edu/
200
http://www.cmb.usc.edu/people/andrewds/rmap
200
http://www.cmb.usc.edu/people/valouev/
java.io.IOException : Server returned HTTP response code: 403 for URL: http://www.cmb.usc.edu/people/valouev/
http://www.cmbi.kun.nl/MGV
200
http://www.cmbi.kun.nl/usage/
java.io.IOException : Server returned HTTP response code: 403 for URL: http://www.cmbi.kun.nl/usage/
http://www.cmbl.uga.edu/software.html
200
http://www.cmis.csiro.au/mpMap
200
http://www.cmm.uchile.cl/genoma/tip/
java.io.FileNotFoundException : http://www.cmm.uchile.cl/genoma/tip/
http://www.cmp.uea.ac.uk/dyndom
200
http://www.cms.liu.se/chemistry/molbiotech/maria_sunnerhagens_group/mtmdat
java.net.UnknownHostException : www.cms.liu.se
http://www.cnb
java.net.UnknownHostException : www.cnb
http://www.cnb.uam
java.net.UnknownHostException : www.cnb.uam
http://www.cnb.uam.es/
200
http://www.cnb.uam.es/bioinfo/Software/so
java.io.FileNotFoundException : http://www.cnb.uam.es/bioinfo/Software/so
http://www.cnbi2.com/cgi-bin/amp.pl
java.io.IOException : Server returned HTTP response code: 403 for URL: http://www.cnbi2.com/cgi-bin/amp.pl
http://www.cnm.es/
200
http://www.cnmcresearch.org/bioinformatics
200
http://www.cns.tau.ac.il/resc.html
200
http://www.coccidia.icb.usp.br/genseed/
200
http://www.columbia.edu/
200
http://www.combinatorics.cn/cbpc/gfold.tar.gz
java.io.FileNotFoundException : http://www.combinatorics.cn/cbpc/gfold.tar.gz
http://www.combinatorics.cn/cbpc/rip.html
java.io.FileNotFoundException : http://www.combinatorics.cn/cbpc/rip.html
http://www.comp-sys-bio.org/SBRML
200
http://www.comp.nus.edu.sg/
200
http://www.compbio.dundee.ac.uk
200
http://www.compbio.dundee.ac.uk/parcrys
200
http://www.compbio.dundee.ac.uk/prophossi
200
http://www.compbio.group.cam.ac.uk/software.html
200
http://www.compbiosci.wfu.edu/tools.htm
200
http://www.compdiag.molgen.mpg.de/software/macat.shtml
java.net.UnknownHostException : www.compdiag.molgen.mpg.de
http://www.compgen.org/tools/PRED-TAT/
200
http://www.compgen.uni-muenster.de/teclass
200
http://www.complex.iastate.edu
200
http://www.compsysbio.org/CellSim/
200
http://www.compsysbio.org/projects/DETECT/
200
http://www.computableplant.org
200
http://www.computationalimmunology.org/utilities/
200
http://www.copasi.org
200
http://www.cosbi.eu/Rpty_Soft_CytoSim.php
200
http://www.cran.org
200
http://www.cran.r-project.org
200
http://www.cran.rproject.org
java.io.IOException : Server returned HTTP response code: 503 for URL: http://www.cran.rproject.org
http://www.crm.umontreal.ca/viart/exemplar_di
java.io.FileNotFoundException : http://www.crm.umontreal.ca/viart/exemplar_di
http://www.crosschip.org
java.net.NoRouteToHostException : No route to host
http://www.CryptoDB.org
200
http://www.cryst.bbk.ac.uk/
200
http://www.cryst.bbk.ac.uk/wernisch/yasma.html
200
http://www.cs
java.net.UnknownHostException : www.cs
http://www.cs.au.dk/
200
http://www.cs.berkeley.edu/
200
http://www.cs.bgu.ac.il/
200
http://www.cs.brown.edu/people/braphael/supplements/
200
http://www.cs.cf.ac.uk/ec/
java.io.IOException : Server returned HTTP response code: 403 for URL: http://www.cs.cf.ac.uk/ec/
http://www.cs.chalmers.se/
200
http://www.cs.cityu.edu.hk/
200
http://www.cs.cmu.edu/
200
http://www.cs.columbia.edu/compbio/backbone
200
http://www.cs.columbia.edu/compbio/geneclass
200
http://www.cs.columbia.edu/compbio/hiclust
200
http://www.cs.cornell.edu/
200
http://www.cs.dartmouth.edu/
200
http://www.cs.dartmouth.edu/gnuplot_inf
java.io.FileNotFoundException : http://www.cs.dartmouth.edu/gnuplot_inf
http://www.cs.duke.edu/
200
http://www.cs.helsinki.fi/group/pssmfind
200
http://www.cs.helsinki.fi/group/suds/cst/
200
http://www.cs.helsinki.fi/u/kpalin/CorrDisrupt/
200
http://www.cs.helsinki.fi/u/lmsalmel/coral/
200
http://www.cs.helsinki.fi/u/lmsalmel/hybrid-shrec/
200
http://www.cs.hku.hk/
200
http://www.cs.man
java.net.UnknownHostException : www.cs.man
http://www.cs.may.ie/distributed
200
http://www.cs.newcastle.edu.au/
200
http://www.cs.niu.edu/
200
http://www.cs.njit.edu/usman/probalign
200
http://www.cs.nott.ac.uk/
200
http://www.cs.purdue.edu/homes/jpandey/narada/
200
http://www.cs.purdue.edu/homes/koyuturk/pathway/
java.io.FileNotFoundException : http://www.cs.purdue.edu/homes/koyuturk/pathway/
http://www.cs.tau.ac.il/
200
http://www.cs.tcd.ie/Nadia.Bolshakova/Machaon.html
java.io.FileNotFoundException : http://www.scss.tcd.ie/Nadia.Bolshakova/Machaon.html
http://www.cs.toronto.edu/
200
http://www.cs.tut.fi/
200
http://www.cs.tut.fi/sgn/csb/spotseg/
200
http://www.cs.ualberta.ca/
301
http://www.cs.ubc.ca/
200
http://www.cs.ubc.ca/labs/beta/genefinding/
200
http://www.cs.ucsb.edu/
200
http://www.cs.uga.edu/
200
http://www.cs.uic.edu/
java.io.IOException : Server returned HTTP response code: 403 for URL: http://www.cs.uic.edu/
http://www.cs.umb.edu/
200
http://www.cs.umd.edu/hcil/hce
200
http://www.cs.umn.edu/
200
http://www.cs.umn.edu/compbio/ProbeAlign
200
http://www.cs.utexas.edu/
200
http://www.cs.utoronto.ca/
200
http://www.cs.uu.nl/people/rainer/conan.html
java.io.FileNotFoundException : http://people.cs.uu.nl/rainer/conan.html
http://www.cs.vu.nl/microgenie
java.io.IOException : Server returned HTTP response code: 403 for URL: http://www.cs.vu.nl/microgenie
http://www.cs.waikato.ac.nz/ml/weka/
200
http://www.cs.washington.edu/homes/kayee/model
200
http://www.cs.wisc.edu/
200
http://www.csail.mit.edu/
200
http://www.csb.ethz.ch
200
http://www.csb.pitt.edu/ProDy/
200
http://www.csd.uwo.ca/
200
http://www.cse.buffalo.edu/DBGROUP/bioinformatics/supplementary/vizstruct
200
http://www.cse.cuhk.edu.hk/
200
http://www.cse.ebuffalo.edu/faculty/mbeal/software.html
java.net.UnknownHostException : www.cse.ebuffalo.edu
http://www.cse.sc.edu/
200
http://www.cse.ucsc
java.net.UnknownHostException : www.cse.ucsc
http://www.cse.ucsc.edu/karplus
java.io.FileNotFoundException : http://www.soe.ucsc.edu/karplus
http://www.cse.ucsc.edu/research/compbi
java.io.FileNotFoundException : http://www.soe.ucsc.edu/research/compbi
http://www.cse.ucsc.edu/research/compbio/HMM-apps/T99-query.html
200
http://www.cse.ucsc.edu/research/compbio/HMM-apps/T99-tuneup.html
200
http://www.cse.ucsc.edu/research/compbio/sam/
java.io.FileNotFoundException : http://compbio.soe.ucsc.edu/sam/
http://www.cse.ucsd.edu/groups/bioinformatics
200
http://www.cse.ucsd.edu/groups/bioinformatics/software.html
200
http://www.cse.ucse
java.net.UnknownHostException : www.cse.ucse
http://www.cse.wustl.edu/
200
http://www.cshl.org/mzhanglab/tabaska/j
java.io.FileNotFoundException : http://www.cshl.edu/mzhanglab/tabaska/j
http://www.csi.uoregon.edu/projects/genetics/GSL
200
http://www.csie.ntu.edu.tw/
200
http://www.csis.hku.hk/
200
http://www.csse.monash.edu.au/
200
http://www.csse.unimelb.edu.au/
200
http://www.cwi.nl/projects/sic/bioinformatics2007/
200
http://www.cyped.uni-stuttgart.de
200
http://www.cytoscape.org
200
http://www.cytoscape.org/plugins/GOlorize/GOlorizeUserGuide.pdf
java.io.FileNotFoundException : http://www.cytoscape.org/plugins/GOlorize/GOlorizeUserGuide.pdf
http://www.cytoscape.org/plugins/index.php
java.io.FileNotFoundException : http://www.cytoscape.org/plugins/index.php
http://www.cytoscape.org/plugins2.php
java.io.FileNotFoundException : http://www.cytoscape.org/plugins2.php
http://www.daimi.au.dk/
200
http://www.dalicon.com/chimera/
200
http://www.dasmi.de/
200
http://www.dasregistry.org/
200
http://www.dat.ruc.dk/keld/research/LKH
200
http://www.data-monkey.org
java.net.UnknownHostException : www.data-monkey.org
http://www.datalab.uci.edu/resources/periodicity/
200
http://www.datamonkey.org
200
http://www.datamonkey.org/GARD/
200
http://www.davidbickel.com
200
http://www.dbi.tju.edu/bioinformatics2004.pdf
200
http://www.dbmi.columbia.edu/
200
http://www.dbmi.columbia.edu/pgviewer/
java.io.FileNotFoundException : http://www.dbmi.columbia.edu/pgviewer/
http://www.dbmi.pitt.edu/EPO-KB
java.io.FileNotFoundException : http://www.dbmi.pitt.edu/EPO-KB
http://www.dbs.ifi.lmu.de/
200
http://www.dbs.ifi.lmu.de/Mitarbeiter/borgwardt.html
200
http://www.dcs.gla.ac.uk/
200
http://www.dcs.gla.ac.uk/inference/metsamp
200
http://www.dcs.shef.ac.uk/
200
http://www.dcs.shef.ac.uk/nlp/pasta/
200
http://www.dddc.ac.cn/adme/myzheng/SOME_1_0.tar.gz
200
http://www.dendroscope.org
200
http://www.dia.fi.upm.es/
200
http://www.dimmic.net/supplement/
java.net.UnknownHostException : www.dimmic.net
http://www.dion.che.udel.edu/multiscale/Introduction.html
200
http://www.disprot.org
200
http://www.disprot.org/predictors.php
200
http://www.dkfz-heidelberg.de/kompl_genome/Other/QuickLims/index.html
java.io.FileNotFoundException : http://www.dkfz.de/kompl_genome/Other/QuickLims/index.html
http://www.dkfz-heidelberg.de/Macromol/ehrlich
java.io.FileNotFoundException : http://www.dkfz.de/Macromol/ehrlich
http://www.dkfz-heidelberg.de/spec/
java.io.FileNotFoundException : http://www.dkfz.de/spec/
http://www.dkfz-heidelberg.de/spec/lox-db/
java.io.FileNotFoundException : http://www.dkfz.de/spec/lox-db/
http://www.dkfz-heidelberg.de/tbi/
200
http://www.dkfz-heidelberg.de/tbi/services/cluster/
java.io.IOException : Server returned HTTP response code: 403 for URL: http://ibios.dkfz.de/tbi_old/services/cluster/
http://www.dkfz-heidelberg.de/tbi/services/modest/b
java.io.FileNotFoundException : http://ibios.dkfz.de/tbi_old/services/modest/b
http://www.dkfz.de/mga2/ddepn/
200
http://www.dkfz.de/mga2/people/buness/CTP/
200
http://www.dkfz.de/tbi
200
http://www.dkfz.de/tbi/projects/modellingAndSimulationOfCelluarSystems/tropical.jsp
java.io.FileNotFoundException : http://ibios.dkfz.de/tbi/projects/modellingAndSimulationOfCelluarSystems/tropical.jsp
http://www.dkfz.de/tbi/services/mchips
200
http://www.dmi.unict.it/CIG/suppdata_bioinf.html
java.net.SocketTimeoutException : connect timed out
http://www.dna.utah.edu/umelt/umelt.html
200
http://www.doe-mbi.ucla.edu/services
200
http://www.doornik.com
200
http://www.dpci.unipd.it/Bioeng/Publications/LAP.htm
java.io.FileNotFoundException : http://www.dpci.unipd.it/Bioeng/Publications/LAP.htm
http://www.dq.fct.unl.pt/qoa/jas/seqrep
200
http://www.dr-spiess.de/qpcR.html
200
http://www.drive5.com/lobster
200
http://www.drive5.com/lobster/index.htm
200
http://www.drive5.com/piler
200
http://www.drive5.com/usearch
200
http://www.ds.unifi.it/
200
http://www.dsba.unisannio.it/Members/ceccarelli/vega
200
http://www.dsi.unifi.it/neural/src/3DDK
200
http://www.dsimb.inserm.fr/dsimb-tools/peeling3
200
http://www.duke.edu/
200
http://www.dynameomics.org
200
http://www.dyogen.ens.fr/genomicus
200
http://www.e-cell.org
200
http://www.earthworms.org/
200
http://www.ebgm.jussieu.fr/
200
http://www.ebi.ac.uk/
200
http://www.ebi.ac.uk/arrayexpress/
200
http://www.ebi.ac.uk/bertone/software
200
http://www.ebi.ac.uk/biocat
200
http://www.ebi.ac.uk/biocat/biocat.html
200
http://www.ebi.ac.uk/biomodels
200
http://www.ebi.ac.uk/clustr/
200
http://www.ebi.ac.uk/dasty/
200
http://www.ebi.ac.uk/efo
200
http://www.ebi.ac.uk/embl/
200
http://www.ebi.ac.uk/embl/Submission/align_top.html
200
http://www.ebi.ac.uk/embl/sva/
200
http://www.ebi.ac.uk/enright/sylarray
200
http://www.ebi.ac.uk/expressionprofiler/
200
http://www.ebi.ac.uk/huber-srv/hilbert/
200
http://www.ebi.ac.uk/interpro/scan.html
200
http://www.ebi.ac.uk/microarray-as/ae/
200
http://www.ebi.ac.uk/microarray/networks
200
http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BS)
200
http://www.ebi.ac.uk/pdbsum
200
http://www.ebi.ac.uk/pratt/
200
http://www.ebi.ac.uk/pride/
200
http://www.ebi.ac.uk/projects/BARGEN/
200
http://www.ebi.ac.uk/QuickGO
200
http://www.ebi.ac.uk/Rebholz-srv/ebimed
200
http://www.ebi.ac.uk/Rebholz-srv/PaperMaker
200
http://www.ebi.ac.uk/Rebholz/software.html
200
http://www.ebi.ac.uk/research/cgg/genomes.html
200
http://www.ebi.ac.uk/research/cgg/services/cast/
200
http://www.ebi.ac.uk/research/cgg/services/layout
200
http://www.ebi.ac.uk/tc-test/textmining/medevi/
200
http://www.ebi.ac.uk/thornton-srv/databases/CoFactor
200
http://www.ebi.ac.uk/thornton-srv/databases/HTHquery
200
http://www.ebi.ac.uk/thornton-srv/databases/Metal_MACiE/home.html
200
http://www.ebi.ac.uk/thornton-srv/databases/WSsas/
200
http://www.ebi.ac.uk/thornton-srv/software/PoreLogo/
200
http://www.ebi.ac.uk/Tools/archschema
200
http://www.ebi.ac.uk/tools/clustalw2
200
http://www.ebi.ac.uk/tools/rcloud
200
http://www.ebi.ac.uk/Tools/rwiki/
200
http://www.ebi.ac.uk/uniprot/unisave
200
http://www.ebi.ac.uk/webservices/whatizit
200
http://www.ebi.ac.uk/xembl/
200
http://www.ebi.uniprot.org/
200
http://www.ece.northwestern.edu/
200
http://www.ee.cityu.edu.hk/
200
http://www.ee.columbia.edu/
200
http://www.ee.nthu.edu.tw/
200
http://www.ee.nthu.edu.tw/bschen/SyntheticBioDesign_supplement.pdf
200
http://www.ee.technion.ac.il/Sites/People/YoninaEldar/
200
http://www.eecs.umich.edu/saga
200
http://www.eee.hku.hk/
200
http://www.efamily.org.uk/software/dasclients/spice/
200
http://www.egs.uu.se/evbiol/Research/JakobssonLab/compass.html
200
http://www.ehscenter.org/dbd/
200
http://www.eidogen-sertanty.com/Documents/convergent_island_stats_sup.pdf
200
http://www.eie.polyu.edu.hk/
200
http://www.embl-ebi.ac
java.net.UnknownHostException : www.embl-ebi.ac
http://www.embl-ebi.ac.uk/FTP/index.html
200
http://www.embl-heidelberg.de/srs5/
java.io.FileNotFoundException : http://www.embl.de/srs5/
http://www.EMBLHeidelberg.de/
200
http://www.embraceregistry.net
200
http://www.emi.unsw.edu.au/
200
http://www.empress.har.mrc.ac.uk
200
http://www.enea.it/hpcn/php/rosato/
java.io.FileNotFoundException : http://www.enea.it/hpcn/php/rosato/
http://www.eng.buffalo.edu/
200
http://www.eng.nus.edu.sg/civil/Labarray/labarray.htm
java.io.FileNotFoundException : http://www.eng.nus.edu.sg/civil/Labarray/labarray.htm
http://www.engg.upd.edu.ph/
java.net.ConnectException : Connection refused
http://www.engr.uconn.edu/
200
http://www.ensembl.org/
200
http://www.enzim.hu/DAS/DAS.html
200
http://www.enzim.hu/hmmtop
200
http://www.enzim.hu/scide
200
http://www.enzome.com
200
http://www.enzyme.chem.msu.ru/hcs/
200
http://www.epfl.ch/
200
http://www.epidkardia.sph.umich.edu/software/chromoscan/
java.net.SocketTimeoutException : connect timed out
http://www.epidkardia.sph.umich.edu/software/kgrapher
java.net.SocketTimeoutException : connect timed out
http://www.epistasis.org
200
http://www.equispharm.com/idmap
200
http://www.erasmusmc.nl/gatcplatform
java.io.FileNotFoundException : http://www.erasmusmc.nl/gatcplatform
http://www.es.embnet.org/SMS
java.net.SocketTimeoutException : Read timed out
http://www.es.embnet.org/SMS/STINGm/consseq/
java.net.SocketTimeoutException : Read timed out
http://www.esat.kuleuven.ac.be/
200
http://www.esat.kuleuven.ac.be/maran/
200
http://www.esat.kuleuven.be/endeavour
200
http://www.ese.u-psud.fr/bases/upresa/pages/devienne/index.html
200
http://www.esid.org/
200
http://www.evolgenics.com/software
java.net.UnknownHostException : www.evolgenics.com
http://www.evolution.reading.ac.uk
200
http://www.evolution.unibas.ch/salzburger/software.htm
200
http://www.ews.uiuc.edu/
200
http://www.expasy.org/databases/prosite/
java.io.FileNotFoundException : http://www.expasy.org/databases/prosite/
http://www.expasy.org/sprot/
200
http://www.expasy.org/swissvar
200
http://www.expasy.org/tools/patoseq/
200
http://www.expasy.org/tools/scanprosite
200
http://www.expasy.org/tools/sulfinator/
200
http://www.expertomicacells.tk
200
http://www.expertomicacells.wu.cz
200
http://www.farma.ku.dk/smartcyp
200
http://www.fas.harvard.edu/
200
http://www.fas.umontreal.ca/biol/casgrain/en/labo/t-rex
java.io.FileNotFoundException : http://www.fas.umontreal.ca/biol/casgrain/en/labo/t-rex
http://www.fda.gov/cber/research/imaging/imageanalysis.htm
java.io.FileNotFoundException : http://www.fda.gov/cber/research/imaging/imageanalysis.htm
http://www.fdm.uni-freiburg.de/
200
http://www.fernandes.org/txp/article/9/site-specific-relative-evolutionary-rates
200
http://www.few.vu.nl/
200
http://www.ff.ul.pt/paginas/jvitor/Bioinformatics/MCRM_algorithm.zip
200
http://www.fgcz.ethz.ch/PhyloDetect
200
http://www.fiserlab.org/servers/mmm
200
http://www.flannotator.org.uk/
200
http://www.fli-leibniz.de/tsb/DASS
200
http://www.flychip.org.uk/kreil/pub/2dgels/
java.io.FileNotFoundException : http://www.flychip.org.uk/missing.php
http://www.flyreg.org/
200
http://www.fmi.ch/groups/functional.genomics/tool-Supp.htm
200
http://www.fmi.ch/groups/functional.genomics/tool.htm
200
http://www.fml.mpg.de/raetsch/projects/palma
200
http://www.fml.mpg.de/raetsch/projects/qpalma
200
http://www.fml.mpg.de/raetsch/suppl/kirmes/
200
http://www.fml.tuebingen.mpg.de/
200
http://www.fml.tuebingen.mpg.de/raetsch/projects/arts
200
http://www.fml.tuebingen.mpg.de/raetsch/projects/POIM
200
http://www.fmp-berlin.de/nmr/cops
200
http://www.fos.su.se/
200
http://www.framinghamheartstudy.org/research/gwas_pleiotropictool.html
200
http://www.fsf.org./copyleft/gpl.html
200
http://www.fujirebio.co.jp/support/index.php
200
http://www.fundp.ac.be/sciences/biologie/bms/
java.io.FileNotFoundException : http://www.fundp.ac.be/sciences/biologie/bms/
http://www.fundp.ac.be/urbm/bioinfo/esypred/
200
http://www.funnet.info
200
http://www.funsimmat.de
200
http://www.fz-juelich.de/nic/cbb
200
http://www.g-language.org/
200
http://www.gatsby.ucl.ac.uk/
200
http://www.gems-system.org
200
http://www.gen-epi.de/mouse
java.net.UnknownHostException : www.gen-epi.de
http://www.genalyzer.de
java.net.SocketException : Unexpected end of file from server
http://www.gene-regulation.com/pub/programs.html
200
http://www.gene.com/share/gmap
200
http://www.genebee.msu.su/services/annot/basic.html
200
http://www.genecruiser.org
200
http://www.genediscovery.org/pgmapper/index.jsp
200
http://www.genemania.org/plugin/
200
http://www.geneontology.org
200
http://www.genepattern.org
200
http://www.genepredictions.org
200
http://www.genereporter.tu-bs.de
200
http://www.genetics.med.ed.ac.uk/suspects/
200
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting
200
http://www.genetics.ucla.edu/labs/horvath/MTOM/
200
http://www.genetics.ucla.edu/labs/sabatti/software.html
200
http://www.genetics.ucla.edu/software/
200
http://www.genetics.uga.edu/sw/
200
http://www.genetics.wustl.edu/eddy/forester
java.io.FileNotFoundException : http://www.genetics.wustl.edu/eddy/forester
http://www.genocad.org
200
http://www.genome.ad.jp/
200
http://www.genome.duke.edu/labs/furey/software/fseq
200
http://www.genome.duke.edu/labs/ohler/research/transcription/fly_enhancer/
200
http://www.genome.ist.i.kyoto-u.ac.jp/
200
http://www.genome.jp/kegg/pathway/hsa/hsa01510.html
java.io.FileNotFoundException : http://www.genome.jp/kegg/pathway/hsa/hsa01510.html
http://www.genome.jp/tools/e-zyme/
200
http://www.genome.kbrin.uky.edu/fungi_tel/terminus/
java.net.UnknownHostException : www.genome.kbrin.uky.edu
http://www.genome.umd.edu
200
http://www.genomecurator.org/ORFcurator/
200
http://www.genomics.csse.unimelb.edu.au/is-rSNP
200
http://www.genomics.mcg.edu/niddkbtc
java.io.FileNotFoundException : http://www.genomics.mcg.edu/niddkbtc
http://www.genomics.med.uu.nl/pub/pk/comb_gen_network
java.io.FileNotFoundException : http://www.genomics.med.uu.nl/pub/pk/comb_gen_network
http://www.genomine.org/eigenr2/
200
http://www.genoplante.org
java.net.UnknownHostException : www.genoplante.org
http://www.genoscope.cns.fr/cycsim
200
http://www.genoscope.fr/ASMC/
200
http://www.genscript.com
200
http://www.genstat.net/genocluster
200
http://www.geocities.com/Athens/4654/POLINA.h
java.io.FileNotFoundException : http://www.geocities.com/Athens/4654/POLINA.h
http://www.geocities.com/jg_liao/software
java.io.FileNotFoundException : http://www.geocities.com/jg_liao/software
http://www.gepas.org/
200
http://www.germonline.org/
200
http://www.gesteland.genetics.utah.edu/freqAnalysis
200
http://www.geworkbench.org
200
http://www.ghmm.org/gql
200
http://www.gis.a-star.edu.sg/
200
http://www.gla.ac.uk/
200
http://www.gluegrant.org
200
http://www.gmod.org
200
http://www.gmod.org/cmap
java.io.FileNotFoundException : http://www.gmod.org/cmap
http://www.gmu.edu/departments/mmb/baranova/pages/bioinformatics
java.io.FileNotFoundException : http://mmb.gmu.edu/baranova/pages/bioinformatics
http://www.gnu.org/
200
http://www.gnu.org/copyleft/lesser.html
200
http://www.gnu.org/licences/gpl
200
http://www.gnu.org/licenses/
200
http://www.gnu.org/licenses/gpl.html
200
http://www.gnu.org/software/mcsim
200
http://www.goat.no
200
http://www.gobics.de/fabian/treephyler.php
200
http://www.gobics.de/thomas
200
http://www.gpcr-okb.org
200
http://www.grad.ttuhsc.edu/archive/
java.net.UnknownHostException : www.grad.ttuhsc.edu
http://www.graphviz.org
200
http://www.gredos.cnb.uam.es/EUCLID
java.io.FileNotFoundException : http://www.gredos.cnb.uam.es/EUCLID
http://www.gridqtl.org.uk
200
http://www.gsf.de/biodv/consinspector.html
java.io.FileNotFoundException : http://www.helmholtz-muenchen.de/en/ieg/group-ag-biodv/consinspector.html
http://www.gsf.de/biodv/dialign.html
java.io.FileNotFoundException : http://www.helmholtz-muenchen.de/en/ieg/group-ag-biodv/dialign.html
http://www.gsf.de/biodv/genomeinspector.html
java.io.FileNotFoundException : http://www.helmholtz-muenchen.de/en/ieg/group-ag-biodv/genomeinspector.html
http://www.gsf.de/biodv/matinspector.html
java.io.FileNotFoundException : http://www.helmholtz-muenchen.de/en/ieg/group-ag-biodv/matinspector.html
http://www.gsf.de/cgi-bin/fastm
java.io.FileNotFoundException : http://www.helmholtz-muenchen.de/cgi-bin/fastm
http://www.gti.ed.ac.uk/pdqwizard/
200
http://www.gusdb.org
200
http://www.gusdb.org/fge.html
200
http://www.gwer.ch/proteinstructure/mdb
java.io.FileNotFoundException : http://www.gwer.ch/proteinstructure/mdb
http://www.h-invitational.jp/g-compass/
200
http://www.healthsciences.columbia.edu/dept/greenwaldlab/links.html
200
http://www.hg.med.umich.edu/labs/douglaslab/software.html
200
http://www.hgc.ims.u-tokyo.ac
200
http://www.hgc.ims.u-tokyo.ac.jp/Melina/
java.io.FileNotFoundException : http://www.hgc.jp/Melina/
http://www.hgc.inc.u-tokyo.ac.jp/service/tooldoc
java.net.UnknownHostException : www.hgc.inc.u-tokyo.ac.jp
http://www.hgmp.mrc.ac.uk/
java.net.UnknownHostException : www.hgmp.mrc.ac.uk
http://www.hgsc.bcm.tms.edu/HTDB/
java.net.UnknownHostException : www.hgsc.bcm.tms.edu
http://www.hh.se/staff/bioinf/
200
http://www.hihg.org
200
http://www.hip.harvard.edu
200
http://www.hiv.lanl.gov/HYPERMUT/hypermut.html
java.io.FileNotFoundException : http://www.hiv.lanl.gov/content/hiv-db/HYPERMUT/hypermut.html
http://www.hnbioinfo.de
java.io.IOException : Server returned HTTP response code: 403 for URL: http://www.hnbioinfo.de
http://www.hpid.org
java.net.UnknownHostException : www.hpid.org
http://www.hri.co.jp/atgpr
java.net.UnknownHostException : www.hri.co.jp
http://www.hri.co.jp/atgpr/ATGpr_sim.html
java.net.UnknownHostException : www.hri.co.jp
http://www.hsph.harvard.edu/
java.net.SocketTimeoutException : connect timed out
http://www.hugenavigator.net/HuGENavigator/startPagePedia.do
200
http://www.hugenavigator.net/HuGENavigator/startPagePhenoPedia.do
200
http://www.hy8.com/
200
http://www.hy8.com/bioinformatics.htm
200
http://www.hybrow.org
200
http://www.hyphy.org
200
http://www.i-cancer.fen.bilkent.edu.tr/p2sl
200
http://www.iac.cnr.it/
200
http://www.iba.muni.cz/
200
http://www.ibb.waw.pl/stocks
java.io.FileNotFoundException : http://www.ibb.waw.pl/stocks
http://www.ibc.wustl.edu/pub/zuker/zuker
java.net.UnknownHostException : www.ibc.wustl.edu
http://www.ibcp.fr/mpsa/
java.io.FileNotFoundException : http://www.ibcp.fr/mpsa/
http://www.ibcp.fr/predict.html
java.io.FileNotFoundException : http://www.ibcp.fr/predict.html
http://www.ibe.med.uni-muenchen.de/organisation/mitarbeiter/020_professuren/boulesteix/overoptimism/
200
http://www.ibi.vu.nl/programs/
200
http://www.ibi.vu.nl/programs/multirelief
200
http://www.ibi.vu.nl/programs/pralinewww
200
http://www.ibt.lt/bioinformatics/coma/
200
http://www.ibt.lt/bioinformatics/voroprot/
200
http://www.ibt.unam.mx/biocomputo/gecont.html
200
http://www.icgeb.org/pride
200
http://www.icgeb.trieste.it/dna/
200
http://www.icgeb.trieste.it/domain
java.io.FileNotFoundException : http://www.icgeb.trieste.it/domain
http://www.icgeb.trieste.it/introns
200
http://www.icgeb.trieste.it/p450/
200
http://www.ichip.de/software/pathwave.html
200
http://www.icis.cgiar.org
200
http://www.icrea.es/pag.asp?id=Miguel.Perez
java.io.FileNotFoundException : http://www.icrea.cat/pag.asp?id=Miguel.Perez
http://www.ics.uci.edu/
200
http://www.icsn.cnrs-gif.fr/download/nmr
200
http://www.idav.ucdavis.edu/
200
http://www.idi.ntnu.no/
200
http://www.ifom-firc.it/RESEARCH/Appl_Bioinfo/tools.html
200
http://www.ifomis.org/bfo/fol
200
http://www.ifr.ac.uk/dass/gui/
200
http://www.igb.illinois.edu/labs/price/downloads/
200
http://www.igb.uci.edu
200
http://www.igb.uci.edu/index.php?page=tools
200
http://www.igb.uci.edu/servers/cgss.html
200
http://www.igb.uci.edu/servers/icbs/
200
http://www.igb.uci.edu/servers/psss.html
200
http://www.igb.uci.edu/servers/servers.html
java.io.FileNotFoundException : http://www.igb.uci.edu/servers/servers.html
http://www.igib.res.in/sarsanalysis.html
java.io.FileNotFoundException : http://www.igib.res.in/sarsanalysis.html
http://www.igmors.u-psud.fr/rousset/bioinformatics/
java.io.FileNotFoundException : http://www.igmors.u-psud.fr/rousset/bioinformatics/
http://www.ihes.fr/
200
http://www.ihes.fr/carbone/data8/
java.io.FileNotFoundException : http://www.ihes.fr/carbone/data8/
http://www.ii.uib.no/
200
http://www.iim.csic.es/
200
http://www.iim.nctu.edu.tw/
200
http://www.iipl.fudan.edu.cn/demo/accpkg.html
200
http://www.ikbar.org/
java.net.UnknownHostException : www.ikbar.org
http://www.iki.fi/
200
http://www.ikmb.uni-kiel.de/CNVineta/
200
http://www.illumina.com
200
http://www.imagenix.com/
200
http://www.imb-jena.de/IMAGE.html
200
http://www.imb-jena.de/tsb/pad
java.io.FileNotFoundException : http://www.imb-jena.de/tsb/pad
http://www.imb.ac.ru/compbio/basio
200
http://www.imbi.uni-freiburg.de/parallel
200
http://www.ime.usp.br/
200
http://www.immunogrid.eu/atherogenesis/
200
http://www.immunomics.eu/SA/
java.io.FileNotFoundException : http://www.immunomics.eu/SA/
http://www.imperial.ac.uk/medicine/people/l.coin
200
http://www.imtech.res.in/raghava/betaturns/
200
http://www.imtech.res.in/raghava/haptendb/
200
http://www.imtech.res.in/raghava/propred/
200
http://www.imtech.res.in/raghava/propred1/
200
http://www.imtech.res.in/raghava/pslpred/
200
http://www.imtech.res.in/raghava/srf
200
http://www.in-silico.com
200
http://www.inab.org
200
http://www.inab.org/MOWServ
200
http://www.inapg.inra.fr/ens_rech/mathinfo/recherche/mathematique
java.net.UnknownHostException : www.inapg.inra.fr
http://www.inapg.inra.fr/ens_rech/mathinfo/recherche/mathematique/outil.html
java.net.UnknownHostException : www.inapg.inra.fr
http://www.inf.fu-berlin.de/inst/ag-bio
200
http://www.inference.phy.cam.ac.uk/os252/projects/quadruplexes
200
http://www.info.uqam.ca/
200
http://www.infobiogen
java.net.UnknownHostException : www.infobiogen
http://www.infobiogen.fr/services/CoPE
java.io.FileNotFoundException : http://www.infobiogen.fr/services/CoPE
http://www.infobiogen.fr/services/Hugemap/IOR
java.io.FileNotFoundException : http://www.infobiogen.fr/services/Hugemap/IOR
http://www.infobiogen.fr/services/zomit
java.io.FileNotFoundException : http://www.infobiogen.fr/services/zomit
http://www.infobiogen.fr/srs5/
java.io.FileNotFoundException : http://www.infobiogen.fr/srs5/
http://www.infobiosud.cnrs.fr/bioserver
200
http://www.infobiotics.net/topogsa
200
http://www.informatics.indiana.edu/predrag/
200
http://www.informatics.jax.org/report.html
java.io.FileNotFoundException : http://www.informatics.jax.org/report.html
http://www.informatik.uni-ulm.de/ni/mitarbeiter/HKestler/boolnet/
200
http://www.informatik.uni-ulm.de/ni/mitarbeiter/HKestler/vennm
200
http://www.informatik.uni-ulm.de/ni/staff/HKestler/ideo/
200
http://www.infornomics.utoronto.ca/downloads/EMRF
200
http://www.ingenovis.com/tripletrepeats
java.io.IOException : Server returned HTTP response code: 403 for URL: http://www.ingenovis.com/tripletrepeats
http://www.ini.uzh.ch/
200
http://www.inra.fr/bia/J/imaste/Projets/PARIS/index.html
java.io.FileNotFoundException : http://w3.jouy.inra.fr/unites/miaj//imaste/Projets/PARIS/index.html
http://www.inra.fr/bia/T/CarthaGene
200
http://www.inra.fr/mia/T/CarthaGene/
200
http://www.inria.fr
200
http://www.inrialpes.fr/helix/people/viari/cccpart
200
http://www.insun.hit.edu.cn/
200
http://www.intergalact.com
java.net.SocketException : Connection reset
http://www.introni.it/splicing.html
200
http://www.iop.kcl.ac.uk/IoP/Departments/PsychMed/GEpiBSt/software.shtml
200
http://www.ipbs.fr/ESPript
java.io.FileNotFoundException : http://www.ipbs.fr/ESPript
http://www.iris.irri.org
200
http://www.irisa.fr/SAMBA/
200
http://www.irisa.fr/symbiose/DomainOrganizer/
java.io.FileNotFoundException : http://www.irisa.fr/symbiose/DomainOrganizer/
http://www.irisa.fr/symbiose/projects/gassst/
200
http://www.irnase.csic.es/users/jmgrau/index.html
java.io.FileNotFoundException : http://www.irnase.csic.es/users/jmgrau/index.html
http://www.iro.umontreal.ca/
200
http://www.isa-tools.org
200
http://www.isds.duke.edu/
200
http://www.isical.ac.in/
200
http://www.ism.ac.jp/
200
http://www.isrec.isb-sib.ch/java/dotlet/
java.io.FileNotFoundException : http://ccg.vital-it.ch/java/dotlet/
http://www.issb.genopole.fr
200
http://www.isye.gatech.edu/
200
http://www.it.iitb.ac.in/
200
http://www.itb.cnr.it/gosh/
200
http://www.itba.mi
java.net.UnknownHostException : www.itba.mi
http://www.itba.mi.cnr.it/webgene
200
http://www.its.caltech.edu/
200
http://www.ittc.ku.edu/
200
http://www.iubio.bio.indiana.edu/soft/molbio/qtl/flipper/
java.net.UnknownHostException : www.iubio.bio.indiana.edu
http://www.ivia.es/centrodegenomica/bioinformatics.htm
java.io.FileNotFoundException : http://www.ivia.es/centrodegenomica/bioinformatics.htm
http://www.izbi.uni-leipzig.de/services/NetwPartLearn.html
java.io.FileNotFoundException : http://www.izbi.uni-leipzig.de/services/NetwPartLearn.html
http://www.jainlab.org/downloads.html
200
http://www.jaist.ac.jp/
200
http://www.jalview.org
200
http://www.jarvislab.net/Bioinformatics/BNAdvances/
200
http://www.java.sun.com
200
http://www.jax.org/phenome
200
http://www.jax.org/staff/churchill/labsite/pubs/yong
java.io.FileNotFoundException : http://churchill.jax.org/labsite/pubs/yong
http://www.jax.org/staff/churchill/labsite/software
java.io.FileNotFoundException : http://churchill.jax.org/labsite/software
http://www.jcvi.org/metarep
200
http://www.jcvi.org/mpidb/
200
http://www.jcvi.org/mpidb/interaction.php?dbsource=MPI-LIT
200
http://www.jdl.ac.cn/user/yfu/pfind/index.html
java.io.FileNotFoundException : http://www.jdl.ac.cn/user/yfu/pfind/index.html
http://www.jenner.ac.uk/JenPep
java.io.FileNotFoundException : http://www.jenner.ac.uk/JenPep
http://www.jenner.ac.uk/MHCPred
java.io.FileNotFoundException : http://www.jenner.ac.uk/MHCPred
http://www.jenti.org
200
http://www.jjj.bio.vu.nl/
200
http://www.jncasr.ac.in/cremofac/
200
http://www.julielab.de
200
http://www.jvirgel.de
200
http://www.kavrakilab.org/atommetanet
200
http://www.kennedykrieger.org/pevsnerlab/dragon.htm
java.io.FileNotFoundException : http://www.kennedykrieger.org/pevsnerlab/dragon.htm
http://www.kermit.ugent.be/taxongap
200
http://www.kingston.ac.uk/
200
http://www.knotplot.com/download
200
http://www.kofler.or.at/Bioinformatics
java.io.FileNotFoundException : http://www.kofler.or.at/Bioinformatics
http://www.ks.uiuc.edu/Research/vmd
200
http://www.ksu.edu/bioinformatics/supplementary.htm
java.io.FileNotFoundException : http://www.k-state.edu/bioinformatics/supplementary.htm
http://www.kumc.edu/biochemistry/resmap/
200
http://www.kyb.mpg.de/bs/people/hiroto/iboost/
java.io.FileNotFoundException : http://people.kyb.tuebingen.mpg.de/hiroto/iboost/
http://www.kyb.tuebingen.mpg.de/
200
http://www.kyb.tuebingen.mpg.de/bs/people/spider
200
http://www.kyb.tuebingen.mpg.de/bs/people/weston/semiprot
200
http://www.lam-mpi.org/mpi/implementations/
200
http://www.lbm.fmvz.usp.br/egene/
200
http://www.lcb.uu.se/
200
http://www.lcb.uu.se/lcbdw.php
200
http://www.ldc.upenn.edu
200
http://www.le.ac.uk/mrctox/microarray_lab/Microarray_Softwares/Microarray_Softwares.htm
java.io.FileNotFoundException : http://www.le.ac.uk/mrctox/microarray_lab/Microarray_Softwares/Microarray_Softwares.htm
http://www.led.uni-stuttgart.de
200
http://www.leonxie.com/targetAlign.php
200
http://www.lg.ndirect.co.uk/chroma
java.net.SocketTimeoutException : connect timed out
http://www.liacs.nl/home/kosters/pg/
200
http://www.lifl.fr/
200
http://www.lina.univ-nantes.fr/combi/DH/Home.html
200
http://www.lindo.com
200
http://www.lirmm.fr/
200
http://www.lirmm.fr/w3ifa/MAAS/
java.io.FileNotFoundException : http://www.lirmm.fr/w3ifa/MAAS/
http://www.lmcp.jussieu.fr/
200
http://www.lps.ens.fr/
200
http://www.lri.fr/
200
http://www.lsi.upc.es/
200
http://www.lsi.us.es/isanepo/toolsSaturno/
200
http://www.ltdk.helsinki.fi/sysbio/csb/downloads/CohortComparator/
200
http://www.lycaenid.org/augist/
200
http://www.maayanlab.net/FNV
200
http://www.mabs.at/ewing/msms/
200
http://www.madtools.org
200
http://www.maizegenetics.net/gdpc/index.html
200
http://www.maizemap.org
200
http://www.maizemap.org/bioinformatics.htm
200
http://www.mame.mu.oz.au/mechatronics/journalinfo/Hsu2003supp.pdf
java.io.FileNotFoundException : http://www.mech.eng.unimelb.edu.au/mechatronics/journalinfo/Hsu2003supp.pdf
http://www.mammibase.lncc.br
200
http://www.mammot.org.uk/
200
http://www.manchester.ac.uk/bioinformatics/ctree
200
http://www.mantisdb.org
200
http://www.marcottelab.org/MSpresso/
200
http://www.mas.ecp.fr/labo/equipe/gagneur/hierarchy/hierarchy.html
java.io.FileNotFoundException : http://www.mas.ecp.fr/labo/equipe/gagneur/hierarchy/hierarchy.html
http://www.massey.ac.nz/
200
http://www.massmatrix.net
200
http://www.massxpert.org
200
http://www.matfys.kvl.dk/
200
http://www.math.kyushu-u.ac.jp/
200
http://www.math.psu.edu/koslicki/entropy.nb
200
http://www.math.tau.ac.il/
200
http://www.math.umn.edu/
200
http://www.math.uni-bremen.de/
200
http://www.math.uni-frankfurt.de/
200
http://www.math.unipa.it/
200
http://www.math.uwaterloo.ca/
200
http://www.mathbio.nimr.mrc.ac.uk
java.net.UnknownHostException : www.mathbio.nimr.mrc.ac.uk
http://www.mathpreprints.com
java.net.SocketTimeoutException : Read timed out
http://www.maths.bris.ac.uk/
200
http://www.maths.lancs.ac.uk/
200
http://www.maths.ox.ac.uk/cmb/STOCHSIMGPU
301
http://www.maths.qut.edu.au/profiles/wood/permr.jsp
302
http://www.maths.strath.ac.uk/
200
http://www.maths.uq.edu.au/
200
http://www.maths.usyd.edu.au/u/johnr/testsym/
200
http://www.maths.usyd.edu.au/u/penghao/index.html
200
http://www.mathsource.com/cgi-bin/msitem?0209-30
java.io.FileNotFoundException : http://library.wolfram.com/redir/cgi-bin/msitem?0209-30
http://www.mathstat.dal.ca/
200
http://www.mathstat.gsu.edu/
200
http://www.may.ie/academic/biology/staff/mfmolecevolandbioinf.shtml
200
http://www.mcb.mcgill.ca/
200
http://www.mchips.org
200
http://www.mchips.org/supplements/moghaddasi_source.tgz
200
http://www.mcisb.org/resources/kipar/
200
http://www.mcisb.org/resources/putmedid.html
200
http://www.mcs.kent.edu/arvind/intellibio
java.net.ConnectException : Connection refused
http://www.mdc-berlin.de/unihi
200
http://www.me.chalmers.se/
java.io.IOException : Server returned HTTP response code: 403 for URL: http://www.me.chalmers.se/
http://www.meb.ki.se/
200
http://www.med.miami.edu/medicine/x2691.xml
200
http://www.med.uio.no/imb/stat/bmms/software/microsurv/
200
http://www.mediawiki.org/wiki/Extension
200
http://www.medicine.manchester.ac.uk/musculoskeletal/research/arc/genetics/bioinformatics/assimilator/
200
http://www.medicine.uiowa.edu/Labs/tan/CSIANNsoft.zip
java.io.FileNotFoundException : http://www.medicine.uiowa.edu/Labs/tan/CSIANNsoft.zip
http://www.medicine.uiowa.edu/Labs/Xing/MADSplus/
200
http://www.medinfopoli.polimi.it/MyWEST/
200
http://www.medit.fr
200
http://www.meduohio.edu/bioinfo/eid
java.net.SocketTimeoutException : connect timed out
http://www.meduohio.edu/bioinfo/software.html
java.net.SocketTimeoutException : connect timed out
http://www.meduohio.edu/medicine/fedorov
java.net.SocketTimeoutException : connect timed out
http://www.megasoftware.net
200
http://www.membraneproteins.org/TMCompare
java.net.UnknownHostException : www.membraneproteins.org
http://www.mensxmachina.org
200
http://www.mgs.bionet.nsc
java.net.UnknownHostException : www.mgs.bionet.nsc
http://www.micrel.deis.unibo.it/
200
http://www.microarray-quality.org
200
http://www.microarray.fr
200
http://www.microarray.fr:8080/miRonTop/index
200
http://www.minet.uni-jena.de/csb/prj/ot/tools
200
http://www.minituba.org
200
http://www.minomics.nl
200
http://www.mips.biochem.mpg.de
java.net.UnknownHostException : www.mips.biochem.mpg.de
http://www.mips.biochem.mpg.de/mips/yeast/
java.net.UnknownHostException : www.mips.biochem.mpg.de
http://www.mitochondria.org/protocols/FALCOR.html
200
http://www.mlst.net
200
http://www.mns.brain.riken.go.jp/
java.net.UnknownHostException : www.mns.brain.riken.go.jp
http://www.mobius.uiuc.edu
301
http://www.molbiol.saitama-u.ac.jp/
200
http://www.molevol.org/nexplorer
200
http://www.molgen.mpg.de/
200
http://www.molgenis.nl
200
http://www.molpopgen.org
200
http://www.montpellier.inra.fr/CBGP/diyabc
200
http://www.motifator.nl
200
http://www.mpi-inf.mpg.de/
200
http://www.mpi-magdeburg.mpg.de/people/kre/robust/
200
http://www.mpi-magdeburg.mpg.de/projects/fluxanalyzer
java.io.FileNotFoundException : http://www.mpi-magdeburg.mpg.de/projects/fluxanalyzer
http://www.mpi-magdeburg.mpg.de/projects/promot/
200
http://www.mpibpc.mpg.de/go-cluster/
200
http://www.mpimg-berlin-dahlem.mpg
java.net.UnknownHostException : www.mpimg-berlin-dahlem.mpg
http://www.mpimp-golm.mpg.de/fiehn/projekte/data-mining-e.html
java.io.FileNotFoundException : http://www.mpimp-golm.mpg.de/fiehn/projekte/data-mining-e.html
http://www.mpisb.mpg.de/
java.net.UnknownHostException : www.mpisb.mpg.de
http://www.mpiz-koeln.mpg.de/GABI-Kat/
200
http://www.mrc-1mb.cam.ac
java.net.UnknownHostException : www.mrc-1mb.cam.ac
http://www.mrc-bsu.cam.ac.uk/personal/thomas/phylo_comparison/comparison_page.html
java.io.FileNotFoundException : http://www.mrc-bsu.cam.ac.uk/personal/thomas/phylo_comparison/comparison_page.html
http://www.mrc-lmb.cam.ac.uk/genomes/
200
http://www.mrc-lmb.cam.ac.uk/genomes/dolop
200
http://www.mrc-lmb.cam.ac.uk/genomes/SAT
200
http://www.mrc-lmb.cam.ac.uk/genomes/spial/
200
http://www.mrl.ubc.ca/who/who_bios_scott_tebbutt.shtml
java.io.FileNotFoundException : http://www.mrl.ubc.ca/who/who_bios_scott_tebbutt.shtml
http://www.mshri.on.ca/mitacs/software/SOFTWARE.HTML
200
http://www.mskcc.org/mskcc/html/85130.cfm
200
http://www.mtt.fi/AlignmentQuality/
java.io.IOException : Server returned HTTP response code: 403 for URL: http://www.mtt.fi/AlignmentQuality/
http://www.mucosa.de/
200
http://www.multiloc.org/YLoc
200
http://www.myexperiment.org/workflows/1283.html
200
http://www.mygrid.org.uk
200
http://www.mysmu.edu/faculty/jingjiang/software/DALR.html
200
http://www.naaan.org/anvo/Software/Software.htm
200
http://www.naaan.org/nhanguyen/archive.htm
200
http://www.nactem.ac.uk/deca_details/start.cgi
200
http://www.nactem.ac.uk/software/acromine/
200
http://www.nactem.ac.uk/software/acromine_disambiguation/
200
http://www.nactem.ac.uk/software/facta/
200
http://www.nas.nasa.gov/Groups/SciTech/nano/msamanta/projects/percolation/index.php
200
http://www.naskitis.com
200
http://www.nature.com
200
http://www.nbpp.nl/warp2d.html
200
http://www.nbpp.nl/Warp2D_commandline.zip
200
http://www.ncbi.nlm.nih.gov
200
http://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/SimBoolNet
java.io.FileNotFoundException : http://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/SimBoolNet
http://www.ncbi.nlm.nih.gov/CBBresearch/qmbp/mn/enrich/
200
http://www.ncbi.nlm.nih.gov/CBBresearch/qmbp/mn/itm_probe
200
http://www.ncbi.nlm.nih.gov/CBBresearch/Spouge/html.ncbi/tap/
200
http://www.ncbi.nlm.nih.gov/Entrez/Genome/
java.io.FileNotFoundException : http://www.ncbi.nlm.nih.gov/Entrez/Genome/
http://www.ncbi.nlm.nih.gov/geo/
200
http://www.ncbi.nlm.nih.gov/IRET/Journals
200
http://www.ncbi.nlm.nih.gov/projects/SNP/
200
http://www.ncbi.nlm.nih.gov/Structure/cdtree/cdtree.shtml
200
http://www.ncbs.res.in/
200
http://www.ncbs.res.in/kinetikit/download.html
java.io.FileNotFoundException : http://www.ncbs.res.in/kinetikit/download.html
http://www.ncmls.eu/bioinfo/gimmemotifs/
200
http://www.ncrg.aston.ac.uk/Projects/milva
200
http://www.ncrna.org/idiographica/
200
http://www.ncrna.org/papers/McCaskillMEA/
200
http://www.ncrna.org/papers/Murlet/
200
http://www.ncrna.org/software/centroidalign/
200
http://www.ncrna.org/software/centroidfold/
200
http://www.ncrna.org/software/centroidfold/ismb2009/
200
http://www.ncrna.org/software/ractip/
200
http://www.ncrna.org/software/Rfold/
200
http://www.ncrna.org/software/scarna_lm/download
200
http://www.ncyc.co.uk/software/turnip.html
200
http://www.nematodes.org
200
http://www.nematodes.org/SimiTri/
java.io.FileNotFoundException : http://www.nematodes.org/SimiTri/
http://www.nersc.gov/
200
http://www.nervenet.org/genome_mixer/
200
http://www.net-machine.net/
java.io.IOException : Server returned HTTP response code: 403 for URL: http://www.net-machine.net/
http://www.netasa.org
200
http://www.netasa.org/rvp-net/
java.io.FileNotFoundException : http://www.netasa.org/rvp-net/
http://www.netlab.uky.edu/p/bioinfo/MapSplice/PER
java.io.FileNotFoundException : http://www.netlab.uky.edu/p/bioinfo/MapSplice/PER
http://www.ngic.re.kr/togo/index.html
java.net.UnknownHostException : www.ngic.re.kr
http://www.nibsc.ac.uk/dg3dseq/
java.io.FileNotFoundException : http://www.nibsc.ac.uk/dg3dseq/
http://www.niehs.nih.gov/research/resources/software/fdrMotif/
200
http://www.niehs.nih.gov/research/resources/software/tagster/
200
http://www.niss.org/irMF
200
http://www.nlm.nih.gov/research/umls/
200
http://www.nmr.chem.uu.nl/haddock
200
http://www.nmsu.edu/molbio/bioABACUShome.htm
java.io.FileNotFoundException : http://www.nmsu.edu/molbio/bioABACUShome.htm
http://www.noble.org/MedicCyc/
200
http://www.noble.org/PlantBio/MS/MSFACTs/MSFACTs.html
200
http://www.ntu.edu.sg/home/ChenXin/Gibbs
200
http://www.ntu.edu.sg/home/jyli/dwe.html
java.io.FileNotFoundException : http://www.ntu.edu.sg/home/jyli/dwe.html
http://www.ntu.edu.sg/home5/pg02776030/lsbound/
java.io.FileNotFoundException : http://www3.ntu.edu.sg/home5/pg02776030/lsbound/
http://www.ntu.edu.sg/home5/pg02776030/wrappers/
java.io.FileNotFoundException : http://www3.ntu.edu.sg/home5/pg02776030/wrappers/
http://www.nubio.nagoya-u.ac.jp/proc/index.html
200
http://www.nus-cme.org.sg/sgvp/software/hapfinder.html
200
http://www.nus-cme.org.sg/software/varld.html
200
http://www.nybg.org/files/scientists/dlittle/B.html
200
http://www.obigrid.org
200
http://www.oboedit.org
200
http://www.odeidentification.org
200
http://www.oeb.harvard.edu/hartl/lab/publications/GeneMerge.html
java.io.FileNotFoundException : http://www.oeb.harvard.edu/hartl/lab/publications/GeneMerge.html
http://www.ohsu.edu/cellbio/dev_biol_prog/affinitydensity/
200
http://www.ohsucancer.com/isrdev/tandtraq/
200
http://www.oisb.ca
200
http://www.oligofaktory.org/
200
http://www.omniarray.com/bioinformatics/GA
java.net.SocketException : Connection reset
http://www.oncoproteomics.nl/
200
http://www.openms.de
200
http://www.opensource.org/licenses/artistic-license.php
200
http://www.opensource.org/licenses/gpl-3.0.html
200
http://www.opensource.org/licenses/mit-license.php
200
http://www.openstructure.org
200
http://www.oreganno.org
200
http://www.oregonstate.edu/dept/comes/genetics/software.htm
200
http://www.oxagen.co.uk
200
http://www.oxfordjournals.org/our_journals/databa/
200
http://www.oxmol.com/biolib/webmap/
200
http://www.paintomics.org
200
http://www.pal-project.org
200
http://www.pangeasystems.com
java.net.UnknownHostException : www.pangeasystems.com
http://www.panix.com/
200
http://www.panzea.org
200
http://www.pasteur.fr/recherche/unites/Binfs/aria/
200
http://www.pasteur.fr/recherche/unites/Binfs/aria2
200
http://www.pasteur.fr/recherche/unites/Gim/genoscape/
200
http://www.pasteur.fr/recherche/unites/neubiomol/meltinghome.html
java.io.FileNotFoundException : http://www.pasteur.fr/recherche/unites/neubiomol/meltinghome.html
http://www.patcar.org/Databases/Tumor_Suppressor_Genes
200
http://www.patgendb.com
java.net.SocketTimeoutException : connect timed out
http://www.pathogenomics.ca/cerebral
200
http://www.pathogenomics.sfu.ca/islandpath
200
http://www.pathogenomics.sfu.ca/islandviewer
java.net.SocketTimeoutException : Read timed out
http://www.patronov.net/sciencevr/mnv/indexmake.html
java.io.FileNotFoundException : http://www.patronov.net/sciencevr/mnv/indexmake.html
http://www.patronov.net/sciencevr/mnv/indexview.html
java.io.FileNotFoundException : http://www.patronov.net/sciencevr/mnv/indexview.html
http://www.patronov.net/sciencevr/mnv/screenshots.html
java.io.FileNotFoundException : http://www.patronov.net/sciencevr/mnv/screenshots.html
http://www.paulmcnicholas.info
200
http://www.payaologue.org
200
http://www.pdb.bnl
java.net.UnknownHostException : www.pdb.bnl
http://www.pdbj.org/eF-site/
java.io.FileNotFoundException : http://www.pdbj.org/eF-site/
http://www.pdbj.org/SeSAW/
200
http://www.pdg.cnb.uam.es/GenoClustering.html
200
http://www.pdg.cnb.uam.es/UniPub/iHOP/
java.io.IOException : Server returned HTTP response code: 502 for URL: http://www.pdg.cnb.uam.es/UniPub/iHOP/
http://www.pedvizapi.org
200
http://www.pence.ca/
java.io.IOException : Server returned HTTP response code: 403 for URL: http://www.pence.ca/
http://www.people.fas.harvard.edu/
200
http://www.people.vcu.edu/
200
http://www.peptidecheck.org
200
http://www.permory.org
200
http://www.personal.psu.edu/nhs109/Clench
java.io.FileNotFoundException : http://www.personal.psu.edu/nhs109/Clench
http://www.personal.psu.edu/nhs109/Programs/
java.io.FileNotFoundException : http://www.personal.psu.edu/nhs109/Programs/
http://www.pesolelab.it/Tools/WebVar.html
java.io.FileNotFoundException : http://www.pesolelab.it/Tools/WebVar.html
http://www.pfizerdtc.com
200
http://www.pharmacogenetics.ca
200
http://www.pharmfac.net/EpiTOP
200
http://www.phenomicdb.de
200
http://www.phoenix.hydra.mki.co.jp/CabosDemo.html
java.net.UnknownHostException : www.phoenix.hydra.mki.co.jp
http://www.phosida.com
200
http://www.phosite.com
200
http://www.php.net
200
http://www.pht.uni-koeln.de
200
http://www.phylo.unm.edu/
java.net.UnknownHostException : www.phylo.unm.edu
http://www.phylodiversity.net/bmoore/software.html
200
http://www.phylowidget.org/
200
http://www.phys.psu.edu/
200
http://www.physiologie.uni-freiburg.de/download.html
200
http://www.pi.csiro.au/gena/
200
http://www.picb.ac.cn/ClinicalGenomicNTW/temp2.html
200
http://www.picb.ac.cn/patterns/Software/ct3d
200
http://www.picb.ac.cn/patterns/Supplements/ct3d
200
http://www.pitt.edu/
200
http://www.pkdb.ifsc.usp.br
200
http://www.planet-lisa.net
200
http://www.plantbio.uga.edu/
200
http://www.plantgdb.org/cgi-bin/AtGeneSeqer.cgi
java.io.FileNotFoundException : http://www.plantgdb.org/cgi-bin/AtGeneSeqer.cgi
http://www.plantgdb.org/cgi-bin/GeneSeqer.cgi
java.io.FileNotFoundException : http://www.plantgdb.org/cgi-bin/GeneSeqer.cgi
http://www.plantgdb.org/PlantGDB-cgi/GeneSeqer/AtGDBgs.cgi
200
http://www.plantgdb.org/PlantGDB-cgi/GeneSeqer/OsGDBgs.cgi
200
http://www.plantgdb.org/PlantGDB-cgi/GeneSeqer/PlantGDBgs.cgi
200
http://www.plantgenomics.iastate.edu/PathBinderH
java.io.FileNotFoundException : http://www.plantgenomics.iastate.edu/PathBinderH
http://www.PlasmoDB.org
200
http://www.pnl.gov/statistics/amia
200
http://www.pnl.gov/statistics/BEPro3
200
http://www.pnl.gov/statistics/ProMAT
200
http://www.pnl.gov/statistics/ProMAT/ELISA-BASE.stm
200
http://www.postgresql.org
200
http://www.PottersWheel.de/
200
http://www.powermarker.net
200
http://www.predictive-toxicology.org/ptc/
200
http://www.predictprotein.org/submit_ucon.html
java.io.FileNotFoundException : http://www.predictprotein.org/submit_ucon.html
http://www.primate.or.kr/HESAS
java.io.IOException : Server returned HTTP response code: 403 for URL: http://www.primate.or.kr/HESAS/
http://www.prodoric.de/vfp
200
http://www.progenetix.net
200
http://www.projects.bioinformatics.northwestern.edu/fundo
java.net.UnknownHostException : www.projects.bioinformatics.northwestern.edu
http://www.protarget.cs.huji.ac.il
java.net.UnknownHostException : www.protarget.cs.huji.ac.il
http://www.protein-ms.de
200
http://www.protein-nmr.org/
200
http://www.proteios.org
200
http://www.proteomatic.org
200
http://www.proteome.ca/opensource.html
java.io.FileNotFoundException : http://www.proteome.ca/opensource.html
http://www.proteomecommons.org
302
http://www.proteomecommons.org/current/511/
200
http://www.proteomecommons.org/current/531/
200
http://www.proteomegrid.org/rain/
200
http://www.proteometrics.com/BIOML/
java.io.FileNotFoundException : http://www.proteometrics.com/BIOML/
http://www.proteomicsresource.org/
200
http://www.proto.cs.huji.ac.il/mirror
200
http://www.protonet.cs.huji.ac.il/dots
200
http://www.protonet.cs.huji.ac.il/sprint
200
http://www.protonet.cs.huji.ac.il/TM/
java.io.FileNotFoundException : http://www.protonet.cs.huji.ac.il/TM/
http://www.protsuggest.org
java.net.UnknownHostException : www.protsuggest.org
http://www.psb.rug.ac.be/gps
200
http://www.psb.ugent.be/cbd/
java.io.IOException : Server returned HTTP response code: 403 for URL: http://www.psb.ugent.be/cbd/
http://www.psb.ugent.be/cbd/papers/gentxwarper/
200
http://www.psb.ugent.be/cbd/publications.php
java.io.FileNotFoundException : http://www.psb.ugent.be/cbd/publications.php
http://www.psb.ugent.be/esb/PiNGO
200
http://www.psi.toronto.edu/GenASAP
200
http://www.psipred.net
java.net.ConnectException : Connection refused
http://www.psort.org/psortb
200
http://www.ptools.ua.ac.be/CRPhos/
200
http://www.ptools.ua.ac.be/pProRep
200
http://www.public.asu.edu/
200
http://www.purl.org/biotop/
200
http://www.pyrosetta.org
200
http://www.pysolo.net
200
http://www.python.org
200
http://www.qanswers.net/GeneTUKit/
200
http://www.QueryChem.com
200
http://www.r-project.org
200
http://www.r.project.org/
200
http://www.ra.cs.uni-tuebingen.de/software/SBML2LaTeX
200
http://www.randomjungle.org
200
http://www.rbvi.ucsf.edu/Research/cytoscape/threshold_scripts.zip
200
http://www.rcsb.org/pdb/workbench/workbench.do
200
http://www.reading.ac.uk/
200
http://www.reading.ac.uk/bioinf/DISOclust/
200
http://www.reading.ac.uk/bioinf/downloads/
200
http://www.rejector.org
200
http://www.renyi.hu/
200
http://www.research.ibm.com/bioinformatics
200
http://www.research.ibm.com/FunGen
200
http://www.research.ibm.com/splash
200
http://www.research.microsoft.com/
200
http://www.rfcgr.mrc.ac.uk/Software/PELICAN/
java.net.UnknownHostException : www.rfcgr.mrc.ac.uk
http://www.ri.bbsrc.ac.uk/
java.net.UnknownHostException : www.ri.bbsrc.ac.uk
http://www.ri.bbsrc.ac.uk/ark_corba/
java.net.UnknownHostException : www.ri.bbsrc.ac.uk
http://www.rii.com/publications/2003/HE_SDS.htm
java.net.UnknownHostException : www.rii.com
http://www.riken.jp/zhangiru/software/durandal_released.tgz
200
http://www.rinst.org/ICS/ICS_Programs.tar.gz
200
http://www.rnasoft.ca/CG/
200
http://www.rni.helsinki.fi/
200
http://www.rni.helsinki.fi/jic/softa.html
java.io.FileNotFoundException : http://www.rni.helsinki.fi/jic/softa.html
http://www.rosettacommons.org
200
http://www.rostlab.org/services/consensus/
200
http://www.rostlab.org/services/pinat
200
http://www.rostlab.org/services/profbval
200
http://www.rostlab.org/services/SNAP
200
http://www.rpgroup.caltech.edu/publications/supplements/alphabets
200
http://www.rqtl.org/
200
http://www.rsc.anu.edu.au/
java.net.UnknownHostException : www.rsc.anu.edu.au
http://www.rtc.riken.go.jp/3DinSight.h
java.net.UnknownHostException : www.rtc.riken.go.jp
http://www.rtc.riken.go.jp/jouhou/ORI-GENE
java.net.UnknownHostException : www.rtc.riken.go.jp
http://www.rtc.riken.go.jp/jouhou/pronit/pronit.html
java.net.UnknownHostException : www.rtc.riken.go.jp
http://www.rtphc.csic.es/download.html
200
http://www.rubic.rdg.ac.uk/
200
http://www.rubic.reading.ac.uk/lvb/
200
http://www.ruffus.org.uk
200
http://www.russell.embl.de/interprets
java.io.FileNotFoundException : http://www.russelllab.org/interprets
http://www.russet.org.uk
200
http://www.sabia.lncc.br
200
http://www.sailing.cs.cmu.edu/
200
http://www.sailing.cs.cmu.edu/discover.html
200
http://www.sailing.cs.cmu.edu/gflasso.html
200
http://www.sailing.cs.cmu.edu/keller
200
http://www.salilab.org/LS-SNP
200
http://www.sander.ebi.ac
java.net.UnknownHostException : www.sander.ebi.ac
http://www.sander.ebi.ac.uk/frame/
java.net.UnknownHostException : www.sander.ebi.ac.uk
http://www.sander.ebi.ac.uk/mview/
java.net.UnknownHostException : www.sander.ebi.ac.uk
http://www.sanger.ac
java.net.UnknownHostException : www.sanger.ac
http://www.sanger.ac.uk/cgi-bin/teams/team113/imapper.cgi
200
http://www.sanger.ac.uk/genetics/CGP/Software/AutoCSA
200
http://www.sanger.ac.uk/proserver/
200
http://www.sanger.ac.uk/resources/software/evoker/
200
http://www.sanger.ac.uk/resources/software/genevar
200
http://www.sanger.ac.uk/Software/ACT/
200
http://www.sanger.ac.uk/Software/analysis/alien_hunter
200
http://www.sanger.ac.uk/Software/analysis/doublescan/
200
http://www.sanger.ac.uk/Software/analysis/genomix
200
http://www.sanger.ac.uk/Software/analysis/logomat-p
200
http://www.sanger.ac.uk/Software/Artemis/
200
http://www.sanger.ac.uk/Software/Artemis/circular/
200
http://www.sanger.ac.uk/Software/Pfam/iPfam/
200
http://www.sanger.ac.uk/Software/PSILC
200
http://www.sanger.ac.uk/Software/Wise2
200
http://www.sanger.ac.uk/Users/agb/SCOOP/
200
http://www.sanger.ac.uk/Users/cari/Z.shtml
200
http://www.sanger.ac.uk/Users/lp1/MaxBench/
200
http://www.sanger.ac.uk/Users/sgj/alignments/map.html
200
http://www.sanger.ac.uk/Users/sgj/ralee/
200
http://www.santafe.edu/
200
http://www.sas.com/
200
http://www.sbc.su.se/
200
http://www.sbg.bio.ic.ac.uk/
200
http://www.sbg.bio.ic.ac.uk/3dgarden
200
http://www.sbg.bio.ic.ac.uk/confunc
200
http://www.sbml.org
200
http://www.sbml.org/software/libsbml/
200
http://www.sbml2tikz.org
200
http://www.sbmm.uma.es
200
http://www.sbos.eu
200
http://www.sbtoolbox.org
200
http://www.sbtoolbox.org/SBaddon
200
http://www.sbtoolbox2.org
200
http://www.scandb.org
200
http://www.scarna.org/
java.net.SocketTimeoutException : connect timed out
http://www.scbit.org/mpss/
200
http://www.scfarm.unibo.it
java.net.SocketTimeoutException : connect timed out
http://www.sci.brooklyn.cuny.edu/
200
http://www.sci.muni.cz/LMFR/vpcr.html
200
http://www.science.uva.nl/research/scs/CellMath/GMP
200
http://www.scriptree.org
java.net.SocketTimeoutException : connect timed out
http://www.scsb.utmb.edu/comp_biol.html/DNA_repair/publication.html
java.io.FileNotFoundException : http://www.scsb.utmb.edu/comp_biol.html/DNA_repair/publication.html
http://www.scsb.utmb.edu/masia/ma
java.io.FileNotFoundException : http://www.scsb.utmb.edu/masia/ma
http://www.scsb.utmb.edu/masia/masia.html
java.io.FileNotFoundException : http://www.scsb.utmb.edu/masia/masia.html
http://www.sdsc.edu/CompSci/Biomed/
java.io.FileNotFoundException : http://www.sdsc.edu/CompSci/Biomed/
http://www.sdsc.edu/pb/software.htm
java.io.FileNotFoundException : http://www.sdsc.edu/pb/software.htm
http://www.seas.ucla.edu/
200
http://www.seas.upenn.edu/
200
http://www.sebida.de
200
http://www.semantic-systems-biology.org/metarel
200
http://www.semanticsbml.org
200
http://www.semedico.org
200
http://www.seqan.de/projects/consensus.html
java.io.FileNotFoundException : http://www.seqan.de/projects/consensus.html
http://www.seqan.de/projects/MicroRazerS.html
200
http://www.seqan.de/projects/msa.html
java.io.FileNotFoundException : http://www.seqan.de/projects/msa.html
http://www.seqexpress.com
200
http://www.sf.net/projects/sbml
200
http://www.sickkids.ca/Robinsonlab/
java.io.FileNotFoundException : http://www.sickkids.ca/Robinsonlab/
http://www.sicuma.uma.es/multicore
200
http://www.Sienabiogzefix.com/publication
java.net.UnknownHostException : www.Sienabiogzefix.com
http://www.simtec.mb.uni-siegen.de/
java.net.UnknownHostException : www.simtec.mb.uni-siegen.de
http://www.simtk.org/home/c2a
302
http://www.simtk.org/home/ifba/
302
http://www.slv.se/templatesSLV/SLV_Page____9343.asp
java.io.FileNotFoundException : http://www.slv.se/templatesSLV/SLV_Page____9343.asp
http://www.snp-nexus.org
200
http://www.snpator.com/public/downloads/aRamirez/FABSIM/
200
http://www.snpator.org
200
http://www.snpchart.ca
java.net.UnknownHostException : www.snpchart.ca
http://www.snubi.org/software/ChromoViz/
200
http://www.soe.ucsc.edu/
200
http://www.soe.ucsc.edu/compbio/SAM_T08/T08-query.html
200
http://www.soe.ucsc.edu/research/compbio/gen_sequence
200
http://www.soe.ucsc.edu/research/compbio/sam.html
200
http://www.soi.city.ac.uk/
java.net.SocketTimeoutException : Read timed out
http://www.som.soton.ac.uk/research/geneticsdiv/epidemiology/LDMAP
200
http://www.somnathdatta.org/Supp/RankCluster/supp.htm
200
http://www.soph.uab.edu/Statgenetics/People/KZhang/HAPLO-IHP/index.html
200
http://www.soph.uab.edu/Statgenetics/People/XCui/r-codes/
200
http://www.sourceforge.net/projects/CTX-BLAST
java.io.FileNotFoundException : http://sourceforge.net/projects/CTX-BLAST
http://www.sourceforge.net/projects/mdr
200
http://www.soybase.org/publication_data/Nelson/ESTminer/ESTminer.html
200
http://www.spatial.maine.edu/
java.io.IOException : Server returned HTTP response code: 500 for URL: http://www.spatial.maine.edu/
http://www.sph.emory.edu/apLCMS
200
http://www.sph.umich.edu/
200
http://www.sph.umich.edu/csg/abecasis/metal/
200
http://www.sph.umich.edu/csg/liang/genome/
200
http://www.sph.umich.edu/csg/qin/CRC/
200
http://www.sph.umich.edu/csg/qin/FESTA/
200
http://www.sph.umich.edu/csg/szoellner/
200
http://www.sph.uth.tmc.edu:8052/hgc/Downloads.asp
java.net.SocketTimeoutException : connect timed out
http://www.splatche.com
200
http://www.splitstree.org
200
http://www.sta.cuhk.edu.hk/xysong/geneselection/
200
http://www.staff.uni-marburg.de/
200
http://www.stanford.edu/
200
http://www.stanford.edu/group/hadlylab/ssc.html
200
http://www.stat.berkeley.edu/
200
http://www.stat.lsa.umich.edu/
200
http://www.stat.ncku.edu.tw/tjwu
java.io.FileNotFoundException : http://www.stat.ncku.edu.tw/tjwu
http://www.stat.nus.edu.sg/
200
http://www.stat.ohio-state.edu/
200
http://www.stat.osu.edu/
200
http://www.stat.psu.edu/
200
http://www.stat.purdue.edu/
200
http://www.stat.sinica.edu.tw/
200
http://www.stat.ubc.ca/
200
http://www.stat.uchicago.edu/
200
http://www.stat.ucla.edu/
200
http://www.stat.ufl.edu/
200
http://www.stat.uga.edu/
200
http://www.stat.uni-muenchen.de/
200
http://www.stat.washington.edu/fraley/mclust
200
http://www.stat.wisc.edu/
200
http://www.stateslab.org/data/celllineOntology/cellline.zip
java.io.FileNotFoundException : http://www.stateslab.org/data/celllineOntology/cellline.zip
http://www.statgen.ucr.edu
200
http://www.statistik.tu-dortmund.de/
200
http://www.statistik.tu-dortmund.de/bio2010.html
200
http://www.statistik.tu-dortmund.de/genetik-publikationen-alignment.html
200
http://www.stats.gla.ac.uk/
200
http://www.stats.ox.ac.uk/
200
http://www.stats.ox.ac.uk/mathgen/software.html
200
http://www.stats.ox.ac.uk/proteins/resources
200
http://www.stats.ox.ac.uk/research/bioinfo/resources
200
http://www.stefanolandi.eu/
200
http://www.stjuderesearch.org/depts/biostats
200
http://www.stjuderesearch.org/depts/biostats/refnorm
java.io.FileNotFoundException : http://www.stjuderesearch.org/depts/biostats/refnorm
http://www.stjuderesearch.org/statistics
200
http://www.stjuderesearch.org/statistics/splosh.html
java.io.FileNotFoundException : http://www.stjuderesearch.org/site/lab/statistics/splosh.html
http://www.studiofmp.com/plpmdb/index.htm
200
http://www.supertriplets.univ-montp2.fr/
200
http://www.sykacek.net/research.html
200
http://www.sys-bio.org
200
http://www.sys-bio.org/layout
200
http://www.sys-bio.org/sbwWiki
200
http://www.sys.uea.ac.uk/
java.net.UnknownHostException : www.sys.uea.ac.uk
http://www.sys.uea.ac.uk/dyndom
java.net.UnknownHostException : www.sys.uea.ac.uk
http://www.sysbio.ac.cn/datatools.asp
200
http://www.sysbio.org/dataresources/brm.stm
200
http://www.sysbio.org/sysbio/networkbio/svm_hustle
200
http://www.sysdiag.cnrs.fr/BioNetCAD
200
http://www.sysdiag.cnrs.fr/publications/supplementary-materials/BioPsi_Manager/
200
http://www.systemsbiology.co.kr/GEAR/
200
http://www.systemsbiology.co.kr/PathCluster/
200
http://www.tbi.univie.ac.at/
200
http://www.tbi.univie.ac.at/RNA/
200
http://www.tbi.univie.ac.at/RNA/PMcomp/
200
http://www.tbi.univie.ac.at/software/cmcompare/
200
http://www.tcm.phy.cam.ac.uk/
200
http://www.tcoffee.org
200
http://www.tcoffee.org/homepage.html
200
http://www.tdw-prime.webs.com
200
http://www.techfak.uni-bielefeld
java.net.UnknownHostException : www.techfak.uni-bielefeld
http://www.techfak.uni-bielefeld.de/ags/ani/projects/HHSOMSeqData
200
http://www.tgen.org/neurogenomics/data
200
http://www.theseus3d.org
200
http://www.thesgc.org/resources/histone_tails/
200
http://www.tigr.org/
200
http://www.tigr.org/Genome_Properties
200
http://www.tigr.org/softlab
200
http://www.tigr.org/software/pirate
200
http://www.tigr.org/software/pirate/twain/twain.html
200
http://www.tigr.org/tigr-scripts/CMR2/genome_properties_references.spl
200
http://www.tik.ee.ethz.ch/sop/bicat
200
http://www.timetree.net
200
http://www.tm4.org
200
http://www.tmd.ac.jp/mri/mri-end/bio-object/download/
200
http://www.topali.org
200
http://www.tops.leeds.ac.uk
200
http://www.tp.umu.se/forskning/networks/meta/
200
http://www.tree-puzzle.de
200
http://www.tu-plovdiv.bg/Container/bi/DataIntegration/
200
http://www.tuat.ac.jp/mitaku/sosui/
java.io.FileNotFoundException : http://www.tuat.ac.jp/mitaku/sosui/
http://www.tulane.edu/
200
http://www.u-vision-biotech.com
200
http://www.uab.edu/proteinmenu
java.io.FileNotFoundException : http://www.uab.edu/proteinmenu
http://www.ub.edu/dnasp
200
http://www.ub.es/dnasp
200
http://www.ucalgary.ca/
200
http://www.ucmb.ulb.ac.be/SCMBB/Tools.htmland
java.io.FileNotFoundException : http://www.ucmb.ulb.ac.be/SCMBB/Tools.htmland
http://www.uea.ac.uk/cmp/research/cmpbio/PADRE
200
http://www.uhnresearch.ca/labs/tillier/ProDesign/ProDesign.html
200
http://www.uia.ac.be/u/
java.net.UnknownHostException : www.uia.ac.be
http://www.uio.no/
200
http://www.uk.embnet.org/Software/EMBOSS/
java.net.UnknownHostException : www.uk.embnet.org
http://www.ukrv
java.net.UnknownHostException : www.ukrv
http://www.ulb.ac.be/di/map/bhaibeka/software/survcomp/
200
http://www.umich.edu/
200
http://www.umit.at/page.cfm?vpath=departments/technik/iebe/tools/bi
200
http://www.uml.edu/Dept/Chem/UMLBIC/Apps/MEL
java.io.FileNotFoundException : http://www.uml.edu/Dept/Chem/UMLBIC/Apps/MEL
http://www.unc.edu/
200
http://www.uni-muenster.de/Biologie.NeuroVer/Tumorbiologie/DNA-Crypt/index.html
200
http://www.uni-muenster.de/Evolution/ebb/Services/AIDAN
java.io.FileNotFoundException : http://www.uni-muenster.de/Evolution/ebb/Services/AIDAN
http://www.uni-ulm.de/in/theo/research/genesis.html
200
http://www.uni-wuerzburg.de/nephrologie/molecular_genetics/molecular_genetics.htm
200
http://www.unicarb-db.org
200
http://www.unich.it/proteomica/bioinf/
200
http://www.unijena.de/SplamiR.html
java.net.UnknownHostException : www.unijena.de
http://www.unil.ch/cbg/ExpressionView
200
http://www.unil.ch/cbg/ISA
200
http://www.unil.ch/cig/page7858.html
200
http://www.uniprot.org
200
http://www.uniprot.org/mappingandproteininformation-resource.org/pirwww/search/idmapping.shtml
java.io.FileNotFoundException : http://www.uniprot.org/mappingandproteininformation-resource.org/pirwww/search/idmapping.shtml
http://www.univ-montp2.fr/
200
http://www.univ-provence.fr/gsite/Local/egee/dir/meglecz/QDD.html
200
http://www.unix.mcs.anl.gov/mpi/mpich
java.net.UnknownHostException : www.unix.mcs.anl.gov
http://www.unm.edu/
200
http://www.uow.edu.au/
200
http://www.upf.es/cexs/recerca/bioevo/softanddata.htm
java.io.FileNotFoundException : http://www.upf.edu/cexs/recerca/bioevo/softanddata.htm
http://www.uq.edu.au/
200
http://www.urmc.rochester.edu/biostat/people/faculty/hu.cfm
200
http://www.urr.cat/AStream/AStream.html
200
http://www.USherbrooke.ca/vers/MtbRegList
200
http://www.ust.hk/gaba
200
http://www.utdallas.edu/
200
http://www.utoronto.ca/zhanglab/MonoDi/
java.io.FileNotFoundException : http://www.utoronto.ca/zhanglab/MonoDi/
http://www.utoronto.ca/zhanglab/papers/bioinfo_2010/
200
http://www.uv.es/genomica/UVCLUSTER
200
http://www.vardb.org/
200
http://www.vbi.vt.edu/
200
http://www.vbi.vt.edu/pathport/pathinfo/
200
http://www.vicc.org/biostatistics/supp.php
200
http://www.visiblecell.com/illoura
200
http://www.vital-it.ch/Software/
java.io.FileNotFoundException : http://www.vital-it.ch/Software/
http://www.vital-it.ch/software/FastEpistasis
200
http://www.vivas.ufba.br/bone/bone.zip
200
http://www.vrac.iastate.edu/research/sites/metnet/Bioinformatics/SupplementaryInformation.htm
java.io.IOException : Server returned HTTP response code: 403 for URL: http://www.vrac.iastate.edu/research/sites/metnet/Bioinformatics/SupplementaryInformation.htm
http://www.vrac.iastate.edu/research/sites/metnet/Download/Download.htm
java.io.IOException : Server returned HTTP response code: 403 for URL: http://www.vrac.iastate.edu/research/sites/metnet/Download/Download.htm
http://www.wadsworth.org/res
java.io.FileNotFoundException : http://www.wadsworth.org/res
http://www.webact.org
200
http://www.webarraydb.org
200
http://www.wehi.edu.au/bioweb/Mauro/Marcoil
java.io.FileNotFoundException : http://www.wehi.edu.au/bioweb/Mauro/Marcoil
http://www.weizmann.ac.il/
200
http://www.weizmann.ac.il/Chemical_Research_Support/molfit
200
http://www.weizmann.ac.il/mcb/UriAlon/
200
http://www.weizmann.ac.il/mcb/UriAlon/Papers/SOSData/
200
http://www.weizmann.ac.il/physics/complex/compphys/bioinfo2/
200
http://www.weizmann.ac.il/physics/complex/compphys/downloads/liate/
200
http://www.weizmann.ac.il/physics/complex/compphys/f2cs/
200
http://www.well.ox.ac.uk/
200
http://www.well.ox.ac.uk/asthma/GOLD/
java.io.FileNotFoundException : http://www.well.ox.ac.uk/asthma/GOLD/
http://www.wemboss.org
200
http://www.win.tue.nl/
200
http://www.wis.kuleuven.ac.be/stat/robust.html
200
http://www.wsbc.warwick.ac.uk/stevenkiddle/tcap.html
200
http://www.wtccc.org.uk/
200
http://www.xlstat.com/en/home/
200
http://www.yale.edu/townsend/software.html
200
http://www.zaik.uni-koeln.de/
200
http://www.zaik.uni-koeln.de/bioinformatik/fptm.html
200
http://www.zbh.uni-hamburg.de/poseview
200
http://www.zbh.uni-hamburg.de/research/ESB/index.php
200
http://www.zbi.uni-saarland.de/chair/projects/BioMiner
java.io.FileNotFoundException : http://www.zbi.uni-saarland.de/chair/projects/BioMiner
http://www.zbit.uni-tuebingen.de/pas/mayday
200
http://www/bioi/syu/oklc.html
java.net.UnknownHostException : www
http://www/lncc.br/
java.net.UnknownHostException : www
http://www/software/software_index.html
java.net.UnknownHostException : www
http://www1.imperial.ac.uk/medicine/people/r.cavill/
200
http://www1.montpellier.inra.fr/CBGP/NGS/
200
http://www1.ustc.edu.cn/lab/pcrystal/NetAlign
java.net.SocketTimeoutException : connect timed out
http://www2.chem.gu.se/bcbp/nmr/prodecomp.html
java.io.IOException : Server returned HTTP response code: 403 for URL: http://www2.chem.gu.se/bcbp/nmr/prodecomp.html
http://www2.chi.unsw.edu.au/attacca
200
http://www2.docm.mmu.ac.uk/STAFF/L.Han/geneannotation/
200
http://www2.hu-berlin.de/wikizbnutztier/software/CandiSNPer
200
http://www2.imtech.res.in/raghava/srf
java.net.UnknownHostException : www2.imtech.res.in
http://www2.isye.gatech.edu/
200
http://www2.mdanderson.org/app/ilya/PBN/PBN.htm
java.io.FileNotFoundException : http://www2.mdanderson.org/app/ilya/PBN/PBN.htm
http://www2.renci.org/
java.io.IOException : Server returned HTTP response code: 403 for URL: http://www2.renci.org/
http://www2.unil.ch/popgen/softwares/quantinemo
200
http://www2.warwick.ac.uk/fac/sci/systemsbiology/staff/ott/tools_and_software/rrs
200
http://www2.warwick.ac.uk/fac/sci/whri/research/archaeobotany
200
http://www3.imperial.ac.uk/theoreticalsystemsbiology/data-software/
200
http://www3.ntu.edu.sg/home/aspatra/research/Yongjin_BI2010.zip
200
http://www4.dei.isep.ipp.pt/etc/dnapaper2010
200
http://www4.stat.ncsu.edu/jytzeng/software.php
java.io.FileNotFoundException : http://www4.stat.ncsu.edu/jytzeng/software.php
http://wwwabi.snv.jussieu.fr/imagene
java.io.FileNotFoundException : http://wwwabi.snv.jussieu.fr/imagene
http://wwwabi.snv.jussieu.fr/public/RepSeek/
200
http://wwwbode.cs.tum/
java.net.UnknownHostException : wwwbode.cs.tum
http://wwwcsif.cs.ucdavis.edu/
200
http://wwwkramer.in.tum.de/exelixis/software.html
200
http://wwwkramer.in.tum.de/research/applications/biodegradation/data
java.io.FileNotFoundException : http://wwwkramer.in.tum.de/research/applications/biodegradation/data
http://wwwkramer.in.tum.de/research/applications/vorolign-kernel
200
http://wwwmgs
java.net.UnknownHostException : wwwmgs
http://wwwmgs.bionet.nsc
java.net.UnknownHostException : wwwmgs.bionet.nsc
http://wwwmgs.bionet.nsc.ru/Dbases/MATRIX/
java.io.FileNotFoundException : http://wwwmgs.bionet.nsc.ru/Dbases/MATRIX/
http://wwwmgs.bionet.nsc.ru/mgs/programs/prof_pat/
200
http://wwwmgs.bionet.nsc.ru/mgs/programs/recon/
200
http://wwwmgs.bionet.nsc.ru/programs/CRASP/
java.io.FileNotFoundException : http://wwwmgs.bionet.nsc.ru/programs/CRASP/
http://wwwmgs.bionet.nsc.ru/systems/Activity/
java.io.FileNotFoundException : http://wwwmgs.bionet.nsc.ru/systems/Activity/
http://wwwmgs.bionet.nsc.ru/systems/BDNAVideo/
java.io.FileNotFoundException : http://wwwmgs.bionet.nsc.ru/systems/BDNAVideo/
http://wwwmgs.bionet.nsc.ru/systems/MGL/GeneN
java.io.FileNotFoundException : http://wwwmgs.bionet.nsc.ru/systems/MGL/GeneN
http://wwwteor.mi.infn.it/bassetti/downloads.html
java.io.FileNotFoundException : http://wwwteor.mi.infn.it/bassetti/downloads.html
http://xena1.ddns.comp.nus.edu.sg/
java.net.UnknownHostException : xena1.ddns.comp.nus.edu.sg
http://xgu.zool.iastate.edu
java.net.SocketTimeoutException : connect timed out
http://xgu1.zool.iastate.edu/
java.net.UnknownHostException : xgu1.zool.iastate.edu
http://xian.tamu.edu/Arbor3D/
java.net.UnknownHostException : xian.tamu.edu
http://xml.apache.org/xerces-j
200
http://xpdb.nist.gov/enzyme_thermodynamics/
200
http://xqtav.sourceforge.net/
200
http://yangdw.science.nus.edu.sg/SCAssign
200
http://ycmi.med.yale.edu/cyspid/
java.io.FileNotFoundException : http://ycmi.med.yale.edu/cyspid/
http://yeastgfp.ucsf.edu
java.net.SocketTimeoutException : connect timed out
http://yeasthub.gersteinlab.org
java.io.IOException : Server returned HTTP response code: 502 for URL: http://mcdb750.med.yale.edu/yeasthub
http://ymbc.ym.edu.tw/sca/
java.net.SocketTimeoutException : connect timed out
http://zellig.cpmc.columbia.edu/PGschema
200
http://zhanglab.ccmb.med.umich.edu/GPCRRD/
200
http://zhangorup.aporc.org/bioinfo/grninfer/
java.net.UnknownHostException : zhangorup.aporc.org
http://zhangroup.aporc.org/bioinfo/MNAligner
java.io.FileNotFoundException : http://zhangroup.aporc.org/bioinfo/MNAligner
http://zhangroup.aporc.org/bioinfo/ptg/
200
http://zhoulab.usc.edu/CODENSE/
200
http://zhoulab.usc.edu/ContextAnnotation
200
http://zhoulab.usc.edu/NeMo/
200
http://zlab.bu.edu/CisML/
200
http://zlab.bu.edu/m-zdock/
200
http://zlab.bu.edu/site2genome/
200
http://zlab.bu.edu/SMM
200
http://zork.wustl.edu/gin
200
https://access.obigrid.org/ibm/cluspa/
javax.net.ssl.SSLHandshakeException : java.security.cert.CertificateException: No name matching access.obigrid.org found
https://access.obigrid.org/yagns/
javax.net.ssl.SSLHandshakeException : java.security.cert.CertificateException: No name matching access.obigrid.org found
https://bioinfo.affymetrix.com/Papers/ANOSVA/
200
https://bitbucket.org/
200
https://cabig-kc.nci.nih.gov/Molecular/forums/
200
https://cabig.nci.nih.gov/workspaces/Architecture/caGrid/
200
https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html
200
https://compbio.iupui.edu/xiaomanli/LiSoftware/retrieve.php?ID=tgs
java.io.FileNotFoundException : https://compbio.iupui.edu/xiaomanli/LiSoftware/retrieve.php?ID=tgs
https://cpfp-master.molbiol.ox.ac.uk/cpfp_demo
200
https://demo1.interagon.com/miRNA/
java.net.ConnectException : Connection refused
https://dw.lcb.uu.se/index.phtml?i_login=test
java.net.SocketTimeoutException : connect timed out
https://genome.unc.edu/pubsup/dwd/
200
https://genome.unc.edu/xpn
200
https://gforge.nbic.nl/projects/mariboes/
200
https://gforge.nbic.nl/projects/statquant/
200
https://github.com/sail
200
https://hippocrates.duhs.duke.edu/soda
java.net.SocketTimeoutException : Read timed out
https://sites.google.com/site/carlovittoriocannistraci/home
200
https://sourceforge.net/project/showfiles.php?group_id=36855
302
https://sourceforge.net/projects/distmatcomp/
302
https://sourceforge.net/projects/diyg/
302
https://sourceforge.net/projects/snpratiotest/
302
https://webtools.imbs.uni-luebeck.de/snptogo
javax.net.ssl.SSLHandshakeException : sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
https://wiki.nci.nih.gov/display/NOBbioinf/FastMEDUSA
200
https://wiki.nci.nih.gov/x/OFNyAQ
200
https://www-lgc.toulouse.inra.fr/nemo
200
https://www.cistrack.org/flynet/
200
https://www.emsl.pnl.gov/NIT/NIT.html
200
https://www.omnifung.hki-jena.de/Rpad/Distance_Scan/index.htm
javax.net.ssl.SSLHandshakeException : sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
https://www.sapac.edu.au/gosling
javax.net.ssl.SSLHandshakeException : sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments.
1995
8808585
Image library of biological macromolecules.
1996
8872391
Development of an animal genome database and its search system.
1996
8872392
The directory of P450-containing systems on WorldWide Web.
1996
8872393
GEOMETRY: a software package for nucleotide sequence analysis using statistical geometry in sequence space.
1996
8902356
ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool.
1996
8902357
GenomeInspector: a new approach to detect correlation patterns of elements on genomic sequences.
1996
8996789
Software for DNA sequencing by hybridization.
1997
9146969
Construction of evolutionary distance trees with TREECON for Windows: accounting for variation in nucleotide substitution rate among sites.
1997
9183524
Match-Box_server: a multiple sequence alignment tool placing emphasis on reliability.
1997
9183529
A Brownian dynamics model for the chromatin fiber.
1997
9183532
Using explicitly represented biological relationships for database navigation and searching via the World-Wide Web.
1997
9183533
End-Epi: an application for inferring phylogenetic and population dynamical processes from molecular sequences.
1997
9183536
Displaying the information contents of structural RNA alignments: the structure logos.
1997
9475985
Q-RT-PCR: data analysis software for measurement of gene expression by competitive RT-PCR.
1997
9475986
XDOM, a graphical tool to analyse domain arrangements in any set of protein sequences.
1997
9475988
SAMBA: hardware accelerator for biological sequence comparison.
1997
9475989
The Sequence Alerting Server--a new WEB server.
1997
9475991
Two applications to facilitate the viewing of database search result files on the Macintosh.
1997
9475993
DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment.
1997
9475994
Mapper: an intelligent restriction mapping tool.
1998
9545441
Design and implementation of a CORBA-based genome mapping system prototype.
1998
9545442
Feature selection for genetic sequence classification.
1998
9545445
DIVCLUS: an automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteins.
1998
9545446
Rose: generating sequence families.
1998
9545448
Automated protein sequence database classification. I. Integration of compositional similarity search, local similarity search, and multiple sequence alignment.
1998
9545449
Automated protein sequence database classification. II. Delineation Of domain boundaries from sequence similarities.
1998
9545450
3DinSight: an integrated relational database and search tool for the structure, function and properties of biomolecules.
1998
9545451
Incremental threading optimization (TITO) to help alignment and modelling of remote homologues.
1998
9545453
TOPAL: recombination detection in DNA and protein sequences.
1998
9545456
GeneFIND web server for protein family identification and information retrieval.
1998
9545458
An EXCEL template for calculation of enzyme kinetic parameters by non-linear regression.
1998
9545460
A distributed environment for physical map construction.
1998
9614268
A genetic algorithm for designing gene family-specific oligonucleotide sets used for hybridization: the G protein-coupled receptor protein superfamily.
1998
9614269
DIALIGN: finding local similarities by multiple sequence alignment.
1998
9614273
New scoring schemes for protein fold recognition based on Voronoi contacts.
1998
9614274
DIAMOD: display and modeling of DNA bending.
1998
9632827
The new Virgil database: a service of rich links.
1998
9632829
Frame: detection of genomic sequencing errors.
1998
9632832
POLINA: detection and evaluation of single amino acid substitutions in protein superfamilies.
1998
9632834
Self-organizing tree growing network for classifying amino acids.
1998
9632835
SOSUI: classification and secondary structure prediction system for membrane proteins.
1998
9632836
MView: a web-compatible database search or multiple alignment viewer.
1998
9632837
Assessing protein coding region integrity in cDNA sequencing projects.
1998
9682051
Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12.
1998
9682052
Reduced space hidden Markov model training.
1998
9682053
COFFEE: an objective function for multiple sequence alignments.
1998
9682054
Removing near-neighbour redundancy from large protein sequence collections.
1998
9682055
A set-theoretic approach to database searching and clustering.
1998
9682056
Computational space reduction and parallelization of a new clustering approach for large groups of sequences.
1998
9682057
POPSIM: a general population simulation program.
1998
9682059
CloneIt: finding cloning strategies, in-frame deletions and frameshifts.
1998
9682060
SWAN: sliding window analysis of nucleotide sequence variability.
1998
9682061
The BioCatalog.
1998
9682062
Formal design and implementation of an improved DDBJ DNA database with a new schema and object-oriented library.
1998
9694985
SSMAL: similarity searching with alignment graphs.
1998
9694989
A geometric algorithm to find small but highly similar 3D substructures in proteins.
1998
9694990
Homology modeling, model and software evaluation: three related resources.
1998
9694991
GeneNet: a gene network database and its automated visualization.
1998
9694992
Z extensions to the RHMAPPER package.
1998
9694993
EUCLID: automatic classification of proteins in functional classes by their database annotations.
1998
9694995
New phylogenetic venues opened by a novel implementation of the DNAml algorithm.
1998
9694996
Graphical interface to the genetic network database GeNet.
1998
9694997
Comprehensive, comprehensible, distributed and intelligent databases: current status.
1998
9730920
Issues in developing integrated genomic databases and application to the human X chromosome.
1998
9730923
LIGAND: chemical database for enzyme reactions.
1998
9730924
Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families.
1998
9730925
JOY: protein sequence-structure representation and analysis.
1998
9730927
An NMR assignment module implemented in the Gifa NMR processing program.
1998
9730928
QU-GENE: a simulation platform for quantitative analysis of genetic models.
1998
9730929
GeneCards: a novel functional genomics compendium with automated data mining and query reformulation support.
1998
9789091
Gene recognition by combination of several gene-finding programs.
1998
9789092
An RNA folding method capable of identifying pseudoknots and base triples.
1998
9789095
Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence.
1998
9789096
PASSML: combining evolutionary inference and protein secondary structure prediction.
1998
9789098
Mapplet: a CORBA-based genome map viewer.
1998
9789099
A web server to locate periodicities in a sequence
1998
9789101
PPCMatrix: a PowerPC dotmatrix program to compare large genomic sequences against protein sequences
1998
9789102
Weighting hidden Markov models for maximum discrimination.
1998
9918947
Representing metabolic pathway information: an object-oriented approach.
1998
9918950
Zomit: biological data visualization and browsing.
1998
9918951
VIRTLAB: a virtual molecular biology laboratory.
1998
9918952
MODELTEST: testing the model of DNA substitution.
1998
9918953
GeneTree: comparing gene and species phylogenies using reconciled trees.
1998
9918954
JavaShade: multiple sequence alignment box-and-shading on the World Wide Web.
1998
9918955
SPEM: a parser for EMBL style flat file database entries.
1998
9918956
WEBMAP: radiation hybrid mapping on the WWW.
1998
9918957
An Internet linkage and mutation database for the complex phenotype asthma.
1998
9918958
SALSA: improved protein database searching by a new algorithm for assembly of sequence fragments into gapped alignments.
1998
9927712
Hidden Markov models for detecting remote protein homologies.
1998
9927713
VHMPT: a graphical viewer and editor for helical membrane protein topologies.
1998
9927715
Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation.
1998
9927716
BioABACUS: a database of abbreviations and acronyms in biotechnology and computer science.
1998
9927719
BEAUTY-X: enhanced BLAST searches for DNA queries.
1998
9927720
JPred: a consensus secondary structure prediction server.
1998
9927721
Imagene: an integrated computer environment for sequence annotation and analysis.
1999
10068688
RNA movies: visualizing RNA secondary structure spaces.
1999
10068690
Bayesian inference on biopolymer models.
1999
10068691
E-CELL: software environment for whole-cell simulation.
1999
10068694
Genetic Simulation Library.
1999
10068695
BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs.
1999
10068696
Application of distance geometry to 3D visualization of sequence relationships.
1999
10068697
Establishing a method of vector contamination identification in database sequences.
1999
10089195
A RAPID algorithm for sequence database comparisons: application to the identification of vector contamination in the EMBL databases.
1999
10089196
Combining many multiple alignments in one improved alignment.
1999
10089197
FORESST: fold recognition from secondary structure predictions of proteins.
1999
10089198
The hydrophobic cores of proteins predicted by wavelet analysis.
1999
10089199
HICLAS: a taxonomic database system for displaying and comparing biological classification and phylogenetic trees.
1999
10089200
A proposal for a standard CORBA interface for genome maps.
1999
10089201
An extensive list of genes that produce alternative transcripts in the mouse.
1999
10089202
TargetFinder: searching annotated sequence databases for target genes of transcription factors.
1999
10089203
DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis.
1999
10089204
PredAcc: prediction of solvent accessibility.
1999
10089205
Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity.
1999
10222404
10-11 bp periodicities in complete genomes reflect protein structure and DNA folding.
1999
10222405
Transformation distances: a family of dissimilarity measures based on movements of segments.
1999
10222406
DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment.
1999
10222408
Docking of hydrophobic ligands with interaction-based matching algorithms.
1999
10222412
METATOOL: for studying metabolic networks.
1999
10222413
WWW access to the SYSTERS protein sequence cluster set.
1999
10222416
DNA-binding requirements of the yeast protein Rap1p as selected in silico from ribosomal protein gene promoter sequences.
1999
10320394
A vector-based method for drawing RNA secondary structure.
1999
10320396
Calign: aligning sequences with restricted affine gap penalties.
1999
10320397
ESPript: analysis of multiple sequence alignments in PostScript.
1999
10320398
DINAMO: interactive protein alignment and model building.
1999
10320399
Motif-based searching in TOPS protein topology databases.
1999
10320400
Automated analysis of interatomic contacts in proteins.
1999
10320401
The Biopolymer Markup Language.
1999
10320402
MIAH: automatic alignment of eukaryotic SSU rRNAs.
1999
10320403
The domain-server: direct prediction of protein domain-homologies from BLAST search.
1999
10320404
CoPE: a collaborative pedigree drawing environment.
1999
10320405
Wrapping SRS with CORBA: from textual data to distributed objects.
1999
10320658
Promoter2.0: for the recognition of PolII promoter sequences.
1999
10366655
Statistical mechanical simulation of polymeric DNA melting with MELTSIM.
1999
10366657
CRAWview: for viewing splicing variation, gene families, and polymorphism in clusters of ESTs and full-length sequences.
1999
10366658
Automated genome sequence analysis and annotation.
1999
10366660
Improved performance in protein secondary structure prediction by inhomogeneous score combination.
1999
10366661
WebBLAST 2.0: an integrated solution for organizing and analyzing sequence data.
1999
10366662
JaDis: computing distances between nucleic acid sequences.
1999
10366663
REPuter: fast computation of maximal repeats in complete genomes.
1999
10366664
Fast evaluation of internal loops in RNA secondary structure prediction.
1999
10383469
Family pairwise search with embedded motif models.
1999
10383471
Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations.
1999
10383472
An ontology for bioinformatics applications.
1999
10383475
Protein analyst--a distributed object environment for protein sequence and structure analysis.
1999
10383476
BLAST PRINTS--alternative perspectives on sequence similarity.
1999
10383477
Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries.
10487860
Complete genomes in WWW Entrez: data representation and analysis.
10487861
Development of the receptor database (RDB): application to the endocrine disruptor problem.
10487862
Nucleosomal DNA property database.
10487866
SCPD: a promoter database of the yeast Saccharomyces cerevisiae.
10487868
GeneBuilder: interactive in silico prediction of gene structure.
10487869
Estimating transcription factor bindability on DNA.
10487870
Oligonucleotide frequency matrices addressed to recognizing functional DNA sites.
10487871
Investigating extended regulatory regions of genomic DNA sequences.
10487872
Conformational and physicochemical DNA features specific for transcription factor binding sites.
10487873
Integrated databases and computer systems for studying eukaryotic gene expression.
10487874
Identification of sequence-dependent DNA features correlating to activity of DNA sites interacting with proteins.
10487875
Prediction of eukaryotic mRNA translational properties.
10487876
Interactive data input into the GeneNet database.
10487877
Shotgun: getting more from sequence similarity searches.
1999
10498773
Associative database of protein sequences.
1999
10498774
Mathematical simulation and analysis of cellular metabolism and regulation.
1999
10498775
TargetDB: a database of peptides targeting proteins to subcellular locations.
1999
10498778
SWEET - WWW-based rapid 3D construction of oligo- and polysaccharides.
1999
10498779
MatrixPlot: visualizing sequence constraints.
1999
10498780
Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide.
1999
10498782
Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences.
1999
10743555
An automated comparative analysis of 17 complete microbial genomes.
1999
10743556
Genome rearrangement with gene families.
1999
10743557
Darwin v. 2.0: an interpreted computer language for the biosciences.
2000
10842729
Sequence search algorithm assessment and testing toolkit (SAT).
2000
10842730
ProtEST: protein multiple sequence alignments from expressed sequence tags.
2000
10842731
Fast assignment of protein structures to sequences using the intermediate sequence library PDB-ISL.
2000
10842732
SAWTED: structure assignment with text description--enhanced detection of remote homologues with automated SWISS-PROT annotation comparisons.
2000
10842733
TOPAL 2.0: improved detection of mosaic sequences within multiple alignments.
2000
10842734
TEXshade: shading and labeling of multiple sequence alignments using LATEX2 epsilon.
2000
10842735
Modeling splice sites with Bayes networks.
2000
10842737
STAR/mmCIF: an ontology for macromolecular structure.
2000
10842738
PNAD-CSS: a workbench for constructing a protein name abbreviation dictionary.
2000
10842739
The human transcript database: a catalogue of full length cDNA inserts.
2000
10842740
Dotlet: diagonal plots in a web browser.
2000
10842741
SISEQ: manipulation of multiple sequence and large database files for common platforms.
2000
10842742
GOLD--graphical overview of linkage disequilibrium.
2000
10842743
TAMBIS: transparent access to multiple bioinformatics information sources.
2000
10842744
Optimal spliced alignment of homologous cDNA to a genomic DNA template.
2000
10869013
Net nearest neighbor analysis (NNNA) summarizes non-compensated dinucleotides within gene sequences.
2000
10869014
Fast probabilistic analysis of sequence function using scoring matrices.
2000
10869016
Adaptive encoding neural networks for the recognition of human signal peptide cleavage sites.
2000
10869017
Predicting the oxidation state of cysteines by multiple sequence alignment.
2000
10869018
MPSA: integrated system for multiple protein sequence analysis with client/server capabilities.
2000
10869021
PIR: a new resource for bioinformatics.
2000
10869023
HELM: searching for helix motifs within protein sequences.
2000
10869024
EDIBLE: experimental design and information calculations in phylogenetics.
2000
10869025
RRTree: relative-rate tests between groups of sequences on a phylogenetic tree.
2000
10869026
PRoMT: inferring demographic history from DNA sequences.
2000
10869027
GABAagent: a system for integrating data on GABA receptors.
2000
10869028
JESAM: CORBA software components to create and publish EST alignments and clusters.
2000
10869029
SPLASH: structural pattern localization analysis by sequential histograms.
2000
10869032
PROF_ PAT 1.3: updated database of patterns used to detect local similarities.
2000
10869033
Database of structural motifs in proteins.
2000
10869035
TrExML: a maximum-likelihood approach for extensive tree-space exploration.
2000
10869037
Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies.
2000
10869038
Detecting hypermutations in viral sequences with an emphasis on G --> A hypermutation.
2000
10869039
A browser for expression data.
2000
10869040
The PSIPRED protein structure prediction server.
2000
10869041
Taxonomic markup language: applying XML to systematic data.
2000
10869042
Mathematica packages for simulation of experimental genetics.
2000
10869043
Prediction of genetic structure in eukaryotic DNA using reference point logistic regression and sequence alignment.
2000
10871265
PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance.
2000
10871266
RSDB: representative protein sequence databases have high information content.
2000
10871268
BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways.
2000
10871269
A homolog of mammalian antizyme is present in fission yeast Schizosaccharomyces pombe but not detected in budding yeast Saccharomyces cerevisiae.
2000
10871270
GESTALT: a workbench for automatic integration and visualization of large-scale genomic sequence analyses.
2000
10871271
Viral Genome DataBase: storing and analyzing genes and proteins from complete viral genomes.
2000
10871272
RadCon: phylogenetic tree comparison and consensus.
2000
10871273
Browsing the SLoop database of structurally classified loops connecting elements of protein secondary structure.
2000
10980148
Bioinorganic motifs: towards functional classification of metalloproteins.
2000
11120676
Information theoretical probe selection for hybridisation experiments.
2000
11120678
USAGE: a web-based approach towards the analysis of SAGE data. Serial Analysis of Gene Expression.
2000
11120679
Support vector machine classification and validation of cancer tissue samples using microarray expression data.
2000
11120680
CAST: an iterative algorithm for the complexity analysis of sequence tracts. Complexity analysis of sequence tracts.
2000
11120681
The reduction of large molecular profiles to informative components using a genetic algorithm.
2000
11120682
Artemis: sequence visualization and annotation.
2000
11120685
MAD: a suite of tools for microarray data management and processing.
2000
11120686
A space-efficient algorithm for aligning large genomic sequences.
2000
11120687
MASIA: recognition of common patterns and properties in multiple aligned protein sequences.
2000
11120688
Prediction whether a human cDNA sequence contains initiation codon by combining statistical information and similarity with protein sequences.
2000
11159307
Short interrupted palindromes on the extragenic DNA of Escherichia coli K-12, Haemophilus influenzae and Neisseria meningitidis.
2000
11159308
Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases.
2000
11159310
Arbor 3D: an interactive environment for examining phylogenetic and taxonomic trees in multiple dimensions.
2000
11159311
Fels-Rand: an Xlisp-Stat program for the comparative analysis of data under phylogenetic uncertainty.
2000
11159312
Processing and quality control of DNA array hybridization data.
2000
11159313
Biochemical systems analysis of genome-wide expression data.
2000
11159314
DRAGON: Database Referencing of Array Genes Online.
2000
11159315
MaskerAid: a performance enhancement to RepeatMasker.
2000
11159316
Circles: automating the comparative analysis of RNA secondary structure.
2000
11159317
VISTA : visualizing global DNA sequence alignments of arbitrary length.
2000
11159318
T(E)Xtopo: shaded membrane protein topology plots in LAT(E)X2epsilon.
2000
11159320
MPBLAST : improved BLAST performance with multiplexed queries.
2000
11159321
BLAST Search Updater: a notification system for new database matches.
2000
11159322
PhyloDraw: a phylogenetic tree drawing system.
2000
11159323
TRITON: in silico construction of protein mutants and prediction of their activities.
2000
11187152
A hierarchical unsupervised growing neural network for clustering gene expression patterns.
2001
11238068
An information-based sequence distance and its application to whole mitochondrial genome phylogeny.
2001
11238070
GeneOrder: comparing the order of genes in small genomes.
2001
11238072
ORI-GENE: gene classification based on the evolutionary tree.
2001
11238073
Virtual PCR.
2001
11238077
COMBOSA3D: combining sequence alignments with three-dimensional structures.
2001
11238080
3Dee: a database of protein structural domains.
2001
11238081
RCNPRED: prediction of the residue co-ordination numbers in proteins.
2001
11238082
Model.it: building three dimensional DNA models from sequence data.
2000
11269231
NIFAS: visual analysis of domain evolution in proteins.
2001
11301303
Identifying the 3'-terminal exon in human DNA.
2001
11448878
Identifying target sites for cooperatively binding factors.
2001
11448879
Conformational model for binding site recognition by the E.coli MetJ transcription factor.
2001
11448880
Semi-automated update and cleanup of structural RNA alignment databases.
2001
11448882
An integrated system for high throughput TaqMan based SNP genotyping.
2001
11448884
MEDUSA: large scale automatic selection and visual assessment of PCR primer pairs.
2001
11448885
ADAPTSITE: detecting natural selection at single amino acid sites.
2001
11448887
PAL: an object-oriented programming library for molecular evolution and phylogenetics.
2001
11448888
T-REX: reconstructing and visualizing phylogenetic trees and reticulation networks.
2001
11448889
A Java applet for visualizing protein-protein interaction.
2001
11448890
Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles.
2001
11472992
Generating protein interaction maps from incomplete data: application to fold assignment.
2001
11473004
Prediction of the coupling specificity of G protein coupled receptors to their G proteins.
2001
11473007
Improved prediction of the number of residue contacts in proteins by recurrent neural networks.
2001
11473014
Probabilistic approaches to the use of higher order clone relationships in physical map assembly.
2001
11473017
Generation of a database containing discordant intron positions in eukaryotic genes (MIDB).
2001
11524368
Amino acid similarity matrices based on force fields.
2001
11524370
Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set.
2001
11524372
Support vector machine approach for protein subcellular localization prediction.
2001
11524373
The Bioinformatics Template Library--generic components for biocomputing.
2001
11524374
Genotype transposer: automated genotype manipulation for linkage disequilibrium analysis.
2001
11524375
GRR: graphical representation of relationship errors.
2001
11524377
Multi-query sequence BLAST output examination with MuSeqBox.
2001
11524378
DBAli: a database of protein structure alignments.
2001
11524379
HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families.
2001
11524380
Structure prediction meta server.
2001
11524381
Easier threading through web-based comparisons and cross-validations.
2001
11524382
MRBAYES: Bayesian inference of phylogenetic trees.
2001
11524383
SIR: a simple indexing and retrieval system for biological flat file databases.
2001
11524384
Evolutionary HMMs: a Bayesian approach to multiple alignment.
2001
11590097
A simple algorithm to infer gene duplication and speciation events on a gene tree.
2001
11590098
PIRA PCR designer for restriction analysis of single nucleotide polymorphisms.
2001
11590100
GeneMachine: gene prediction and sequence annotation.
2001
11590102
CHROMA: consensus-based colouring of multiple alignments for publication.
2001
11590103
InterProScan--an integration platform for the signature-recognition methods in InterPro.
2001
11590104
The HMMTOP transmembrane topology prediction server.
2001
11590105
BioLayout--an automatic graph layout algorithm for similarity visualization.
2001
11590107
BioWAP, mobile Internet service for bioinformatics.
2001
11590108
Critical assessment of microarray data analysis: the 2001 challenge.
2001
11590109
Detection of cis-element clusters in higher eukaryotic DNA.
2001
11673232
Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a 'weak' context of the start codon.
2001
11673233
An analysis of gene-finding programs for Neurospora crassa.
2001
11673234
Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROT.
2001
11673236
Clustering protein sequences--structure prediction by transitive homology.
2001
11673238
Predicting class II MHC/peptide multi-level binding with an iterative stepwise discriminant analysis meta-algorithm.
2001
11673239
Determining the minimum number of types necessary to represent the sizes of protein atoms.
2001
11673240
Model-based clustering and data transformations for gene expression data.
2001
11673243
Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis.
2001
11724728
Gene recognition in eukaryotic DNA by comparison of genomic sequences.
2001
11724729
Thermodynamic database for protein-nucleic acid interactions (ProNIT).
2001
11724731
Detection of conserved physico-chemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutions.
2001
11724732
MDB: a database system utilizing automatic construction of modules and STAR-derived universal language.
2001
11724733
The TRANSPATH signal transduction database: a knowledge base on signal transduction networks.
2001
11724734
Nucleosome formation potential of exons, introns, and Alu repeats.
2001
11724736
Segmentation of long genomic sequences into domains with homogeneous composition with BASIO software.
2001
11724737
Selection of optimal DNA oligos for gene expression arrays.
2001
11724738
Database-driven multi locus sequence typing (MLST) of bacterial pathogens.
2001
11724739
DNA sequence quality trimming and vector removal.
2001
11751217
Tricross : using dot-plots in sequence-id space to detect uncataloged intergenic features.
2001
11751218
A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling.
2001
11751219
Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN method.
2001
11751221
Differential expression of genes coding for ribosomal proteins in different human tissues.
2001
11751223
Estimation of P-values for global alignments of protein sequences.
2001
11751224
Minimum conflict: a divide-and-conquer approach to phylogeny estimation.
2001
11751225
Taxonomy workbench.
2001
11751226
Visualizing plant metabolomic correlation networks using clique-metabolite matrices.
2001
11751228
SPiD: a subtilis protein interaction database.
2001
11751229
A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cells.
2001
11751230
MELTING, computing the melting temperature of nucleic acid duplex.
2001
11751232
Progenetix.net: an online repository for molecular cytogenetic aberration data.
2001
11751233
Sequence type analysis and recombinational tests (START).
2001
11751234
mmsearch: a motif arrangement language and search program.
2001
11751236
ProPred: prediction of HLA-DR binding sites.
2001
11751237
TMCompare: transmembrane region sequence and structure.
2001
11751238
ToolShop: prerelease inspections for protein structure prediction servers.
2001
11751239
EVA: continuous automatic evaluation of protein structure prediction servers.
2001
11751240
MEGA2: molecular evolutionary genetics analysis software.
2001
11751241
CONSEL: for assessing the confidence of phylogenetic tree selection.
2001
11751242
Geno3D: automatic comparative molecular modelling of protein.
2002
11836238
Models@Home: distributed computing in bioinformatics using a screensaver based approach.
2002
11847079
The EBI SRS server--recent developments.
2002
11847095
Assessing the significance of consistently mis-regulated genes in cancer associated gene expression matrices.
2002
11934737
A mixture model-based approach to the clustering of microarray expression data.
2002
11934740
Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysis.
2002
11934741
JenPep: a database of quantitative functional peptide data for immunology.
2002
11934742
PatternHunter: faster and more sensitive homology search.
2002
11934743
Multiple sequence alignment using partial order graphs.
2002
11934745
STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm.
2002
11934747
ProbeMatchDB--a web database for finding equivalent probes across microarray platforms and species.
2002
11934751
GRIMM: genome rearrangements web server.
2002
11934753
MaxBench: evaluation of sequence and structure comparison methods.
2002
11934754
CASA: a server for the critical assessment of protein sequence alignment accuracy.
2002
11934755
BetaTPred: prediction of beta-TURNS in a protein using statistical algorithms.
2002
11934756
DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family.
2002
11934757
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing.
2002
11934758
A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments.
2002
12016052
Application of Bayesian decomposition for analysing microarray data.
2002
12016054
Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts.
2002
12016056
TranScout: prediction of gene expression regulatory proteins from their sequences.
2002
12016057
Amphiphilicity index of polar amino acids as an aid in the characterization of amino acid preference at membrane-water interfaces.
2002
12016058
An HMM model for coiled-coil domains and a comparison with PSSM-based predictions.
2002
12016059
CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences.
2002
12016061
TROLL--tandem repeat occurrence locator.
2002
12016062
Advanced pairwise structure alignments of proteins and analysis of conformational changes.
2002
12016063
DOLOP--database of bacterial lipoproteins.
2002
12016064
Desktop prediction/analysis of mass spectrometric data in proteomic projects by using massXpert.
2002
12016065
PATH: a task for the inference of phylogenies.
2002
12016066
Detecting cryptically simple protein sequences using the SIMPLE algorithm.
2002
12050063
Sequence complexity profiles of prokaryotic genomic sequences: a fast algorithm for calculating linguistic complexity.
2002
12050064
Evaluation of computational metabolic-pathway predictions for Helicobacter pylori.
2002
12050068
Adaptive quality-based clustering of gene expression profiles.
2002
12050070
Xdigitise: visualization of hybridization experiments.
2002
12050072
Gene structure identification with MyGV using cDNA evidence and protein homologs to improve ab initio predictions.
2002
12050073
EMBL-Align: a new public nucleotide and amino acid multiple sequence alignment database.
2002
12050074
BeoBLAST: distributed BLAST and PSI-BLAST on a Beowulf cluster.
2002
12050075
ENDscript: a workflow to display sequence and structure information.
2002
12050076
The Sulfinator: predicting tyrosine sulfation sites in protein sequences.
2002
12050077
GP3: GenePix post-processing program for automated analysis of raw microarray data.
2002
12050078
A bioinformatics tool to select sequences for microarray studies of mouse models of oncogenesis.
2002
12050079
Exon discovery by genomic sequence alignment.
2002
12075013
NETASA: neural network based prediction of solvent accessibility.
2002
12075017
Modelling biological processes using workflow and Petri Net models.
2002
12075018
Adaptive algorithm of automated annotation.
2002
12075019
The chemical organization of signaling interactions.
2002
12075021
AiO, combining DNA/protein programs and oligo-management.
2002
12075025
Synonymous-non-synonymous mutation rates between sequences containing ambiguous nucleotides (Syn-SCAN).
2002
12075026
Arrayplot for visualization and normalization of cDNA microarray data.
2002
12075027
MOUSE (Mitochondrial and Other Useful SEquences) a compilation of population genetic markers.
2002
12075028
BAOBAB: a Java editor for large phylogenetic trees.
2002
12075029
DMLE+: Bayesian linkage disequilibrium gene mapping.
2002
12075030
Selecting targets for structural determination by navigating in a graph of protein families.
2002
12117787
Clustering of proximal sequence space for the identification of protein families.
2002
12117788
Target space for structural genomics revisited.
2002
12117789
Deriving quantitative conclusions from microarray expression data.
2002
12117794
Comparative genomics study of inverted repeats in bacteria.
2002
12117795
Determining a unique defining DNA sequence for yeast species using hashing techniques.
2002
12117799
TangleSolve: topological analysis of site-specific recombination.
2002
12117800
CaGE: cardiac gene expression knowledgebase.
2002
12117801
CS-PSeq-Gen: simulating the evolution of protein sequence under constraints.
2002
12117802
SNAPper: gene order predicts gene function.
2002
12117803
The Pathway Tools software.
2002
12169551
Improving gene recognition accuracy by combining predictions from two gene-finding programs.
2002
12176826
Computational identification of putative programmed translational frameshift sites.
2002
12176827
Analysis of expression profile using fuzzy adaptive resonance theory.
2002
12176830
Probabilistic alignment of motifs with sequences.
2002
12176832
Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices.
2002
12176833
Prediction of Golgi Type II membrane proteins based on their transmembrane domains.
2002
12176834
A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families.
2002
12176835
TFBS: Computational framework for transcription factor binding site analysis.
2002
12176838
ShiftDetector: detection of shift mutations.
2002
12176839
MArray: analysing single, replicated or reversed microarray experiments.
2002
12176840
Domain fishing: a first step in protein comparative modelling.
2002
12176841
DiffTool: building, visualizing and querying protein clusters.
2002
12176842
The NCTU BioInfo Archive of biological data sets for bioinformatics research and experimentation.
2002
12176843
XEMBL: distributing EMBL data in XML format.
2002
12176844
The EBI SRS server-new features.
2002
12176845
Genome structures embossed by oligonucleotide-stickiness.
2002
12217906
Pooled library tissue tags for EST-based gene discovery.
2002
12217907
Identification of regulatory elements using a feature selection method.
2002
12217908
Bayesian infinite mixture model based clustering of gene expression profiles.
2002
12217911
The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs.
2002
12217916
ESyPred3D: Prediction of proteins 3D structures.
2002
12217917
VIZARD: analysis of Affymetrix Arabidopsis GeneChip data.
2002
12217919
SEGE: A database on 'intron less/single exonic' genes from eukaryotes.
2002
12217920
UniBLAST: a system to filter, cluster, and display BLAST results and assign unique gene annotation.
2002
12217921
Parallelized multiple alignment.
2002
12217922
OrthoGUI: graphical presentation of Orthostrapper results.
2002
12217923
A kinase sequence database: sequence alignments and family assignment.
2002
12217924
PeCoP: automatic determination of persistently conserved positions in protein families.
2002
12217925
Applications of Tree-Maps to hierarchical biological data.
2002
12217926
An ontology driven architecture for derived representations of macromolecular structure.
2002
12217927
Condition specific transcription factor binding site characterization in Saccharomyces cerevisiae.
2002
12376372
Comparative ab initio prediction of gene structures using pair HMMs.
2002
12376375
Threading using neural nEtwork (TUNE): the measure of protein sequence-structure compatibility.
2002
12376379
Data mining of sequences and 3D structures of allergenic proteins.
2002
12376380
Finding motifs in the twilight zone.
2002
12376382
GENOTRACE: cDNA-based local GENOme assembly from TRACE archives.
2002
12376385
Genquire: genome annotation browser/editor.
2002
12376386
Genexp--a genetic network simulation environment.
2002
12376387
CINEMA-MX: a modular multiple alignment editor.
2002
12376388
GENIE: estimating demographic history from molecular phylogenies.
2002
12376389
Feature subset selection for splice site prediction.
2002
12385987
An efficient and accurate distance based algorithm to reconstruct tandem duplication trees.
2002
12385990
Biological information: making it accessible and integrated (and trying to make sense of it).
2002
12385995
Stochastic pairwise alignments.
2002
12385998
Proteome analysis based on motif statistics.
2002
12385999
Correlating gene promoters and expression in gene disruption experiments.
2002
12386000
ProClust: improved clustering of protein sequences with an extended graph-based approach.
2002
12386002
Building an automated classification of DNA-binding protein domains.
2002
12386003
Building and analysing genome-wide gene disruption networks.
2002
12386004
BioMiner--modeling, analyzing, and visualizing biochemical pathways and networks.
2002
12386006
Representation of DNA sequences with virtual potentials and their processing by (SEQREP) Kohonen self-organizing maps.
2003
12499290
Genetic algorithms applied to multi-class prediction for the analysis of gene expression data.
2003
12499291
Evolutionary algorithms for finding optimal gene sets in microarray prediction.
2003
12499292
Analysis of whole-genome microarray replicates using mixed models.
2003
12499293
Simple rules underlying gene expression profiles of more than six subtypes of acute lymphoblastic leukemia (ALL) patients.
2003
12499295
Mining gene expression databases for association rules.
2003
12499296
MADGE: scalable distributed data management software for cDNA microarrays.
2003
12499297
Gene selection: a Bayesian variable selection approach.
2003
12499298
Finding the common structure shared by two homologous RNAs.
2003
12499300
Protein structures and information extraction from biological texts: the PASTA system.
2003
12499303
Simulating complex traits influenced by genes with fuzzy-valued effects in pedigreed populations.
2003
12499304
Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits.
2003
12499305
MAVG: locating non-overlapping maximum average segments in a given sequence.
2003
12499306
An integrated genetic data environment (GDE)-based LINUX interface for analysis of HIV-1 and other microbial sequences.
2003
12499307
An extensible application for assembling annotation for genomic data.
2003
12499308
XdomView: protein domain and exon position visualization.
2003
12499310
InterPreTS: protein interaction prediction through tertiary structure.
2003
12499311
ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information.
2003
12499312
ModView, visualization of multiple protein sequences and structures.
2003
12499313
Detection of hydrogen-bond signature patterns in protein families.
2003
12499314
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.
2003
12538238
Combinatorial image analysis of DNA microarray features.
2003
12538239
Gene finding with a hidden Markov model of genome structure and evolution.
2003
12538242
A generalized global alignment algorithm.
2003
12538243
A naive Bayes model to predict coupling between seven transmembrane domain receptors and G-proteins.
2003
12538244
Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO).
2003
12538245
Fractional populations in multiple gene inheritance.
2003
12538247
FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps.
2003
12538248
A task framework for the web interface W2H.
2003
12538250
QuickLIMS: facilitating the data management for DNA-microarray fabrication.
2003
12538251
An efficient algorithm for minimal primer set selection.
2003
12538252
Efficient selective screening of haplotype tag SNPs.
2003
12538253
Simulating haplotype blocks in the human genome.
2003
12538254
Pedstrip: extracting a maximal subset of available, unrelated individuals from a pedigree.
2003
12538255
Matrix2png: a utility for visualizing matrix data.
2003
12538257
SEGID: identifying interesting segments in (multiple) sequence alignments.
2003
12538258
RnaViz 2: an improved representation of RNA secondary structure.
2003
12538259
r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock.
2003
12538260
Chimera: construction of chimeric sequences for phylogenetic analysis.
2003
12538261
G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining.
2003
12538262
A profile hidden Markov model for signal peptides generated by HMMER.
2003
12538263
MPID: MHC-Peptide Interaction Database for sequence-structure-function information on peptides binding to MHC molecules.
2003
12538264
TopDraw: a sketchpad for protein structure topology cartoons.
2003
12538265
ARIA: automated NOE assignment and NMR structure calculation.
2003
12538267
Visualization and analysis of protein interactions.
2003
12538268
Towards a computational model for -1 eukaryotic frameshifting sites.
2003
12584117
Genetic Network Analyzer: qualitative simulation of genetic regulatory networks.
2003
12584118
Identifying differentially expressed genes using false discovery rate controlling procedures.
2003
12584122
Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions.
2003
12584123
GenePath: a system for automated construction of genetic networks from mutant data.
2003
12584124
SimiTri--visualizing similarity relationships for groups of sequences.
2003
12584125
The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks.
2003
12584128
cMap: the comparative genetic map viewer.
2003
12584129
IslandPath: aiding detection of genomic islands in prokaryotes.
2003
12584130
Melina: motif extraction from promoter regions of potentially co-regulated genes.
2003
12584132
AltAVisT: comparing alternative multiple sequence alignments.
2003
12584133
PDP: protein domain parser.
2003
12584135
pathSCOUT: exploration and analysis of biochemical pathways.
2003
12584136
KnowledgeEditor: a new tool for interactive modeling and analyzing biological pathways based on microarray data.
2003
12584137
Modeling biological systems using Dynetica--a simulator of dynamic networks.
2003
12584138
GSCope: a clipped fisheye viewer effective for highly complicated biomolecular network graphs.
2003
12584139
WiGID: wireless genome information database.
2003
12584140
Wrapping up BLAST and other applications for use on Unix clusters.
2003
12584141
Comparisons and validation of statistical clustering techniques for microarray gene expression data.
2003
12611800
Statistical alignment based on fragment insertion and deletion models.
2003
12611804
MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segments.
2003
12611805
Detection of unrelated proteins in sequences multiple alignments by using predicted secondary structures.
2003
12611806
Alignment-free sequence comparison-a review.
2003
12611807
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
2003
12611808
Subnetwork hierarchies of biochemical pathways.
2003
12611809
PopHist: inferring population history from the spectrum of allele frequencies.
2003
12611810
3MOTIF: visualizing conserved protein sequence motifs in the protein structure database.
2003
12611811
IS: a web-site for intron statistics.
2003
12611812
Protein family annotation in a multiple alignment viewer.
2003
12611813
The European Bioinformatics Institute web site: a new view.
2003
12611814
Triplet repeats in human genome: distribution and their association with genes and other genomic regions.
2003
12651711
AFLPinSilico, simulating AFLP fingerprints.
2003
12691992
SamCluster: an integrated scheme for automatic discovery of sample classes using gene expression profile.
2003
12724290
Robust cluster analysis of microarray gene expression data with the number of clusters determined biologically.
2003
12724291
Reconstructing the temporal ordering of biological samples using microarray data.
2003
12724294
ALES: cell lineage analysis and mapping of developmental events.
2003
12724295
MuGeN: simultaneous exploration of multiple genomes and computer analysis results.
2003
12724296
Improvement of the GenTHREADER method for genomic fold recognition.
2003
12724298
Towards optimal views of proteins.
2003
12724299
R/qtl: QTL mapping in experimental crosses.
2003
12724300
GeneMerge--post-genomic analysis, data mining, and hypothesis testing.
2003
12724301
MARAN: normalizing micro-array data.
2003
12724302
BioEditor-simplifying macromolecular structure annotation.
2003
12724304
SCide: identification of stabilization centers in proteins.
2003
12724305
BioQuery: an object framework for building queries to biomedical databases.
2003
12724306
IPPRED: server for proteins interactions inference.
2003
12724307
FPV: fast protein visualization using Java 3D.
2003
12761052
Integrative approach for computationally inferring protein domain interactions.
2003
12761053
Corrected small-sample estimation of the Bayes error.
2003
12761056
Computation method to identify differential allelic gene expression and novel imprinted genes.
2003
12761057
Microarray standard data set and figures of merit for comparing data processing methods and experiment designs.
2003
12761058
Fuzzy C-means method for clustering microarray data.
2003
12761060
Codon pairs in the genome of Escherichia coli.
2003
12761062
Generating consensus sequences from partial order multiple sequence alignment graphs.
2003
12761063
ProPred1: prediction of promiscuous MHC Class-I binding sites.
2003
12761064
3D-Jury: a simple approach to improve protein structure predictions.
2003
12761065
Hierarchical analysis of dependency in metabolic networks.
2003
12761067
Zerg: a very fast BLAST parser library.
2003
12761068
Visual representation of database search results: the RHIMS Plot.
2003
12761069
ACGT-a comparative genomics tool.
2003
12761070
Ligand-Info, searching for similar small compounds using index profiles.
2003
12761071
CAP: conformation angles package-displaying the conformation angles of side chains in proteins.
2003
12761072
Statistical adjustment of signal censoring in gene expression experiments.
2003
12801865
Boosting for tumor classification with gene expression data.
2003
12801866
Coupled two-way clustering analysis of breast cancer and colon cancer gene expression data.
2003
12801868
Bagging to improve the accuracy of a clustering procedure.
2003
12801869
Novel clustering algorithm for microarray expression data in a truncated SVD space.
2003
12801871
Learning rule-based models of biological process from gene expression time profiles using gene ontology.
2003
12801872
Gene interaction in DNA microarray data is decomposed by information geometric measure.
2003
12801873
Classification of multiple cancer types by multicategory support vector machines using gene expression data.
2003
12801874
eXPatGen: generating dynamic expression patterns for the systematic evaluation of analytical methods.
2003
12801875
Coupled two-way clustering server.
2003
12801877
RASCAL: rapid scanning and correction of multiple sequence alignments.
2003
12801878
The small-world dynamics of tree networks and data mining in phyloinformatics.
2003
12801879
Modular modeling of cellular systems with ProMoT/Diva.
2003
12801880
A survey of the Predictive Toxicology Challenge 2000-2001.
2003
12835259
Statistical evaluation of the Predictive Toxicology Challenge 2000-2001.
2003
12835260
Toxicology analysis by means of the JSM-method.
2003
12835262
Characteristic substructures and properties in chemical carcinogens studied by the cascade model.
2003
12835263
Fast sequence clustering using a suffix array algorithm.
2003
12835265
A Bayesian network approach to operon prediction.
2003
12835266
Estimating the occurrence of false positives and false negatives in microarray studies by approximating and partitioning the empirical distribution of p-values.
2003
12835267
Unsupervised feature selection via two-way ordering in gene expression analysis.
2003
12835270
Local structure prediction with local structure-based sequence profiles.
2003
12835271
Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation.
2003
12835272
The DynDom database of protein domain motions.
2003
12835274
TableView: portable genomic data visualization.
2003
12835275
Longest biased interval and longest non-negative sum interval.
2003
12835276
GeneComber: combining outputs of gene prediction programs for improved results.
2003
12835277
Calculation of helix packing angles in protein structures.
2003
12835278
HaploBlockFinder: haplotype block analyses.
2003
12835279
Linking genotype to phenotype: the International Rice Information System (IRIS).
2003
12855438
A tool to assist the study of specific features at protein binding sites.
2003
12855466
ESTprep: preprocessing cDNA sequence reads.
2003
12874042
New normalization methods for cDNA microarray data.
2003
12874043
Exact significance levels for the maximum chi(2) method of detecting recombination.
2003
12874048
Identifying property based sequence motifs in protein families and superfamilies: application to DNase-1 related endonucleases.
2003
12874050
SATCHMO: sequence alignment and tree construction using hidden Markov models.
2003
12874053
MeKE: discovering the functions of gene products from biomedical literature via sentence alignment.
2003
12874055
The connectivity structure, giant strong component and centrality of metabolic networks.
2003
12874056
Which genetic loci have greater population assignment power?
2003
12874058
Q-Gene: processing quantitative real-time RT-PCR data.
2003
12874059
GABI-Kat SimpleSearch: a flanking sequence tag (FST) database for the identification of T-DNA insertion mutants in Arabidopsis thaliana.
2003
12874060
2HAPI: a microarray data analysis system.
2003
12874061
POAVIZ: a Partial order multiple sequence alignment visualizer.
2003
12874062
COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics.
2003
12874064
The binding interface database (BID): a compilation of amino acid hot spots in protein interfaces.
2003
12874065
AGenDA: homology-based gene prediction.
2003
12912840
STRING: finding tandem repeats in DNA sequences.
2003
14512342
Designing hardware for protein sequence analysis.
2003
14512343
Recognizing the fold of a protein structure.
2003
14512345
DDBASE2.0: updated domain database with improved identification of structural domains.
2003
14512346
Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules.
2003
14512347
CLICK and EXPANDER: a system for clustering and visualizing gene expression data.
2003
14512350
Controlling false-negative errors in microarray differential expression analysis: a PRIM approach.
2003
14512352
Automatic registration of microarray images. I. Rectangular grid.
2003
14512354
Automatic registration of microarray images. II. Hexagonal grid.
2003
14512355
The design of Jemboss: a graphical user interface to EMBOSS.
2003
14512356
An XML message broker framework for exchange and integration of microarray data.
2003
14512357
A tool-kit for cDNA microarray and promoter analysis.
2003
14512358
RVP-net: online prediction of real valued accessible surface area of proteins from single sequences.
2003
14512359
Disulfide by Design: a computational method for the rational design of disulfide bonds in proteins.
2003
14512360
Batch mode generation of residue-based diagrams of proteins.
2003
14512361
L/D Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein-ligand complexes.
2003
14512362
MutDB: annotating human variation with functionally relevant data.
2003
14512363
The EMBL sequence version archive.
2003
14512364
Soap-HT-BLAST: high throughput BLAST based on Web services.
2003
14512365
Computational detection of cis -regulatory modules.
2003
14534164
Searching for statistically significant regulatory modules.
2003
14534166
Predicting gene function in Saccharomyces cerevisiae.
2003
14534170
A suffix tree approach to the interpretation of tandem mass spectra: applications to peptides of non-specific digestion and post-translational modifications.
2003
14534180
Artificial gene networks for objective comparison of analysis algorithms.
2003
14534181
Finding subtle motifs by branching from sample strings.
2003
14534184
The shortest common supersequence problem in a microarray production setting.
2003
14534185
Finding optimal degenerate patterns in DNA sequences.
2003
14534191
Gene prediction with a hidden Markov model and a new intron submodel.
2003
14534192
A fast layout algorithm for protein interaction networks.
2003
14555620
A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens.
2003
14555622
Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data.
2003
14555624
Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays.
2003
14555628
Background rareness-based iterative multiple sequence alignment algorithm for regulatory element detection.
2003
14555629
Sequence alignment kernel for recognition of promoter regions.
2003
14555630
Application of support vector machines for T-cell epitopes prediction.
2003
14555632
A computational pipeline for protein structure prediction and analysis at genome scale.
2003
14555633
Intersect: identification and visualization of overlaps in database search results.
2003
14555634
Analysing gene expressions with GRANK.
2003
14555635
Codon adaptation index as a measure of dominating codon bias.
2003
14594704
Applying signal theory to the analysis of biomolecules.
2003
14594705
Development of an integrated laboratory information management system for the maize mapping project.
2003
14594706
A novel strategy for microarray quality control using Bayesian networks.
2003
14594707
Venn Mapping: clustering of heterologous microarray data based on the number of co-occurring differentially expressed genes.
2003
14594711
A Bayesian missing value estimation method for gene expression profile data.
2003
14594714
Kernel hierarchical gene clustering from microarray expression data.
2003
14594715
iMap: a database-driven utility to integrate and access the genetic and physical maps of maize.
2003
14594716
An unsupervised hierarchical dynamic self-organizing approach to cancer class discovery and marker gene identification in microarray data.
2003
14594719
SNP cherry picker: maximizing the chance of finding an association with a disease SNP.
2003
14594720
MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis.
2003
14594721
LDA--a java-based linkage disequilibrium analyzer.
2003
14594722
The UAB Proteomics Database.
2003
14594723
RED-T: utilizing the Ratios of Evolutionary Distances for determination of alternative phylogenetic events.
2003
14594724
Pathway studio--the analysis and navigation of molecular networks.
2003
14594725
GARBAN: genomic analysis and rapid biological annotation of cDNA microarray and proteomic data.
2003
14594726
RankViaContact: ranking and visualization of amino acid contacts.
2003
14594727
Electrophoretic data classification for phylogenetics and biostatistics.
2003
14594728
Automatic design of gene-specific sequence tags for genome-wide functional studies.
2003
14630647
MGraph: graphical models for microarray data analysis.
2003
14630649
In silico analysis reveals substantial variability in the gene contents of the gamma proteobacteria LexA-regulon.
2003
14630651
Parametric alignment of ordered trees.
2003
14630652
A simple and efficient algorithm for gene selection using sparse logistic regression.
2003
14630653
Towards the in silico identification of class II restricted T-cell epitopes: a partial least squares iterative self-consistent algorithm for affinity prediction.
2003
14630655
Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks.
2003
14630656
Metabolomics spectral formatting, alignment and conversion tools (MSFACTs).
2003
14630657
Efficient remote homology detection using local structure.
2003
14630658
Missing-value estimation using linear and non-linear regression with Bayesian gene selection.
2003
14630659
PDB file parser and structure class implemented in Python.
2003
14630660
TSGDB: a database system for tumor suppressor genes.
2003
14630661
MASV--Multiple (BLAST) Annotation System Viewer.
2003
14630662
BioWareDB: the biomedical software and database search engine.
2003
14630664
Gene Expression Dynamics Inspector (GEDI): for integrative analysis of expression profiles.
2003
14630665
BLAST++: BLASTing queries in batches.
2003
14630666
Libsequence: a C++ class library for evolutionary genetic analysis.
2003
14630667
PreP: gene expression data pre-processing.
2003
14630668
NCL: a C++ class library for interpreting data files in NEXUS format.
2003
14630669
MetaGeneAlyse: analysis of integrated transcriptional and metabolite data.
2003
14630670
Combining DNA expression with positional information to detect functional silencing of chromosomal regions.
2003
14668216
JXP4BIGI: a generalized, Java XML-based approach for biological information gathering and integration.
2003
14668218
Combining phylogenetic data with co-regulated genes to identify regulatory motifs.
2003
14668220
Algorithms for large-scale genotyping microarrays.
2003
14668223
caCORE: a common infrastructure for cancer informatics.
2003
14668224
Global snapshot of a protein interaction network-a percolation based approach.
2003
14668225
SEMEDA: ontology based semantic integration of biological databases.
2003
14668226
Susceptibility of non-linear systems as an approach to metabolic responses.
2003
14668227
Metabolic pathways in three dimensions.
2003
14668228
A random variance model for detection of differential gene expression in small microarray experiments.
2003
14668230
Using credibility intervals instead of hypothesis tests in SAGE analysis.
2003
14668232
A CART-based approach to discover emerging patterns in microarray data.
2003
14668233
The MUSC DNA Microarray Database.
2003
14668234
MREPATT: detection and analysis of exact consecutive repeats in genomic sequences.
2003
14668235
gff2aplot: Plotting sequence comparisons.
2003
14668236
MUTAGEN: multi-user tool for annotating genomes.
2003
14668237
LOX-DB-- database on lipoxygenases.
2003
14668238
GoFigure: automated Gene Ontology annotation.
2003
14668239
PRIMEX: rapid identification of oligonucleotide matches in whole genomes.
2003
14668240
KISS for STRAP: user extensions for a protein alignment editor.
2003
14668241
SNOW: standard nomenclature wizard to help searching for (bio) chemical standardized names.
2003
14668242
Machaon CVE: cluster validation for gene expression data.
2003
14668243
DnaSP, DNA polymorphism analyses by the coalescent and other methods.
2003
14668244
SPEPlip: the detection of signal peptide and lipoprotein cleavage sites.
2003
14668245
ModLoop: automated modeling of loops in protein structures.
2003
14668246
Characterizing gene sets with FuncAssociate.
2003
14668247
Identifying periodically expressed transcripts in microarray time series data.
2004
14693803
Prediction of protein subcellular locations using fuzzy k-NN method.
2004
14693804
Efficient filtering methods for clustering cDNAs with spliced sequence alignment.
2004
14693805
ClusPro: an automated docking and discrimination method for the prediction of protein complexes.
2004
14693807
An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots.
2004
14693809
MedBlast: searching articles related to a biological sequence.
2004
14693811
Adaptive stochastic-deterministic chemical kinetic simulations.
2004
14693812
VizStruct: exploratory visualization for gene expression profiling.
2004
14693813
A global test for groups of genes: testing association with a clinical outcome.
2004
14693814
A generalized likelihood ratio test to identify differentially expressed genes from microarray data.
2004
14693815
Adjustment of systematic microarray data biases.
2004
14693816
GIS: a biomedical text-mining system for gene information discovery.
2004
14693818
GRIL: genome rearrangement and inversion locator.
2004
14693819
HOMGL-comparing genelists across species and with different accession numbers.
2004
14693820
WILMA-automated annotation of protein sequences.
2004
14693821
BugView: a browser for comparing genomes.
2004
14693822
The genomic threading database.
2004
14693823
PARIS: a proteomic analysis and resources indexation system.
2004
14693824
TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter.
2004
14693825
Multi-species comparative mapping in silico using the COMPASS strategy.
2004
14734304
Computational identification of novel chitinase-like proteins in the Drosophila melanogaster genome.
2004
14734306
Phylogenomic inference of protein molecular function: advances and challenges.
2004
14734307
A comparative phylogenetic approach for dating whole genome duplication events.
2004
14734308
Prediction of locally stable RNA secondary structures for genome-wide surveys.
2004
14734309
Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network.
2004
14734310
Comparative evaluation of word composition distances for the recognition of SCOP relationships.
2004
14734312
GAPSCORE: finding gene and protein names one word at a time.
2004
14734313
Minimal cut sets in biochemical reaction networks.
2004
14734314
An empirical bayes adjustment to increase the sensitivity of detecting differentially expressed genes in microarray experiments.
2004
14734315
Graph-based clustering for finding distant relationships in a large set of protein sequences.
2004
14734316
Formalization of mouse embryo anatomy.
2004
14734318
The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources.
2004
14734319
ROSO: optimizing oligonucleotide probes for microarrays.
2004
14734320
LVB: parsimony and simulated annealing in the search for phylogenetic trees.
2004
14734321
PGTdb: a database providing growth temperatures of prokaryotes.
2004
14734322
JDotter: a Java interface to multiple dotplots generated by dotter.
2004
14734323
FGDP: functional genomics data pipeline for automated, multiple microarray data analyses.
2004
14734324
YETI: Yeast Exploration Tool Integrator.
2004
14734325
EST-PAGE--managing and analyzing EST data.
2004
14734326
APE: Analyses of Phylogenetics and Evolution in R language.
2004
14734327
AnaGram: protein function assignment.
2004
14734328
Gene Unscrambler for detangling scrambled genes in ciliates.
2004
14751966
ReDiT: Repeat Discrepancy Tagger--a shotgun assembly finishing aid.
2004
14751967
ClusterControl: a web interface for distributing and monitoring bioinformatics applications on a Linux cluster.
2004
14751976
Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms.
2004
14751981
Database model and specification of GermOnline Release 2.0, a cross-species community annotation knowledgebase on germ cell differentiation.
2004
14751982
Measuring the similarity of protein structures by means of the universal similarity metric.
2004
14751983
Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases.
2004
14751985
Java-based application framework for visualization of gene regulatory region annotations.
2004
14751988
Regression trees for regulatory element identification.
2004
14751992
Predicting protein structure classes from function predictions.
2004
14751994
Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments.
2004
14751995
Algorithms for variable length Markov chain modeling.
2004
14751999
In silico analysis of complete bacterial genomes: PCR, AFLP-PCR and endonuclease restriction.
2004
14752001
Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment.
2004
14764543
SPI: a tool for incorporating gene expression data into a four-dimensional database of Caenorhabditis elegans embryogenesis.
2004
14764544
Confirmation of data mining based predictions of protein function.
2004
14764546
CompuCell, a multi-model framework for simulation of morphogenesis.
2004
14764549
ChromoViz: multimodal visualization of gene expression data onto chromosomes using scalable vector graphics.
2004
14764551
Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP).
2004
14764552
CLENCH: a program for calculating Cluster ENriCHment using the Gene Ontology.
2004
14764555
Cluster Analyzer for Transcription Sites (CATS): a C++-based program for identifying clustered transcription factor binding sites.
2004
14764556
Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus.
2004
14764557
An evaluation of new criteria for CpG islands in the human genome as gene markers.
2004
14764558
Plotting haplotype-specific linkage disequilibrium patterns by extended haplotype homozygosity.
2004
14764566
Genes@Work: an efficient algorithm for pattern discovery and multivariate feature selection in gene expression data.
2004
14764572
Statistically rigorous automated protein annotation.
2004
14764575
Recognition and analysis of protein-coding genes in severe acute respiratory syndrome associated coronavirus.
2004
14764577
CNplot: visualizing pre-clustered networks.
2004
14871859
Open source clustering software.
2004
14871861
WebVar: A resource for the rapid estimation of relative site variability from multiple sequence alignments.
2004
14871863
Growing genetic regulatory networks from seed genes.
2004
14871865
eF-site and PDBjViewer: database and viewer for protein functional sites.
2004
14871866
CVD: the intestinal crypt/villus in situ hybridization database.
2004
14871867
2LD, GENECOUNTING and HAP: Computer programs for linkage disequilibrium analysis.
2004
14871868
ConSeq: the identification of functionally and structurally important residues in protein sequences.
2004
14871869
dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data.
2004
14871870
Bayesian mixture model based clustering of replicated microarray data.
2004
14871871
Cellware--a multi-algorithmic software for computational systems biology.
2004
14871872
Protein isoelectric point as a predictor for increased crystallization screening efficiency.
2004
14871873
NvAssign: protein NMR spectral assignment with NMRView.
2004
14871875
Recognizing names in biomedical texts: a machine learning approach.
2004
14871877
Simple sequence repeat marker loci discovery using SSR primer.
2004
14962913
Align-m--a new algorithm for multiple alignment of highly divergent sequences.
2004
14962914
VARAN: a web server for variability analysis of DNA microarray experiments.
2004
14962915
Amplicon: software for designing PCR primers on aligned DNA sequences.
2004
14962918
OBIYagns: a grid-based biochemical simulator with a parameter estimator.
2004
14962919
A general computational model of mitochondrial metabolism in a whole organelle scale.
2004
14962921
Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems.
2004
14962922
BioOptimizer: a Bayesian scoring function approach to motif discovery.
2004
14962923
A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments.
2004
14962924
Evaluating the predictability of conformational switching in RNA.
2004
14962925
A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences.
2004
14962926
Rapid 3D protein structure database searching using information retrieval techniques.
2004
14962928
GeneAnnot: comprehensive two-way linking between oligonucleotide array probesets and GeneCards genes.
2004
14962929
ParSeq: searching motifs with structural and biochemical properties.
2004
14962930
RAG: RNA-As-Graphs database--concepts, analysis, and features.
2004
14962931
Automatic prediction of protein domains from sequence information using a hybrid learning system.
2004
14962932
NetAffx Gene Ontology Mining Tool: a visual approach for microarray data analysis.
2004
14962933
GOstat: find statistically overrepresented Gene Ontologies within a group of genes.
2004
14962934
ACID: a database for microarray clone information.
2004
14962935
A comparison of scoring functions for protein sequence profile alignment.
2004
14962936
COACH: profile-profile alignment of protein families using hidden Markov models.
2004
14962937
Modeling T-cell activation using gene expression profiling and state-space models.
2004
14962938
Site2genome: locating short DNA sequences in whole genomes.
2004
14962939
ToPNet--an application for interactive analysis of expression data and biological networks.
2004
14962941
QDist--quartet distance between evolutionary trees.
2004
14962942
Application of the GA/KNN method to SELDI proteomics data.
2004
14962943
TANDEM: matching proteins with tandem mass spectra.
2004
14976030
Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation.
2004
14976032
galaxie--CGI scripts for sequence identification through automated phylogenetic analysis.
2004
14976034
Haplotypes histories as pathways of recombinations.
2004
14988100
Haplotype reconstruction from genotype data using Imperfect Phylogeny.
2004
14988101
Structural exon database, SEDB, mapping exon boundaries on multiple protein structures.
2004
14988102
Sight: automating genomic data-mining without programming skills.
2004
14988103
Multiple-sequence functional annotation and the generalized hidden Markov phylogeny.
2004
14988105
Genomic data visualization on the Web.
2004
14988106
TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments.
2004
14988107
FunMap: functional mapping of complex traits.
2004
14988108
Robust PCA and classification in biosciences.
2004
14988110
Visualization for genomics: the Microbial Genome Viewer.
2004
14988111
Improving false discovery rate estimation.
2004
14988112
GenAlyzer: interactive visualization of sequence similarities between entire genomes.
2004
14988113
'Harvester': a fast meta search engine of human protein resources.
2004
14988114
PartiGene--constructing partial genomes.
2004
14988115
SeqExpress: desktop analysis and visualization tool for gene expression experiments.
2004
14988116
Protein secondary structure: entropy, correlations and prediction.
2004
14988117
matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements.
2004
14988118
Protein backbone angle prediction with machine learning approaches.
2004
14988121
GeneCluster 2.0: an advanced toolset for bioarray analysis.
2004
14988123
Mixture models for assessing differential expression in complex tissues using microarray data.
2004
14988124
Decoupling dynamical systems for pathway identification from metabolic profiles.
2004
14988125
A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins.
2004
14988128
Why neural networks should not be used for HIV-1 protease cleavage site prediction.
2004
14988129
HMMGEP: clustering gene expression data using hidden Markov models.
2004
14988130
RAD and the RAD Study-Annotator: an approach to collection, organization and exchange of all relevant information for high-throughput gene expression studies.
2004
14990441
CisML: an XML-based format for sequence motif detection software.
2004
15001475
Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs.
2004
15001476
A Web-based design center for vector-based siRNA and siRNA cassette.
2004
15001477
Conservation analysis of small RNA genes in Escherichia coli.
2004
15033865
PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes.
2004
15033869
Phylo-VISTA: interactive visualization of multiple DNA sequence alignments.
2004
15033870
Optimization models for cancer classification: extracting gene interaction information from microarray expression data.
2004
15033871
Disulfide connectivity prediction using recursive neural networks and evolutionary information.
2004
15033872
Degrees of differential gene expression: detecting biologically significant expression differences and estimating their magnitudes.
2004
15033875
A statistical framework for combining and interpreting proteomic datasets.
2004
15033876
Omic space: coordinate-based integration and analysis of genomic phenomic interactions.
2004
15037505
Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph.
2004
15037506
Non-linear conversion between genetic and physical chromosomal distances.
2004
15037507
MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins.
2004
15037509
BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments.
2004
15037510
Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data.
2004
15037511
Identifying multiple alignment regions satisfying simple formulas and patterns.
2004
15044226
The DISOPRED server for the prediction of protein disorder.
2004
15044227
Repair-FunMap: a functional database of proteins of the DNA repair systems.
2004
15044228
DNA microarray normalization methods can remove bias from differential protein expression analysis of 2D difference gel electrophoresis results.
2004
15044229
Defining 3D residue environment in protein structures using SCORPION and FORMIGA.
2004
15044232
CEBS object model for systems biology data, SysBio-OM.
2004
15044233
Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry.
2004
15044235
ConSSeq: a web-based application for analysis of amino acid conservation based on HSSP database and within context of structure.
2004
15044236
A tool for gene expression based PubMed search through combining data sources.
2004
15044238
Hypothesis-driven approach to predict transcriptional units from gene expression data.
2004
15044239
LumberJack: a heuristic tool for sequence alignment exploration and phylogenetic inference.
2004
15044241
A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes.
2004
15044242
Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle.
2004
15044243
Supervised cluster analysis for microarray data based on multivariate Gaussian mixture.
2004
15044244
A comparison of cluster analysis methods using DNA methylation data.
2004
15044245
Simultaneous search for multiple QTL using the global optimization algorithm DIRECT.
2004
15044246
Defining transcription modules using large-scale gene expression data.
2004
15044247
Phylogenetic trees based on gene content.
2004
15044248
AliasServer: a web server to handle multiple aliases used to refer to proteins.
2004
15059813
Estimating and comparing the rates of gene discovery and expressed sequence tag (EST) frequencies in EST surveys.
2004
15059814
INCA: synonymous codon usage analysis and clustering by means of self-organizing map.
2004
15059815
Spot shape modelling and data transformations for microarrays.
2004
15059816
TRMP: a database of therapeutically relevant multiple pathways.
2004
15059817
Arby: automatic protein structure prediction using profile-profile alignment and confidence measures.
2004
15059818
Pelican: pedigree editor for linkage computer analysis.
2004
15059819
BioMercator: integrating genetic maps and QTL towards discovery of candidate genes.
2004
15059820
Drawing phylogenetic trees in LATEX and Microsoft Word.
2004
15059821
PedSplit: pedigree management for stratified analysis.
2004
15059823
SPrCY: comparison of structural predictions in the Saccharomyces cerevisiae genome.
2004
15059824
A database for management of gene expression data in situ.
2004
15059825
SCANMS: adjusting for multiple comparisons in sliding window neutrality tests.
2004
15059827
ProMode: a database of normal mode analyses on protein molecules with a full-atom model.
2004
15059828
TIP: protein backtranslation aided by genetic algorithms.
2004
15059829
Fragment assembly with short reads.
2004
15059830
Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases.
2004
15059831
Gene annotation from scientific literature using mappings between keyword systems.
2004
15059832
F2CS: FSSP to CATH and SCOP prediction server.
2004
15059833
Designing and executing scientific workflows with a programmable integrator.
2004
15059834
A weighted least-squares approach for inferring phylogenies from incomplete distance matrices.
2004
15059836
Ligand Depot: a data warehouse for ligands bound to macromolecules.
2004
15059838
MuSiC: a tool for multiple sequence alignment with constraints.
2004
15059840
Web-based kinetic modelling using JWS Online.
2004
15072998
Probabilistic nucleotide assembling method for sequencing by hybridization.
2004
15073000
STING Contacts: a web-based application for identification and analysis of amino acid contacts within protein structure and across protein interfaces.
2004
15073001
Speeding up whole-genome alignment by indexing frequency vectors.
2004
15073002
GeConT: gene context analysis.
2004
15073003
PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR.
2004
15073005
Sequence patterns derived from the automated prediction of functional residues in structurally-aligned homologous protein families.
2004
15073006
GEPIS--quantitative gene expression profiling in normal and cancer tissues.
2004
15073007
PUNS: transcriptomic- and genomic-in silico PCR for enhanced primer design.
2004
15073008
G-PRIMER: greedy algorithm for selecting minimal primer set.
2004
15073009
Data mining in bioinformatics using Weka.
2004
15073010
The PDB-Preview database: a repository of in-silico models of 'on-hold' PDB entries.
2004
15073011
Constructing an enzyme-centric view of metabolism.
2004
15073012
An examination of the conservation of surface patch polarity for proteins.
2004
15073014
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments.
2004
15073015
Alignment of RNA base pairing probability matrices.
2004
15073017
A novel method for estimating ancestral amino acid composition and its application to proteins of the Last Universal Ancestor.
2004
15073018
Supertree algorithms for ancestral divergence dates and nested taxa.
2004
15073021
An interactive triple-helical collagen builder.
2004
15073022
POLYVIEW: a flexible visualization tool for structural and functional annotations of proteins.
2004
15073023
BAPS 2: enhanced possibilities for the analysis of genetic population structure.
2004
15073024
Pedro: a configurable data entry tool for XML.
2004
15073025
ArrayNorm: comprehensive normalization and analysis of microarray data.
2004
15073026
A System for Automated Bacterial (genome) Integrated Annotation--SABIA.
2004
15087310
MathSBML: a package for manipulating SBML-based biological models.
2004
15087311
Analysis of longitudinal metabolomics data.
2004
15087313
Sfixem--graphical sequence feature display in Java.
2004
15087316
The SRS 3D module: integrating structures, sequences and features.
2004
15087318
An online database for the detection of novel archaeal sequences in human ESTs.
2004
15087319
SAD--a normalized structural alignment database: improving sequence-structure alignments.
2004
15087320
PINdb: a database of nuclear protein complexes from human and yeast.
2004
15087322
ProteoMix: an integrated and flexible system for interactively analyzing large numbers of protein sequences.
2004
15105278
GDPC: connecting researchers with multiple integrated data sources.
2004
15105279
PaVESy: Pathway Visualization and Editing System.
2004
15105280
HPID: the Human Protein Interaction Database.
2004
15117749
SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history.
2004
15117750
Efficient combination of multiple word models for improved sequence comparison.
2004
15117751
Interactively optimizing signal-to-noise ratios in expression profiling: project-specific algorithm selection and detection p-value weighting in Affymetrix microarrays.
2004
15117752
The database of epoxide hydrolases and haloalkane dehalogenases: one structure, many functions.
2004
15117755
A mixture model-based strategy for selecting sets of genes in multiclass response microarray experiments.
2004
15117756
RRE: a tool for the extraction of non-coding regions surrounding annotated genes from genomic datasets.
2004
15117758
Genome wide identification and classification of alternative splicing based on EST data.
2004
15117759
Gene-Ontology-based clustering of gene expression data.
2004
15117760
WebSIDD: server for predicting stress-induced duplex destabilized (SIDD) sites in superhelical DNA.
2004
15130924
SWAPSC: sliding window analysis procedure to detect selective constraints.
2004
15130925
LUCY2: an interactive DNA sequence quality trimming and vector removal tool.
2004
15130926
Heterogeneity detector: finding heterogeneous positions in Phred/Phrap assemblies.
2004
15130927
TargetDB: a target registration database for structural genomics projects.
2004
15130928
A collaborative database of inbred mouse strain characteristics.
2004
15130929
ASIAN: a website for network inference.
2004
15130931
THEA: ontology-driven analysis of microarray data.
2004
15130932
A statistical framework for genomic data fusion.
2004
15130933
A neural network method for prediction of beta-turn types in proteins using evolutionary information.
2004
15145798
GeneRecords: a relational database for GenBank flat file parsing and data manipulation in personal computers.
2004
15145799
Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura.
2004
15145800
FigSearch: a figure legend indexing and classification system.
2004
15145804
TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders.
2004
15145805
Thermodynamics of enzyme-catalyzed reactions--a database for quantitative biochemistry.
2004
15145806
Rainbow: a toolbox for phylogenetic supertree construction and analysis.
2004
15145807
A mixture model for estimating the local false discovery rate in DNA microarray analysis.
2004
15145810
An efficient algorithm for optimizing whole genome alignment with noise.
2004
15145812
ClutrFree: cluster tree visualization and interpretation.
2004
15145813
Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathway.
2004
15145814
Dblox: a genome-wide test for ancient segmental duplication.
2004
15145815
Pathway Miner: extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data.
2004
15145817
An object model and database for functional genomics.
2004
15145818
CoPS: Comprehensive Peptide Signature database.
2004
15166019
ICBS: a database of interactions between protein chains mediated by beta-sheet formation.
2004
15166020
Command line tool for calculating theoretical MS spectra for given sequences.
2004
15166022
BacTregulators: a database of transcriptional regulators in bacteria and archaea.
2004
15166024
Qxpak: a versatile mixed model application for genetical genomics and QTL analyses.
2004
15166025
Regulatory motif finding by logic regression.
2004
15166027
A statistical framework for the design of microarray experiments and effective detection of differential gene expression.
2004
15180939
STAR: an algorithm to Search for Tandem Approximate Repeats.
2004
15180940
Breakpoint identification and smoothing of array comparative genomic hybridization data.
2004
15201182
Voro3D: 3D Voronoi tessellations applied to protein structures.
2005
15217822
SCA db: spinocerebellar ataxia candidate gene database.
2004
15217823
HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination.
2005
15231536
Recognition of multiple patterns in unaligned sets of sequences: comparison of kernel clustering method with other methods.
2004
15231544
Conserved network motifs allow protein-protein interaction prediction.
2004
15247093
DNMAD: web-based diagnosis and normalization for microarray data.
2004
15247094
VisRD--visual recombination detection.
2004
15247095
PLPMDB: pyridoxal-5'-phosphate dependent enzymes mutants database.
2004
15247096
CSB.DB: a comprehensive systems-biology database.
2004
15247097
SARGE: a tool for creation of putative genetic networks.
2004
15247099
A computational search for box C/D snoRNA genes in the Drosophila melanogaster genome.
2004
15247100
MyWEST: my Web Extraction Software Tool for effective mining of annotations from web-based databanks.
2004
15247102
Effects of pooling mRNA in microarray class comparisons.
2004
15247103
Accuracy improvement for identifying translation initiation sites in microbial genomes.
2004
15247104
CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data.
2004
15256401
DNAfan: a software tool for automated extraction and analysis of user-defined sequence regions.
2004
15256403
Gene selection using a two-level hierarchical Bayesian model.
2004
15256404
GenePicker: replicate analysis of Affymetrix gene expression microarrays.
2004
15256405
Dimension reduction methods for microarrays with application to censored survival data.
2004
15256406
An optimized algorithm for flux estimation from isotopomer distribution in glucose metabolites.
2004
15256408
CRH_Server: an online comparative and radiation hybrid mapping server for the canine genome.
2004
15256409
Extracting gene pathway relations using a hybrid grammar: the Arizona Relation Parser.
2004
15256411
Preferred in vivo ubiquitination sites.
2004
15256413
Interactive gene-order comparison for multiple small genomes.
2004
15256414
A graph-theoretic approach to testing associations between disparate sources of functional genomics data.
2004
15256415
Importing MAGE-ML format microarray data into BioConductor.
2004
15256416
A knowledge based approach for representing and reasoning about signaling networks.
2004
15262776
Deconvolving cell cycle expression data with complementary information.
2004
15262777
Statistical modeling of sequencing errors in SAGE libraries.
2004
15262778
Into the heart of darkness: large-scale clustering of human non-coding DNA.
2004
15262779
A neural-network-based method for predicting protein stability changes upon single point mutations.
2004
15262782
Selecting biomedical data sources according to user preferences.
2004
15262785
Improved techniques for the identification of pseudogenes.
2004
15262786
Functional inference from non-random distributions of conserved predicted transcription factor binding sites.
2004
15262788
Assigning transmembrane segments to helices in intermediate-resolution structures.
2004
15262790
SCOPEC: a database of protein catalytic domains.
2004
15262791
High density linkage disequilibrium mapping using models of haplotype block variation.
2004
15262792
TraitMap: an XML-based genetic-map database combining multigenic loci and biomolecular networks.
2004
15262794
Optimal robust non-unique probe selection using Integer Linear Programming.
2004
15262798
An efficient algorithm for detecting frequent subgraphs in biological networks.
2004
15262800
Striped sheets and protein contact prediction.
2004
15262803
Predicting genetic regulatory response using classification.
2004
15262804
Protein names precisely peeled off free text.
2004
15262805
HyBrow: a prototype system for computer-aided hypothesis evaluation.
2004
15262807
Predicting protein-peptide interactions via a network-based motif sampler.
2004
15262809
Robust inference of groups in gene expression time-courses using mixtures of HMMs.
2004
15262810
Exploring Williams-Beuren syndrome using myGrid.
2004
15262813
Tracking repeats using significance and transitivity.
2004
15262814
Filtering erroneous protein annotation.
2004
15262818
IMGT/JunctionAnalysis: the first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs.
2004
15262823
SelSim: a program to simulate population genetic data with natural selection and recombination.
2004
15271777
Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data.
2004
15271778
Data exploration tools for the Gene Ontology database.
2004
15271779
ORFcurator: molecular curation of genes and gene clusters in prokaryotic organisms.
2004
15271781
GeneNetwork: an interactive tool for reconstruction of genetic networks using microarray data.
2004
15271782
ViTO: tool for refinement of protein sequence-structure alignments.
2004
15271783
Systematic analysis of snake neurotoxins' functional classification using a data warehousing approach.
2004
15271784
the JigCell model builder and run manager.
2004
15273159
NMRb: a web-site repository for raw NMR datasets.
2004
15284093
Advances to Bayesian network inference for generating causal networks from observational biological data.
2004
15284094
Discovery of meaningful associations in genomic data using partial correlation coefficients.
2004
15284096
CLANS: a Java application for visualizing protein families based on pairwise similarity.
2004
15284097
Accurate detection of aneuploidies in array CGH and gene expression microarray data.
2004
15284100
Primer design and marker clustering for multiplex SNP-IT primer extension genotyping assay using statistical modeling.
2004
15284101
DNAFSMiner: a web-based software toolbox to recognize two types of functional sites in DNA sequences.
2005
15284102
Modeling interactome: scale-free or geometric?
2004
15284103
Ontologies for behavior.
2004
15284105
DIVAA: analysis of amino acid diversity in multiple aligned protein sequences.
2004
15284106
MedlineR: an open source library in R for Medline literature data mining.
2004
15284107
PIML: the Pathogen Information Markup Language.
2005
15297293
Comparative analysis of methods for representing and searching for transcription factor binding sites.
2004
15297295
limmaGUI: a graphical user interface for linear modeling of microarray data.
2004
15297296
Highly specific prediction of phosphorylation sites in proteins.
2004
15297298
GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes.
2004
15297299
Haploview: analysis and visualization of LD and haplotype maps.
2005
15297300
Network structures and algorithms in Bioconductor.
2005
15297301
Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting.
2004
15297302
How many samples are needed to build a classifier: a general sequential approach.
2005
15297303
Gene clustering by latent semantic indexing of MEDLINE abstracts.
2005
15308538
BioLingua: a programmable knowledge environment for biologists.
2005
15308539
Outcome signature genes in breast cancer: is there a unique set?
2005
15308542
SNP Chart: an integrated platform for visualization and interpretation of microarray genotyping data.
2005
15308543
Microarray data mining with visual programming.
2005
15308546
BlastAlign: a program that uses blast to align problematic nucleotide sequences.
2005
15310559
DisProt: a database of protein disorder.
2005
15310560
Supervised identification of allergen-representative peptides for in silico detection of potentially allergenic proteins.
2005
15319257
Simulating genetic networks made easy: network construction with simple building blocks.
2005
15319258
A method for estimating stochastic noise in large genetic regulatory networks.
2005
15319259
Similarity of position frequency matrices for transcription factor binding sites.
2005
15319260
MCQTL: multi-allelic QTL mapping in multi-cross design.
2005
15319261
DWE: discriminating word enumerator.
2005
15333453
HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms.
2005
15333454
OntologyTraverser: an R package for GO analysis.
2005
15333457
A new algorithm for detecting low-complexity regions in protein sequences.
2005
15333459
Filtering of ineffective siRNAs and improved siRNA design tool.
2005
15333460
Missing value estimation for DNA microarray gene expression data: local least squares imputation.
2005
15333461
Recombination Analysis Tool (RAT): a program for the high-throughput detection of recombination.
2005
15333462
Dual-genome primer design for construction of DNA microarrays.
2005
15333463
ProViz: protein interaction visualization and exploration.
2005
15347570
BarleyExpress: a web-based submission tool for enriched microarray database annotations.
2005
15347571
Detecting overlapping coding sequences with pairwise alignments.
2005
15347574
Evaluating putative chimeric sequences from PCR-amplified products.
2005
15347575
easyLINKAGE: a PERL script for easy and automated two-/multi-point linkage analyses.
2005
15347576
Tracker: continuous HMMER and BLAST searching.
2005
15347577
The SSEA server for protein secondary structure alignment.
2005
15347578
Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics.
2005
15347579
SNAP: workbench management tool for evolutionary population genetic analysis.
2005
15353448
Capturing biological information with class-responsibility-collaboration cards.
2005
15353449
iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions.
2005
15353450
A Bayesian approach to reconstructing genetic regulatory networks with hidden factors.
2005
15353451
VizRank: finding informative data projections in functional genomics by machine learning.
2005
15358614
Human-Mouse Gene Searcher: a tool to assist discovery of malformation-associated genes by using phenotype databases.
2005
15358615
Discovery of stable and significant binding motif pairs from PDB complexes and protein interaction datasets.
2005
15374856
RAP: a new computer program for de novo identification of repeated sequences in whole genomes.
2005
15374857
Online synonymous codon usage analyses with the ade4 and seqinR packages.
2005
15374859
Reliability analysis of microarray data using fuzzy c-means and normal mixture modeling based classification methods.
2005
15374860
tPatternHunter: gapped, fast and sensitive translated homology search.
2005
15374861
A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis.
2005
15374862
ESTminer: a Web interface for mining EST contig and cluster databases.
2005
15374864
Identifying time-lagged gene clusters using gene expression data.
2005
15374868
Prediction of splice sites with dependency graphs and their expanded bayesian networks.
2005
15374869
MAP-O-MAT: internet-based linkage mapping.
2005
15374870
VarMixt: efficient variance modelling for the differential analysis of replicated gene expression data.
2005
15374871
An experimental evaluation of a loop versus a reference design for two-channel microarrays.
2005
15374872
Iterative cluster analysis of protein interaction data.
2005
15374873
Clann: investigating phylogenetic information through supertree analyses.
2005
15374874
PhenomicDB: a multi-species genotype/phenotype database for comparative phenomics.
2005
15374875
A memory-efficient algorithm for multiple sequence alignment with constraints.
2005
15374876
The Los Alamos hepatitis C sequence database.
2005
15377502
SNPP: automating large-scale SNP genotype data management.
2005
15377503
A simple and fast secondary structure prediction method using hidden neural networks.
2005
15377504
HaploPainter: a tool for drawing pedigrees with complex haplotypes.
2005
15377505
RALEE--RNA ALignment editor in Emacs.
2005
15377506
RDP2: recombination detection and analysis from sequence alignments.
2005
15377507
Predicting protein functions with message passing algorithms.
2005
15377508
wEMBOSS: a web interface for EMBOSS.
2005
15388516
Stepwise detection of recombination breakpoints in sequence alignments.
2005
15388518
Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification.
2005
15388519
APART: automated preprocessing for NMR assignments with reduced tedium.
2005
15388520
CIS: compound importance sampling method for protein-DNA binding site p-value estimation.
2005
15454407
Modelling cellular systems with PySCeS.
2005
15454409
Improving promoter prediction for the NNPP2.2 algorithm: a case study using Escherichia coli DNA sequences.
2005
15454410
Seq2Struct: a resource for establishing sequence-structure links.
2005
15454411
arrayMagic: two-colour cDNA microarray quality control and preprocessing.
2005
15454413
TFExplorer: integrated analysis database for predicted transcription regulatory elements.
2005
15466909
BagBoosting for tumor classification with gene expression data.
2004
15466910
GenomeMixer: a complex genetic cross simulator.
2004
15477491
A simple procedure for estimating the false discovery rate.
2005
15479710
Database driven test case generation for protein-protein docking.
2005
15479711
Understanding protein dispensability through machine-learning analysis of high-throughput data.
2005
15479713
Circular genome visualization and exploration using CGView.
2005
15479716
PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis.
2005
15501914
HyPhy: hypothesis testing using phylogenies.
2005
15509596
COPS--cis/trans peptide bond conformation prediction of amino acids on the basis of secondary structure information.
2005
15509597
LabArray: real-time imaging and analytical tool for microarrays.
2005
15509598
MedKit: a helper toolkit for automatic mining of MEDLINE/PubMed citations.
2005
15509599
Implementation of a gene expression index calculation method based on the PDNN model.
2005
15509605
Predicting gene function through systematic analysis and quality assessment of high-throughput data.
2005
15531615
ESTminer: a suite of programs for gene and allele identification.
2005
15531616
SpliceMachine: predicting splice sites from high-dimensional local context representations.
2005
15564294
Wnt pathway curation using automated natural language processing: combining statistical methods with partial and full parse for knowledge extraction.
2005
15564295
A nearest-neighboring-end algorithm for genetic mapping.
2005
15564296
DSEARCH: sensitive database searching using distributed computing.
2005
15564297
Procom: a web-based tool to compare multiple eukaryotic proteomes.
2005
15564299
Evaluation of iterative alignment algorithms for multiple alignment.
2005
15564300
Constructing ontology-driven protein family databases.
2005
15564301
The ArrayExpress gene expression database: a software engineering and implementation perspective.
2005
15564302
Accelerated off-target search algorithm for siRNA.
2005
15564304
Serial SimCoal: a population genetics model for data from multiple populations and points in time.
2005
15564305
VitaPad: visualization tools for the analysis of pathway data.
2005
15564306
The carbohydrate sequence markup language (CabosML): an XML description of carbohydrate structures.
2005
15564307
A graph based algorithm for generating EST consensus sequences.
2005
15572463
MACAT--microarray chromosome analysis tool.
2005
15572464
YODA: selecting signature oligonucleotides.
2005
15572465
SYMMETREE: whole-tree analysis of differential diversification rates.
2005
15572466
Correlation of amino acid preference and mammalian viral genome type.
2005
15572467
Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster.
2005
15572468
Synergy of human Pol II core promoter elements revealed by statistical sequence analysis.
2005
15572469
Optimal number of features as a function of sample size for various classification rules.
2005
15572470
BIAS: Bioinformatics Integrated Application Software.
2005
15572471
Generalized Venn diagrams: a new method of visualizing complex genetic set relations.
2005
15572472
Detecting interspecific recombination with a pruned probabilistic divergence measure.
2005
15572473
Porter: a new, accurate server for protein secondary structure prediction.
2005
15585524
CLUSTAG: hierarchical clustering and graph methods for selecting tag SNPs.
2005
15585525
Support vector machines for separation of mixed plant-pathogen EST collections based on codon usage.
2005
15585526
OLIN: optimized normalization, visualization and quality testing of two-channel microarray data.
2005
15585527
RBT--a tool for building refined Buneman trees.
2005
15585529
A score matrix to reveal the hidden links in glycans.
2005
15585530
HykGene: a hybrid approach for selecting marker genes for phenotype classification using microarray gene expression data.
2005
15585531
TERMINUS--Telomeric End-Read Mining IN Unassembled Sequences.
2005
15585532
Statistical detection of chromosomal homology using shared-gene density alone.
2005
15585535
In silico fine-mapping: narrowing disease-associated loci by intergenomics.
2005
15591355
Highly specific and accurate selection of siRNAs for high-throughput functional assays.
2005
15591357
HESAS: HERVs Expression and Structure Analysis System.
2005
15591358
Statistical evaluation and comparison of a pairwise alignment algorithm that a priori assigns the number of gaps rather than employing gap penalties.
2005
15591359
SITEBLAST--rapid and sensitive local alignment of genomic sequences employing motif anchors.
2005
15598827
Dynamic simulation of protein complex formation on a genomic scale.
2005
15598828
CARHTA GENE: multipopulation integrated genetic and radiation hybrid mapping.
2005
15598829
The WHy domain mediates the response to desiccation in plants and bacteria.
2005
15598830
MultiPLX: automatic grouping and evaluation of PCR primers.
2005
15598831
DbW: automatic update of a functional family-specific multiple alignment.
2005
15598832
Differential gene expression detection using penalized linear regression models: the improved SAM statistics.
2005
15598833
LS Bound based gene selection for DNA microarray data.
2005
15598834
Boolean relationships among genes responsive to ionizing radiation in the NCI 60 ACDS.
2005
15598836
Implicit motif distribution based hybrid computational kernel for sequence classification.
2005
15598837
TargetFinder: a software for antisense oligonucleotide target site selection based on MAST and secondary structures of target mRNA.
2005
15598838
Visualizing information across multidimensional post-genomic structured and textual databases.
2005
15598839
GeneContent: software for whole-genome phylogenetic analysis.
2005
15598840
Investigating the dynamic behavior of biochemical networks using model families.
2005
15604106
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees.
2005
15608047
An integrated tool for microarray data clustering and cluster validity assessment.
2005
15608048
Improved prediction of protein-protein binding sites using a support vector machines approach.
2005
15613384
An enhanced Java graph applet interface for visualizing interactomes.
2005
15613388
GMD@CSB.DB: the Golm Metabolome Database.
2005
15613389
GPSDB: a new database for synonyms expansion of gene and protein names.
2005
15613390
A framework for scientific data modeling and automated software development.
2005
15613391
PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces.
2005
15613393
Bloader--a batch loader application for MIAMExpress.
2005
15613394
M-ZDOCK: a grid-based approach for Cn symmetric multimer docking.
2005
15613396
Expa: a program for calculating extreme pathways in biochemical reaction networks.
2005
15613397
Mapping SNPs to protein sequence and structure data.
2005
15613399
Exploring the diversity of complex metabolic networks.
2005
15613400
ALOHOMORA: a tool for linkage analysis using 10K SNP array data.
2005
15647291
ProtTest: selection of best-fit models of protein evolution.
2005
15647292
Significance analysis of functional categories in gene expression studies: a structured permutation approach.
2005
15647293
Selecton: a server for detecting evolutionary forces at a single amino-acid site.
2005
15647294
Robust estimation of protein expression ratios with lysate microarray technology.
2005
15647295
Transcription factor binding site identification using the self-organizing map.
2005
15647296
Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa).
2005
15647298
GOAnno: GO annotation based on multiple alignment.
2005
15647299
Detecting clusters of different geometrical shapes in microarray gene expression data.
2005
15647300
MAGIC Tool: integrated microarray data analysis.
2005
15647303
AGML Central: web based gel proteomic infrastructure.
2005
15647304
On the quality of tree-based protein classification.
2005
15647305
Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%.
2005
15657094
PIBASE: a comprehensive database of structurally defined protein interfaces.
2005
15657096
Dynamic model based algorithms for screening and genotyping over 100 K SNPs on oligonucleotide microarrays.
2005
15657097
Mtreemix: a software package for learning and using mixture models of mutagenetic trees.
2005
15657098
Online predicted human interaction database.
2005
15657099
Integrative data analysis for functional prediction: a multi-objective optimization approach.
2005
15657100
IntegratedMap: a Web interface for integrating genetic map data.
2005
15657101
Use of within-array replicate spots for assessing differential expression in microarray experiments.
2005
15657102
EPIMHC: a curated database of MHC-binding peptides for customized computational vaccinology.
2005
15657103
Testing association of a pathway with survival using gene expression data.
2005
15657105
Prediction of unfolded segments in a protein sequence based on amino acid composition.
2005
15657106
Topology of small-world networks of protein-protein complex structures.
2005
15659419
Gene finding for the helical cytokines.
2005
15661800
TruMatch--a BLAST post-processor that identifies bona fide sequence matches to genome assemblies.
2005
15671115
Investigating metabolite essentiality through genome-scale analysis of Escherichia coli production capabilities.
2005
15671116
A linear programming approach for identifying a consensus sequence on DNA sequences.
2005
15671117
Computational identification of human mitochondrial proteins based on homology to yeast mitochondrially targeted proteins.
2005
15671119
PERMOL: restraint-based protein homology modeling using DYANA or CNS.
2005
15671120
Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum.
2005
15673564
Molecular decomposition of complex clinical phenotypes using biologically structured analysis of microarray data.
2005
15677704
A grid layout algorithm for automatic drawing of biochemical networks.
2005
15677705
ProfDist: a tool for the construction of large phylogenetic trees based on profile distances.
2005
15677706
TreeScan: a bioinformatic application to search for genotype/phenotype associations using haplotype trees.
2005
15681571
DictyMOLD-a Dictyostelium discoideum genome browser database.
2005
15681572
CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays.
2005
15684227
PROTEIOS: an open source proteomics initiative.
2005
15691852
SNPsFinder--a web-based application for genome-wide discovery of single nucleotide polymorphisms in microbial genomes.
2005
15691853
An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes.
2005
15691854
Evaluation of the gene-specific dye bias in cDNA microarray experiments.
2005
15691855
Empirical Bayes screening of many p-values with applications to microarray studies.
2005
15691856
SpecAlign--processing and alignment of mass spectra datasets.
2005
15691857
Identification of GPI anchor attachment signals by a Kohonen self-organizing map.
2005
15691858
Efficient implementation of a generalized pair hidden Markov model for comparative gene finding.
2005
15691859
BioIE: extracting informative sentences from the biomedical literature.
2005
15691860
SuperDrug: a conformational drug database.
2005
15691861
DNA polymorphism detector: an automated tool that searches for allelic matches in public databases for discrepancies found in clone or cDNA sequences.
2005
15695424
PSLpred: prediction of subcellular localization of bacterial proteins.
2005
15699023
Time accelerated Monte Carlo simulations of biological networks using the binomial tau-leap method.
2005
15699024
A comparative analysis of relative occurrence of transcription factor binding sites in vertebrate genomes and gene promoter areas.
2005
15699025
MPSS: an integrated database system for surveying a set of proteins.
2005
15699026
ExPrimer: to design primers from exon--exon junctions.
2005
15699028
Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites.
2005
15701681
Protein function prediction using the Protein Link EXplorer (PLEX).
2005
15701682
The Graphical Query Language: a tool for analysis of gene expression time-courses.
2005
15701683
Bio-Object, a stochastic simulator for post-transcriptional regulation.
2005
15705653
Estimating cancer survival and clinical outcome based on genetic tumor progression scores.
2005
15705654
PowerMarker: an integrated analysis environment for genetic marker analysis.
2005
15705655
MamMiBase: a mitochondrial genome database for mammalian phylogenetic studies.
2005
15713730
FastContact: rapid estimate of contact and binding free energies.
2005
15713734
Datamonkey: rapid detection of selective pressure on individual sites of codon alignments.
2005
15713735
Applications of beta-mixture models in bioinformatics.
2005
15713737
MtbRegList, a database dedicated to the analysis of transcriptional regulation in Mycobacterium tuberculosis.
2005
15722376
GMAP: a genomic mapping and alignment program for mRNA and EST sequences.
2005
15728110
A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length.
2005
15728117
AutoMotif server: prediction of single residue post-translational modifications in proteins.
2005
15728119
PatGen--a consolidated resource for searching genetic patent sequences.
2005
15728120
PLATCOM: a Platform for Computational Comparative Genomics.
2005
15731206
Predicting a set of minimal free energy RNA secondary structures common to two sequences.
2005
15731207
Self-organizing and self-correcting classifications of biological data.
2005
15731209
Object-oriented biological system integration: a SARS coronavirus example.
2005
15731211
DATF: a database of Arabidopsis transcription factors.
2005
15731212
Using evolutionary Expectation Maximization to estimate indel rates.
2005
15731213
A web-based tool for principal component and significance analysis of microarray data.
2005
15734774
Protein structure topological comparison, discovery and matching service.
2005
15741246
Prediction of subcellular localization using sequence-biased recurrent networks.
2005
15746276
Integration of GO annotations in Correspondence Analysis: facilitating the interpretation of microarray data.
2005
15746280
Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information.
2005
15746281
Mega2: data-handling for facilitating genetic linkage and association analyses.
2005
15746282
Fast tandem mass spectra-based protein identification regardless of the number of spectra or potential modifications examined.
2005
15746284
CoC: a database of universally conserved residues in protein folds.
2005
15746286
ADAPT: a database of affymetrix probesets and transcripts.
2005
15746287
ArrayCyGHt: a web application for analysis and visualization of array-CGH data.
2005
15746288
WebAllergen: a web server for predicting allergenic proteins.
2005
15746289
Gene-Expression Omnibus integration and clustering tools in SeqExpress.
2005
15746290
Multiple flexible structure alignment using partial order graphs.
2005
15746292
PSIbase: a database of Protein Structural Interactome map (PSIMAP).
2005
15749693
MIPS bacterial genomes functional annotation benchmark dataset.
2005
15769832
Using the biological taxonomy to access biological literature with PathBinderH.
2005
15769838
A fractional programming approach to efficient DNA melting temperature calculation.
2005
15769839
SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs).
2005
15769840
Identification and measurement of neighbor-dependent nucleotide substitution processes.
2005
15769841
Mining SARS-CoV protease cleavage data using non-orthogonal decision trees: a novel method for decisive template selection.
2005
15797903
Quasi-consensus-based comparison of profile hidden Markov models for protein sequences.
2005
15797916
A comprehensive and non-redundant database of protein domain movements.
2005
15802286
A stochastic differential equation model for quantifying transcriptional regulatory network in Saccharomyces cerevisiae.
2005
15802287
BEST: binding-site estimation suite of tools.
2005
15814553
EGene: a configurable pipeline generation system for automated sequence analysis.
2005
15814554
Prediction of protein solvent accessibility using fuzzy k-nearest neighbor method.
2005
15814555
twilight; a Bioconductor package for estimating the local false discovery rate.
2005
15817688
Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge.
2005
15817689
Convergent Island Statistics: a fast method for determining local alignment score significance.
2005
15817690
Stochastic reaction-diffusion simulation with MesoRD.
2005
15817692
NodMutDB: a database for genes and mutants involved in symbiosis.
2005
15817696
Modeling and simulation of cancer immunoprevention vaccine.
2005
15817697
STARS: statistics on inter-atomic distances and torsion angles in protein secondary structures.
2005
15827078
Visualizing profile-profile alignment: pairwise HMM logos.
2005
15827079
Three-dimensional computation of atom depth in complex molecular structures.
2005
15827080
LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources.
2005
15827081
EMPReSS: European mouse phenotyping resource for standardized screens.
2005
15827082
Meta-DP: domain prediction meta-server.
2005
15840708
Differential network expression during drug and stress response.
2005
15840709
Donuts, scratches and blanks: robust model-based segmentation of microarray images.
2005
15845656
MollDE: a homology modeling framework you can click with.
2005
15845657
Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces.
2005
15855251
Discovering patterns to extract protein-protein interactions from the literature: Part II.
2005
15890744
Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure.
2005
15905274
MFAML: a standard data structure for representing and exchanging metabolic flux models.
2005
15905275
CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data.
2005
15905276
Prediction error estimation: a comparison of resampling methods.
2005
15905277
Semi-supervised protein classification using cluster kernels.
2005
15905279
Inferring protein-protein interactions through high-throughput interaction data from diverse organisms.
2005
15905281
Computational cluster validation in post-genomic data analysis.
2005
15914541
Efficient recognition of folds in protein 3D structures by the improved PRIDE algorithm.
2005
15914542
Comparative interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map).
2005
15914543
Resmap: automated representation of macromolecular interfaces as two-dimensional networks.
2005
15914544
Mining genetic epidemiology data with Bayesian networks I: Bayesian networks and example application (plasma apoE levels).
2005
15914545
A latent variable model for chemogenomic profiling.
2005
15919724
Functional annotation from predicted protein interaction networks.
2005
15919725
SECISDesign: a server to design SECIS-elements within the coding sequence.
2005
15919727
MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms.
2005
15919728
COREX/BEST server: a web browser-based program that calculates regional stability variations within protein structures.
2005
15923205
HYPROSP II--a knowledge-based hybrid method for protein secondary structure prediction based on local prediction confidence.
2005
15932901
PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes.
2005
15932902
Statistics of protein library construction.
2005
15932904
A new progressive-iterative algorithm for multiple structure alignment.
2005
15941743
A quantitative determination of multi-protein interactions by the analysis of confocal images using a pixel-by-pixel assessment algorithm.
2005
15947019
HEGESMA: genome search meta-analysis and heterogeneity testing.
2005
15955784
The predictive power of the CluSTr database.
2005
15961444
ANOSVA: a statistical method for detecting splice variation from expression data.
2005
15961447
Detecting coevolving amino acid sites using Bayesian mutational mapping.
2005
15961449
A procedure for assessing GO annotation consistency.
2005
15961450
PILER: identification and classification of genomic repeats.
2005
15961452
Clustering short time series gene expression data.
2005
15961453
CaSPredictor: a new computer-based tool for caspase substrate prediction.
2005
15961454
Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli.
2005
15961457
Mining coherent dense subgraphs across massive biological networks for functional discovery.
2005
15961460
Modeling the organization of the WUSCHEL expression domain in the shoot apical meristem.
2005
15961462
An HMM posterior decoder for sequence feature prediction that includes homology information.
2005
15961464
High-recall protein entity recognition using a dictionary.
2005
15961466
A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences.
2005
15961467
Improved detection of DNA motifs using a self-organized clustering of familial binding profiles.
2005
15961468
A systematic approach for comprehensive T-cell epitope discovery using peptide libraries.
2005
15961469
Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps.
2005
15961472
Computing the P-value of the information content from an alignment of multiple sequences.
2005
15961473
In silico identification of functional regions in proteins.
2005
15961475
De novo identification of repeat families in large genomes.
2005
15961478
Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity.
2005
15961479
RASE: recognition of alternatively spliced exons in C.elegans.
2005
15961480
Families of membranous proteins can be characterized by the amino acid composition of their transmembrane domains.
2005
15961481
Kernel methods for predicting protein-protein interactions.
2005
15961482
Search for folding nuclei in native protein structures.
2005
15961484
Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution.
2005
15961486
Robust classification modeling on microarray data using misclassification penalized posterior.
2005
15961487
How old is your fold?
2005
15961490
Experimental design for three-color and four-color gene expression microarrays.
2005
15961491
Protein function prediction via graph kernels.
2005
15961493
Automatic detection of subsystem/pathway variants in genome analysis.
2005
15961494
ExonHunter: a comprehensive approach to gene finding.
2005
15961499
Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithms.
2005
15961501
YeastHub: a semantic web use case for integrating data in the life sciences domain.
2005
15961502
Conservative extraction of over-represented extensible motifs.
2005
15961503
A heuristic approach for detecting RNA H-type pseudoknots.
2005
15994188
The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships.
2005
15994190
TICO: a tool for improving predictions of prokaryotic translation initiation sites.
2005
15994191
MicroRNA identification based on sequence and structure alignment.
2005
15994192
P-cats: prediction of catalytic residues in proteins from their tertiary structures.
2005
15994193
TO-GO: a Java-based Gene Ontology navigation environment.
2005
15994194
SynBrowse: a synteny browser for comparative sequence analysis.
2005
15994196
Local modeling of global interactome networks.
2005
15998662
A precise and scalable method for querying genes in chromosomal banding regions based on cytogenetic annotations.
2005
15998663
Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs.
2005
15998664
Rapid simulation and analysis of isotopomer distributions using constraints based on enzyme mechanisms: an example from HT29 cancer cells.
2005
16002431
A parsimonious tree-grow method for haplotype inference.
2005
16002432
Applying GIFT, a Gene Interactions Finder in Text, to fly literature.
2005
16014369
easyLINKAGE-Plus--automated linkage analyses using large-scale SNP data.
2005
16014370
Integration of metabolic networks and gene expression in virtual reality.
2005
16020466
DEPD: a novel database for differentially expressed proteins.
2005
16020467
goCluster integrates statistical analysis and functional interpretation of microarray expression data.
2005
16020468
simuPOP: a forward-time population genetics simulation environment.
2005
16020469
A tractable probabilistic model for Affymetrix probe-level analysis across multiple chips.
2005
16020470
SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures.
2005
16020471
Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction.
2005
16020472
MAVisto: a tool for the exploration of network motifs.
2005
16020473
PACdb: PolyA Cleavage Site and 3'-UTR Database.
2005
16030070
DBToolkit: processing protein databases for peptide-centric proteomics.
2005
16030071
GeneCruiser: a web service for the annotation of microarray data.
2005
16030072
A multicellular systems biology model predicts epidermal morphology, kinetics and Ca2+ flow.
2005
16030073
HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif.
2005
16030074
Resolving abbreviations to their senses in Medline.
2005
16037121
BlastXtract--a new way of exploring translated searches.
2005
16046492
Extraction of regulatory gene/protein networks from Medline.
2006
16046493
TileMap: create chromosomal map of tiling array hybridizations.
2005
16046496
Automated Microarray Image Analysis Toolbox for MATLAB.
2005
16046497
A statistical model for HIV-1 sequence classification using the subtype analyser (STAR).
2005
16046498
SpA: web-accessible spectratype analysis: data management, statistical analysis and visualization.
2005
16051675
JIGSAW: integration of multiple sources of evidence for gene prediction.
2005
16076884
GenColors: accelerated comparative analysis and annotation of prokaryotic genomes at various stages of completeness.
2005
16076887
Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis.
2005
16076888
Friend, an integrated analytical front-end application for bioinformatics.
2005
16076889
WebACT--an online companion for the Artemis Comparison Tool.
2005
16076890
Study of coordinative gene expression at the biological process level.
2005
16076891
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research.
2005
16081474
Bifurcation discovery tool.
2005
16081475
ProRule: a new database containing functional and structural information on PROSITE profiles.
2005
16091411
ROCR: visualizing classifier performance in R.
2005
16096348
A geometric invariant-based framework for the analysis of protein conformational space.
2005
16096349
Simple decision rules for classifying human cancers from gene expression profiles.
2005
16105897
MESHI: a new library of Java classes for molecular modeling.
2005
16105898
Combining phylogenetic motif discovery and motif clustering to predict co-regulated genes.
2005
16105899
Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap.
2005
16105900
Bias in the estimation of false discovery rate in microarray studies.
2005
16105901
ORIOGEN: order restricted inference for ordered gene expression data.
2005
16109745
A statistical model providing comprehensive predictions for the mRNA differential display.
2005
16109746
Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes.
2005
16109747
Structure clustering features on the Sfold Web server.
2005
16109749
Detecting single-feature polymorphisms using oligonucleotide arrays and robustified projection pursuit.
2005
16118260
PAWE-3D: visualizing power for association with error in case-control genetic studies of complex traits.
2005
16123114
Calibrating E-values for hidden Markov models using reverse-sequence null models.
2005
16123115
HAPLOT: a graphical comparison of haplotype blocks, tagSNP sets and SNP variation for multiple populations.
2005
16131520
Detection of DNA copy number alterations using penalized least squares regression.
2005
16131523
Network constrained clustering for gene microarray data.
2005
16141248
BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing.
2005
16141249
The SuMo server: 3D search for protein functional sites.
2005
16141250
A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings.
2005
16141251
Optimal word sizes for dissimilarity measures and estimation of the degree of dissimilarity between DNA sequences.
2005
16144805
Inference of transcriptional regulatory network by two-stage constrained space factor analysis.
2005
16144806
pTARGET [corrected] a new method for predicting protein subcellular localization in eukaryotes.
2005
16144808
Generating Boolean networks with a prescribed attractor structure.
2005
16150807
BADASP: predicting functional specificity in protein families using ancestral sequences.
2005
16159912
A comparison study: applying segmentation to array CGH data for downstream analyses.
2005
16159913
MILVA: an interactive tool for the exploration of multidimensional microarray data.
2005
16159914
METIS: multiple extraction techniques for informative sentences.
2005
16159915
Design of long oligonucleotide probes for functional gene detection in a microbial community.
2005
16159916
Using information theory to search for co-evolving residues in proteins.
2005
16159918
Analysis of mass spectral serum profiles for biomarker selection.
2005
16159919
A method for detection of differential gene expression in the presence of inter-individual variability in response.
2005
16159922
ChemDB: a public database of small molecules and related chemoinformatics resources.
2005
16174682
Classification of microarrays to nearest centroids.
2005
16174683
Prediction of the coupling specificity of GPCRs to four families of G-proteins using hidden Markov models and artificial neural networks.
2005
16174684
Doelan: a solution for quality control monitoring of microarray production.
2005
16179358
SNPselector: a web tool for selecting SNPs for genetic association studies.
2005
16179360
Mapping PDB chains to UniProtKB entries.
2005
16188924
MACiE: a database of enzyme reaction mechanisms.
2005
16188925
HapSim: a simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients.
2005
16188927
A friendly statistics package for microarray analysis.
2005
16188932
Computational discovery of transcriptional regulatory rules.
2005
16204087
A fully Bayesian model to cluster gene-expression profiles.
2005
16204092
Computing recombination networks from binary sequences.
2005
16204096
Discriminating between rate heterogeneity and interspecific recombination in DNA sequence alignments with phylogenetic factorial hidden Markov models.
2005
16204097
Association Cluster Detector: a tool for heuristic detection of significance clusters in whole-genome scans.
2005
16204099
Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E.coli.
2005
16204102
Knowledge-based framework for hypothesis formation in biochemical networks.
2005
16204106
Decomposing protein networks into domain-domain interactions.
2005
16204107
RNA secondary structural alignment with conditional random fields.
2005
16204111
Fast maximum-likelihood refinement of electron microscopy images.
2005
16204112
Implementing the iHOP concept for navigation of biomedical literature.
2005
16204114
DPDB: a database for the storage, representation and analysis of polymorphism in the Drosophila genus.
2005
16204116
Web servicing the biological office.
2005
16204117
Adding some SPICE to DAS.
2005
16204122
SIMAP--the similarity matrix of proteins.
2005
16204123
ARTS: alignment of RNA tertiary structures.
2005
16204124
Predicting protein stability changes from sequences using support vector machines.
2005
16204125
Evaluating the usefulness of protein structure models for molecular replacement.
2005
16204129
Non-coding RNAs in Ciona intestinalis.
2005
16204130
Pcons5: combining consensus, structural evaluation and fold recognition scores.
2005
16204344
Sample size determination for the false discovery rate.
2005
16204346
Discrimination of outer membrane proteins using support vector machines.
2005
16204348
CREDO: a web-based tool for computational detection of conserved sequence motifs in noncoding sequences.
2005
16204349
GARSA: genomic analysis resources for sequence annotation.
2005
16210424
Syntons, metabolons and interactons: an exact graph-theoretical approach for exploring neighbourhood between genomic and functional data.
2005
16216829
The influence of missing value imputation on detection of differentially expressed genes from microarray data.
2005
16216830
ATID: a web-oriented database for collection of publicly available alternative translational initiation events.
2005
16216831
Identifying genes from up-down properties of microarray expression series.
2005
16221984
A novel algorithm and web-based tool for comparing two alternative phylogenetic trees.
2006
16234319
OligoFaktory: a visual tool for interactive oligonucleotide design.
2006
16239305
Integrating time-course microarray gene expression profiles with cytotoxicity for identification of biomarkers in primary rat hepatocytes exposed to cadmium.
2006
16249259
Automatic term list generation for entity tagging.
2006
16249261
A generic motif discovery algorithm for sequential data.
2006
16257985
Intelligent client for integrating bioinformatics services.
2006
16257987
libSRES: a C library for stochastic ranking evolution strategy for parameter estimation.
2006
16267082
SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles.
2006
16267083
BioThesaurus: a web-based thesaurus of protein and gene names.
2006
16267085
Improved spliced alignment from an information theoretic approach.
2006
16267086
Nexplorer: phylogeny-based exploration of sequence family data.
2006
16267087
An efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria.
2006
16269414
LogoBar: bar graph visualization of protein logos with gaps.
2006
16269415
COMPAM :visualization of combining pairwise alignments for multiple genomes.
2006
16269416
PRODISTIN Web Site: a tool for the functional classification of proteins from interaction networks.
2006
16269417
ClaNC: point-and-click software for classifying microarrays to nearest centroids.
2006
16269418
Pathway recognition and augmentation by computational analysis of microarray expression data.
2006
16278238
Residue-rotamer-reduction algorithm for the protein side-chain conformation problem.
2006
16278239
PCP: a program for supervised classification of gene expression profiles.
2006
16278240
Intervention in a family of Boolean networks.
2006
16286362
Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites.
2006
16287937
Classification of microarray data with factor mixture models.
2006
16287938
Improved prediction of bacterial transcription start sites.
2006
16287942
Gene Time E{chi}pression Warper: a tool for alignment, template matching and visualization of gene expression time series.
2006
16293669
Enhanced recognition of protein transmembrane domains with prediction-based structural profiles.
2006
16293670
'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments.
2006
16301202
Accurate anchoring alignment of divergent sequences.
2006
16301203
The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling.
2006
16301204
Incorporation of splice site probability models for non-canonical introns improves gene structure prediction in plants.
2005
16306388
The choice of optimal distance measure in genome-wide datasets.
2005
16306389
DNA assembly with gaps (Dawg): simulating sequence evolution.
2005
16306390
Mining sequence annotation databanks for association patterns.
2005
16306393
Bioinformatic analysis of exon repetition, exon scrambling and trans-splicing in humans.
2006
16308355
Gene network inference from incomplete expression data: transcriptional control of hematopoietic commitment.
2006
16332705
In silico sequence evolution with site-specific interactions along phylogenetic trees.
2006
16332711
VIS-O-BAC: exploratory visualization of functional genome studies from bacteria.
2006
16339284
Bayesian sparse hidden components analysis for transcription regulation networks.
2006
16368767
BioContrasts: extracting and exploiting protein-protein contrastive relations from biomedical literature.
2006
16368768
Local RNA base pairing probabilities in large sequences.
2006
16368769
Multidimensional local false discovery rate for microarray studies.
2006
16368770
ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression.
2006
16377611
GenomeDiagram: a python package for the visualization of large-scale genomic data.
2006
16377612
Improving missing value estimation in microarray data with gene ontology.
2006
16377613
ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation.
2006
16397004
BuchneraBASE: a post-genomic resource for Buchnera sp. APS.
2006
16397006
OPM: orientations of proteins in membranes database.
2006
16397007
ANDY: a general, fault-tolerant tool for database searching on computer clusters.
2006
16397008
A regularized discriminative model for the prediction of protein-peptide interactions.
2006
16397010
GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing.
2006
16403789
MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data.
2006
16403790
Optimized multilayer perceptrons for molecular classification and diagnosis using genomic data.
2006
16403791
Using a state-space model with hidden variables to infer transcription factor activities.
2006
16403793
IWoCS: analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships.
2006
16403794
Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression.
2006
16403795
Bayesian classifiers for detecting HGT using fixed and variable order markov models of genomic signatures.
2006
16403797
Inferring global levels of alternative splicing isoforms using a generative model of microarray data.
2006
16403798
BioShell--a package of tools for structural biology computations.
2006
16407320
LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters.
2006
16410317
Hierarchical multi-label prediction of gene function.
2006
16410319
Comparison of Affymetrix GeneChip expression measures.
2006
16410320
Chemical effects in biological systems (CEBS) object model for toxicology data, SysTox-OM: design and application.
2006
16410321
LSAT: learning about alternative transcripts in MEDLINE.
2006
16410322
Tools for the SBML Community.
2006
16410323
OrthologID: automation of genome-scale ortholog identification within a parsimony framework.
2006
16410324
Multiple association analysis via simulated annealing (MASSA).
2006
16414961
Panta rhei (QAlign2): an open graphical environment for sequence analysis.
2006
16418234
Inference of gene regulatory networks and compound mode of action from time course gene expression profiles.
2006
16418235
An interactive power analysis tool for microarray hypothesis testing and generation.
2006
16418236
TAMAL: an integrated approach to choosing SNPs for genetic studies of human complex traits.
2006
16418238
REMORA: a pilot in the ocean of BioMoby web-services.
2006
16423924
SUSPECTS: enabling fast and effective prioritization of positional candidates.
2006
16423925
Genetic test bed for feature selection.
2006
16428263
MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition.
2006
16428265
Automatic extension of Gene Ontology with flexible identification of candidate terms.
2006
16428805
The MGED Ontology: a resource for semantics-based description of microarray experiments.
2006
16428806
VISSA: a program to visualize structural features from structure sequence alignment.
2006
16434438
Polynomial model approach for resynchronization analysis of cell-cycle gene expression data.
2006
16434439
CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS).
2006
16434441
ProteomeCommons.org JAF: reference information and tools for proteomics.
2006
16434446
Enhancing instance-based classification with local density: a new algorithm for classifying unbalanced biomedical data.
2006
16443633
HaptenDB: a comprehensive database of haptens, carrier proteins and anti-hapten antibodies.
2006
16443637
siRecords: an extensive database of mammalian siRNAs with efficacy ratings.
2006
16443930
Thermodynamics of RNA-RNA binding.
2006
16446276
AMiGA: the arthropodan mitochondrial genomes accessible database.
2006
16446277
Discovering motif pairs at interaction sites from protein sequences on a proteome-wide scale.
2006
16446278
Capturing expert knowledge with argumentation: a case study in bioinformatics.
2006
16446279
MAMMOT--a set of tools for the design, management and visualization of genomic tiling arrays.
2006
16452111
Efficient estimation of graphlet frequency distributions in protein-protein interaction networks.
2006
16452112
Memory efficient folding algorithms for circular RNA secondary structures.
2006
16452114
The LCB Data Warehouse.
2006
16455749
Detection of gene copy number changes in CGH microarrays using a spatially correlated mixture model.
2006
16455750
PROFbval: predict flexible and rigid residues in proteins.
2006
16455751
affylmGUI: a graphical user interface for linear modeling of single channel microarray data.
2006
16455752
Predicting interactions in protein networks by completing defective cliques.
2006
16455753
CellML2SBML: conversion of CellML into SBML.
2006
16473867
Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations.
2006
16473870
Generation of 3D templates of active sites of proteins with rigid prosthetic groups.
2006
16473871
CFinder: locating cliques and overlapping modules in biological networks.
2006
16473872
A new summarization method for Affymetrix probe level data.
2006
16473874
Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support.
2006
16473875
The DIMA web resource--exploring the protein domain network.
2006
16481337
Pedigree-drawing with R and graphviz.
2006
16488908
Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction.
2006
16489208
Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences.
2006
16492684
Refinement of optical map assemblies.
2006
16500933
START: an automated tool for serial analysis of chromatin occupancy data.
2006
16500934
Mass analysis peptide sequence prediction (MAPSP).
2006
16500935
The UCSC Known Genes.
2006
16500937
Paloverde: an OpenGL 3D phylogeny browser.
2006
16500938
Mayday--a microarray data analysis workbench.
2006
16500939
Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns.
2006
16500940
PIANA: protein interactions and network analysis.
2006
16510498
CAFE: a computational tool for the study of gene family evolution.
2006
16543274
DRTF: a database of rice transcription factors.
2006
16551659
UniSave: the UniProtKB sequence/annotation version database.
2006
16551660
XQTav: an XQuery processor for Taverna environment.
2006
16551662
BicAT: a biclustering analysis toolbox.
2006
16551664
SBMLToolbox: an SBML toolbox for MATLAB users.
2006
16574696
SScore: an R package for detecting differential gene expression without gene expression summaries.
2006
16574698
ProMAT: protein microarray analysis tool.
2006
16595561
Using mRNAs lengths to accurately predict the alternatively spliced gene products in Caenorhabditis elegans.
2006
16595562
Analysis assistant for single-molecule force spectroscopy data on membrane proteins--MPTV.
2006
16606684
Ribosomal RNA as molecular barcodes: a simple correlation analysis without sequence alignment.
2006
16613905
Dragon Promoter Mapper (DPM): a Bayesian framework for modelling promoter structures.
2006
16613910
A probabilistic dynamical model for quantitative inference of the regulatory mechanism of transcription.
2006
16632490
GeneRecon--a coalescent based tool for fine-scale association mapping.
2006
16632491
Molecular complexes at a glance: automated generation of two-dimensional complex diagrams.
2006
16632493
Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques.
2006
16644788
Method for identifying transcription factor binding sites in yeast.
2006
16644789
BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge.
2006
16672256
SHARP2: protein-protein interaction predictions using patch analysis.
2006
16672257
Ensemble classifier for protein fold pattern recognition.
2006
16672258
TopoICE-R: 3D visualization modeling the topology of DNA recombination.
2006
16672259
Query Chem: a Google-powered web search combining text and chemical structures.
2006
16672261
BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny.
2006
16679334
Observing local and global properties of metabolic pathways: 'load points' and 'choke points' in the metabolic networks.
2006
16682421
HoSeqI: automated homologous sequence identification in gene family databases.
2006
16682422
Prelude and Fugue, predicting local protein structure, early folding regions and structural weaknesses.
2006
16682423
PACK: Profile Analysis using Clustering and Kurtosis to find molecular classifiers in cancer.
2006
16682424
SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments.
2006
16690634
Developing a move-set for protein model refinement.
2006
16705011
FCP: functional coverage of the proteome by structures.
2006
16705012
Comparative gene marker selection suite.
2006
16709585
A model diagram layout extension for SBML.
2006
16709586
INFO-RNA--a fast approach to inverse RNA folding.
2006
16709587
Combo: a whole genome comparative browser.
2006
16709588
TRFMA: a web-based tool for terminal restriction fragment length polymorphism analysis based on molecular weight.
2006
16709590
Context-specific infinite mixtures for clustering gene expression profiles across diverse microarray dataset.
2006
16709591
NETGEN: generating phylogenetic networks with diploid hybrids.
2006
16717070
SNPStats: a web tool for the analysis of association studies.
2006
16720584
Identifying sequence regions undergoing conformational change via predicted continuum secondary structure.
2006
16720586
Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli.
2006
16731694
Scanning microarrays at multiple intensities enhances discovery of differentially expressed genes.
2006
16731695
ACE-it: a tool for genome-wide integration of gene dosage and RNA expression data.
2006
16731696
Metatool 5.0: fast and flexible elementary modes analysis.
2006
16731697
PROBER: oligonucleotide FISH probe design software.
2006
16740623
Evolutionary simulations to detect functional lineage-specific genes.
2006
16766551
caGrid: design and implementation of the core architecture of the cancer biomedical informatics grid.
2006
16766552
tuple_plot: fast pairwise nucleotide sequence comparison with noise suppression.
2006
16766553
Transcriptome network component analysis with limited microarray data.
2006
16766556
SeqVis: visualization of compositional heterogeneity in large alignments of nucleotides.
2006
16766557
Combination of text-mining algorithms increases the performance.
2006
16766558
A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS.
2006
16766559
JADE: a distributed Java application for deleterious genomic mutation (DGM) estimation.
2006
16766560
Clustering microarray gene expression data using weighted Chinese restaurant process.
2006
16766561
NetAlign: a web-based tool for comparison of protein interaction networks.
2006
16766562
Robust estimation of the false discovery rate.
2006
16777905
Roundup: a multi-genome repository of orthologs and evolutionary distances.
2006
16777906
THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures.
2006
16777907
JCell--a Java-based framework for inferring regulatory networks from time series data.
2006
16782725
Building chromosome-wide LD maps.
2006
16782726
Additional gene ontology structure for improved biological reasoning.
2006
16787968
Transcript mapping with high-density oligonucleotide tiling arrays.
2006
16787969
Increasing confidence of protein interactomes using network topological metrics.
2006
16787971
DomainSieve: a protein domain-based screen that led to the identification of dam-associated genes with potential link to DNA maintenance.
2006
16787973
HCNet: a database of heart and calcium functional network.
2006
16787974
TSSub: eukaryotic protein subcellular localization by extracting features from profiles.
2006
16787975
Cleaver: software for identifying taxon specific restriction endonuclease recognition sites.
2006
16787976
A lock-and-key model for protein-protein interactions.
2006
16787977
Pathway analysis using random forests classification and regression.
2006
16809386
ET viewer: an application for predicting and visualizing functional sites in protein structures.
2006
16809388
Domain organization within repeated DNA sequences: application to the study of a family of transposable elements.
2006
16809391
PDQ Wizard: automated prioritization and characterization of gene and protein lists using biomedical literature.
2006
16809392
SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs.
2006
16809394
Parallel multifactor dimensionality reduction: a tool for the large-scale analysis of gene-gene interactions.
2006
16809395
ZooDDD: a cross-species database for digital differential display analysis.
2006
16820423
MAGOS: multiple alignment and modelling server.
2006
16820425
Searching RNA motifs and their intermolecular contacts with constraint networks.
2006
16820426
Probe-level measurement error improves accuracy in detecting differential gene expression.
2006
16820429
Ribostral: an RNA 3D alignment analyzer and viewer based on basepair isostericities.
2006
16820430
VAMP: visualization and analysis of array-CGH, transcriptome and other molecular profiles.
2006
16820431
Remote homology detection based on oligomer distances.
2006
16837522
Predicting methylation status of CpG islands in the human brain.
2006
16837523
ADGO: analysis of differentially expressed gene sets using composite GO annotation.
2006
16837524
VISTAL--a new 2D visualization tool of protein 3D structural alignments.
2006
16837525
Mutagenic probability estimation of chemical compounds by a novel molecular electrophilicity vector and support vector machine.
2006
16837526
RBR: library-less repeat detection for ESTs.
2006
16837527
Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands.
2006
16837528
An initial strategy for comparing proteins at the domain architecture level.
2006
16837531
Gene selection in cancer classification using sparse logistic regression with Bayesian regularization.
2006
16844704
Global topological features of cancer proteins in the human interactome.
2006
16844706
CART variance stabilization and regularization for high-throughput genomic data.
2006
16844707
Serial NetEvolve: a flexible utility for generating serially-sampled sequences along a tree or recombinant network.
2006
16844708
SynView: a GBrowse-compatible approach to visualizing comparative genome data.
2006
16844709
Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks.
2006
16844710
Identification of transcription factor cooperativity via stochastic system model.
2006
16844711
OrderedList--a bioconductor package for detecting similarity in ordered gene lists.
2006
16844712
A whole genome long-range haplotype (WGLRH) test for detecting imprints of positive selection in human populations.
2006
16845142
arrayQCplot: software for checking the quality of microarray data.
2006
16864592
Inferring gene regulatory networks from multiple microarray datasets.
2006
16864593
Bio-Ontology and text: bridging the modeling gap.
2006
16870928
ARCS: an aggregated related column scoring scheme for aligned sequences.
2006
16870930
AliBaba: PubMed as a graph.
2006
16870931
Bayesian search of functionally divergent protein subgroups and their function specific residues.
2006
16870932
JVirGel 2.0: computational prediction of proteomes separated via two-dimensional gel electrophoresis under consideration of membrane and secreted proteins.
2006
16870933
What should be expected from feature selection in small-sample settings.
2006
16870934
Finding motifs from all sequences with and without binding sites.
2006
16870937
Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles.
2006
16873460
Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle.
2006
16873462
Semi-supervised LC/MS alignment for differential proteomics.
2006
16873463
Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE.
2006
16873464
Context-specific independence mixture modeling for positional weight matrices.
2006
16873468
ZPRED: predicting the distance to the membrane center for residues in alpha-helical membrane proteins.
2006
16873471
Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data.
2006
16873472
Learning MHC I--peptide binding.
2006
16873476
Comparative genomics reveals unusually long motifs in mammalian genomes.
2006
16873477
Rapid knot detection and application to protein structure prediction.
2006
16873480
Annotating proteins by mining protein interaction networks.
2006
16873481
A combinatorial pattern discovery approach for the prediction of membrane dipping (re-entrant) loops.
2006
16873484
Identifying cycling genes by combining sequence homology and expression data.
2006
16873488
The iRMSD: a local measure of sequence alignment accuracy using structural information.
2006
16873492
Efficient identification of DNA hybridization partners in a sequence database.
2006
16873493
An experimental metagenome data management and analysis system.
2006
16873494
Informative priors based on transcription factor structural class improve de novo motif discovery.
2006
16873497
Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone.
2006
16873498
Create and assess protein networks through molecular characteristics of individual proteins.
2006
16873500
BaCelLo: a balanced subcellular localization predictor.
2006
16873501
Semi-supervised analysis of gene expression profiles for lineage-specific development in the Caenorhabditis elegans embryo.
2006
16873502
Decoding non-unique oligonucleotide hybridization experiments of targets related by a phylogenetic tree.
2006
16873503
Integrating copy number polymorphisms into array CGH analysis using a robust HMM.
2006
16873504
An ontology for a Robot Scientist.
2006
16873508
ARTS: accurate recognition of transcription starts in human.
2006
16873509
Integrating structured biological data by Kernel Maximum Mean Discrepancy.
2006
16873512
SNP Function Portal: a web database for exploring the function implication of SNP alleles.
2006
16873516
Protein classification using ontology classification.
2006
16873517
Inferring functional pathways from multi-perturbation data.
2006
16873518
AClAP, Autonomous hierarchical agglomerative Cluster Analysis based protocol to partition conformational datasets.
2006
16873522
A top-level ontology of functions and its application in the Open Biomedical Ontologies.
2006
16873523
Automatic clustering of orthologs and inparalogs shared by multiple proteomes.
2006
16873526
CONTRAfold: RNA secondary structure prediction without physics-based models.
2006
16873527
General framework for developing and evaluating database scoring algorithms using the TANDEM search engine.
2006
16877754
Hierarchical classification of hydrolases catalytic sites.
2006
16877756
Reliable gene signatures for microarray classification: assessment of stability and performance.
2006
16882647
PYCHEM: a multivariate analysis package for python.
2006
16882648
Nemo: an evolutionary and population genetics programming framework.
2006
16882649
Partial correlation coefficient between distance matrices as a new indicator of protein-protein interactions.
2006
16882650
OSIRIS: a tool for retrieving literature about sequence variants.
2006
16882651
Sebida: a database for the functional and evolutionary analysis of genes with sex-biased expression.
2006
16882652
Few crucial links assure checkpoint efficiency in the yeast cell-cycle network.
2006
16895923
MLR-tagging: informative SNP selection for unphased genotypes based on multiple linear regression.
2006
16895924
Robust inference of positive selection from recombining coding sequences.
2006
16895925
Branch and bound computation of exact p-values.
2006
16895926
HiRes--a tool for comprehensive assessment and interpretation of metabolomic data.
2006
16895927
UniGene Tabulator: a full parser for the UniGene format.
2006
16895929
Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information.
2006
16895930
COPA--cancer outlier profile analysis.
2006
16895932
ARFA: a program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting.
2006
16895933
Solvated docking: introducing water into the modelling of biomolecular complexes.
2006
16899489
MASQOT-GUI: spot quality assessment for the two-channel microarray platform.
2006
16899490
The ties problem resulting from counting-based error estimators and its impact on gene selection algorithms.
2006
16908500
GenePro: a Cytoscape plug-in for advanced visualization and analysis of interaction networks.
2006
16921162
Text similarity: an alternative way to search MEDLINE.
2006
16926219
SBML-PET: a Systems Biology Markup Language-based parameter estimation tool.
2006
16926221
DOCKGROUND resource for studying protein-protein interfaces.
2006
16928732
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.
2006
16928733
TESD: a transposable element dynamics simulation environment.
2006
16928734
Anisotropic network model: systematic evaluation and a new web interface.
2006
16928735
Maximum likelihood of phylogenetic networks.
2006
16928736
MMM: a sequence-to-structure alignment protocol.
2006
16928737
MARD: a new method to detect differential gene expression in treatment-control time courses.
2006
16928738
An application for assessing quality of RNA hybridized to Affymetrix GeneChips.
2006
16935927
ArrayFusion: a web application for multi-dimensional analysis of CGH, SNP and microarray data.
2006
16935928
Bio3d: an R package for the comparative analysis of protein structures.
2006
16940322
Model-based boosting in high dimensions.
2006
16940323
iFold: a platform for interactive folding simulations of proteins.
2006
16940324
Tropical--parameter estimation and simulation of reaction-diffusion models based on spatio-temporal microscopy images.
2006
16940327
IndexToolkit: an open source toolbox to index protein databases for high-throughput proteomics.
2006
16945944
A locally adaptive statistical procedure (LAP) to identify differentially expressed chromosomal regions.
2006
16951291
Targeted projection pursuit for visualizing gene expression data classifications.
2006
16954139
Probalign: multiple sequence alignment using partition function posterior probabilities.
2006
16954142
SEBINI: Software Environment for BIological Network Inference.
2006
16954144
Augur--a computational pipeline for whole genome microbial surface protein prediction and classification.
2006
16966358
SCAssign: a sparky extension for the NMR resonance assignment of aliphatic side-chains of uniformly 13C,15N-labeled large proteins.
2006
16966359
Protein-RNA interactions: exploring binding patterns with a three-dimensional superposition analysis of high resolution structures.
2006
16966360
SPEED: a molecular-evolution-based database of mammalian orthologous groups.
2006
16966361
Probabilistic inference of transcription factor concentrations and gene-specific regulatory activities.
2006
16966362
Support vector machine learning from heterogeneous data: an empirical analysis using protein sequence and structure.
2006
16966363
Clearcut: a fast implementation of relaxed neighbor joining.
2006
16982706
ADAM: another database of abbreviations in MEDLINE.
2006
16982707
RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis.
2006
16982708
Software for dynamic analysis of tracer-based metabolomic data: estimation of metabolic fluxes and their statistical analysis.
2006
17000750
GATHER: a systems approach to interpreting genomic signatures.
2006
17000751
Peptide length-based prediction of peptide-MHC class II binding.
2006
17000752
CAPS: coevolution analysis using protein sequences.
2006
17005535
Support vector machines for prediction of dihedral angle regions.
2006
17005536
BNArray: an R package for constructing gene regulatory networks from microarray data by using Bayesian network.
2006
17005537
GenoProfiler: batch processing of high-throughput capillary fingerprinting data.
2007
17018534
ProtBuD: a database of biological unit structures of protein families and superfamilies.
2006
17018535
Sungear: interactive visualization and functional analysis of genomic datasets.
2007
17018536
P2BAT: a massive parallel implementation of PBAT for genome-wide association studies in R.
2006
17021156
TimeTree: a public knowledge-base of divergence times among organisms.
2006
17021158
CREMOFAC--a database of chromatin remodeling factors.
2006
17021159
The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks.
2006
17021160
FoldUnfold: web server for the prediction of disordered regions in protein chain.
2006
17021161
Evaluating the performance of microarray segmentation algorithms.
2006
17032673
Large scale data mining approach for gene-specific standardization of microarray gene expression data.
2006
17032674
KGraph: a system for visualizing and evaluating complex genetic associations.
2007
17032675
ChromoScan: a scan statistic application for identifying chromosomal regions in genomic studies.
2006
17032677
DASS: efficient discovery and p-value calculation of substructures in unordered data.
2007
17032678
Integration of gel-based proteome data with pProRep.
2006
17032679
Survival analysis of longitudinal microarrays.
2006
17032680
Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA.
2006
17032682
COPASI--a COmplex PAthway SImulator.
2006
17032683
APDB: a web server to evaluate the accuracy of sequence alignments using structural information.
2006
17032685
Measuring covariation in RNA alignments: physical realism improves information measures.
2006
17038338
ssSNPer: identifying statistically similar SNPs to aid interpretation of genetic association studies.
2006
17038340
NMPP: a user-customized NimbleGen microarray data processing pipeline.
2006
17038341
Parameter estimation using Simulated Annealing for S-system models of biochemical networks.
2007
17038344
Repseek, a tool to retrieve approximate repeats from large DNA sequences.
2007
17038345
Supporting the SBML layout extension.
2006
17038346
Cell++--simulating biochemical pathways.
2006
17038347
Inherent limitations in protein-protein docking procedures.
2007
17040920
Extending MapMan: application to legume genome arrays.
2006
17046975
sGAL: a computational method for finding surface exposed sites in proteins suitable for Cys-mediated cross-linking.
2006
17046976
MetaQuant: a tool for the automatic quantification of GC/MS-based metabolome data.
2006
17046977
Estimation of false discovery proportion under general dependence.
2006
17046978
Computational prediction of novel components of lung transcriptional networks.
2007
17050569
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.
2007
17050570
Building an abbreviation dictionary using a term recognition approach.
2006
17050571
Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins.
2006
17060355
SequenceLDhot: detecting recombination hotspots.
2006
17060358
Combining functional and linkage disequilibrium information in the selection of tag SNPs.
2007
17060359
Linkage analysis using sex-specific recombination fractions with GENEHUNTER-MODSCORE.
2007
17060360
A Gibbs sampler for the identification of gene expression and network connectivity consistency.
2006
17060361
SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays.
2007
17062589
Babel's tower revisited: a universal resource for cross-referencing across annotation databases.
2006
17068090
Dependence network modeling for biomarker identification.
2007
17077095
OmicBrowse: a browser of multidimensional omics annotations.
2007
17077097
GECO--linear visualization for comparative genomics.
2007
17077098
Computing the maximum similarity bi-clusters of gene expression data.
2007
17090578
ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes.
2007
17090579
Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes.
2007
17090580
AGScan: a pluggable microarray image quantification software based on the ImageJ library.
2007
17092988
Inferential, robust non-negative matrix factorization analysis of microarray data.
2007
17092989
Pattern locator: a new tool for finding local sequence patterns in genomic DNA sequences.
2006
17095514
PEAKS: identification of regulatory motifs by their position in DNA sequences.
2007
17098773
Using GOstats to test gene lists for GO term association.
2007
17098774
Predicting transcription factor affinities to DNA from a biophysical model.
2007
17098775
Interpretation of ANOVA models for microarray data using PCA.
2007
17105717
Reliable prediction of Drosha processing sites improves microRNA gene prediction.
2007
17105718
Detecting protein dissimilarities in multiple alignments using Bayesian variable selection.
2007
17105719
Striped Smith-Waterman speeds database searches six times over other SIMD implementations.
2007
17110365
Network neighborhood analysis with the multi-node topological overlap measure.
2007
17110366
GARD: a genetic algorithm for recombination detection.
2006
17110367
SAGA: a subgraph matching tool for biological graphs.
2007
17110368
Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment.
2007
17110370
NvMap: automated analysis of NMR chemical shift perturbation data.
2007
17118956
PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences.
2007
17118958
WHAP: haplotype-based association analysis.
2007
17118959
PrepMS: TOF MS data graphical preprocessing tool.
2007
17121773
Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach.
2007
17121774
SNP2NMD: a database of human single nucleotide polymorphisms causing nonsense-mediated mRNA decay.
2007
17121775
ProteomeCommons.org IO Framework: reading and writing multiple proteomics data formats.
2007
17121776
ARIA2: automated NOE assignment and data integration in NMR structure calculation.
2007
17121777
Mosclust: a software library for discovering significant structures in bio-molecular data.
2007
17127677
GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring.
2007
17127678
QSCOP--SCOP quantified by structural relationships.
2007
17127679
Mclip: motif detection based on cliques of gapped local profile-to-profile alignments.
2007
17127680
Improved breast cancer prognosis through the combination of clinical and genetic markers.
2007
17130137
K-Fold: a tool for the prediction of the protein folding kinetic order and rate.
2007
17138584
BioNetBuilder: automatic integration of biological networks.
2007
17138585
Flexible empirical Bayes models for differential gene expression.
2007
17138586
Prophet, a web-based tool for class prediction using microarray data.
2007
17138587
Crystallographic protein model-building on the web.
2007
17138588
Visualization of genomic aberrations using Affymetrix SNP arrays.
2007
17138589
RelEx--relation extraction using dependency parse trees.
2007
17142812
Exploiting large scale computing to construct high resolution linkage disequilibrium maps of the human genome.
2007
17142813
The automation of Nested Clade Phylogeographic Analysis.
2007
17142814
Dynamic exploration and editing of KEGG pathway diagrams.
2007
17142815
cBrother: relaxing parental tree assumptions for Bayesian recombination detection.
2007
17145740
AutoGRAPH: an interactive web server for automating and visualizing comparative genome maps.
2007
17145741
LdCompare: rapid computation of single- and multiple-marker r2 and genetic coverage.
2007
17148510
Genomic sweeping for hypermethylated genes.
2007
17148511
ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage.
2007
17150992
msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots.
2007
17150995
AllerTool: a web server for predicting allergenicity and allergic cross-reactivity in proteins.
2007
17150996
Bayesian-based selection of metabolic objective functions.
2007
17150997
GGtools: analysis of genetics of gene expression in bioconductor.
2007
17158513
Assembling millions of short DNA sequences using SSAKE.
2007
17158514
Functional genomics via multiscale analysis: application to gene expression and ChIP-on-chip data.
2007
17164284
Robust prediction of consensus secondary structures using averaged base pairing probability matrices.
2007
17182698
URec: a system for unrooted reconciliation.
2007
17182699
SNPchip: R classes and methods for SNP array data.
2007
17204461
MinSet: a general approach to derive maximally representative database subsets by using fragment dictionaries and its application to the SCOP database.
2007
17204463
SChiSM2: creating interactive web page annotations of molecular structure models using Jmol.
2007
17204464
In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists.
2007
17204465
Protein-protein interaction site prediction based on conditional random fields.
2007
17234636
snp.plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting package.
2007
17234637
A structural alignment kernel for protein structures.
2007
17234638
Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases.
2007
17234640
CoCo: a web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data.
2007
17234641
Identifying bacterial genes and endosymbiont DNA with Glimmer.
2007
17237039
Modeling nonlinearity in dilution design microarray data.
2007
17237040
A computational system to select candidate genes for complex human traits.
2007
17237041
FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes.
2007
17237043
Computing exact P-values for DNA motifs.
2007
17237046
Structure-based evaluation of in silico predictions of protein-protein interactions using Comparative Docking.
2007
17237047
A new protein-protein docking scoring function based on interface residue properties.
2007
17237048
LFM-Pro: a tool for detecting significant local structural sites in proteins.
2007
17237050
APOPTO-CELL--a simulation tool and interactive database for analyzing cellular susceptibility to apoptosis.
2007
17237051
Comparison of human protein-protein interaction maps.
2007
17237052
AphidBase: a database for aphid genomic resources.
2007
17237053
The Treeterbi and Parallel Treeterbi algorithms: efficient, optimal decoding for ordinary, generalized and pair HMMs.
2007
17237054
SMotif: a server for structural motifs in proteins.
2007
17237055
The ESID Online Database network.
2007
17237056
Identifying clusters of functionally related genes in genomes.
2007
17237058
Analysis of E. coli promoter recognition problem in dinucleotide feature space.
2007
17237059
Software package for automatic microarray image analysis (MAIA).
2007
17237062
Compressed suffix tree--a basis for genome-scale sequence analysis.
2007
17237063
Automatic recognition and annotation of gene expression patterns of fly embryos.
2007
17237064
Peak selection from MALDI-TOF mass spectra using ant colony optimization.
2007
17237065
Improving the accuracy of transmembrane protein topology prediction using evolutionary information.
2007
17237066
Inferring pairwise regulatory relationships from multiple time series datasets.
2007
17237067
DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins.
2007
17237068
BioWeka--extending the Weka framework for bioinformatics.
2007
17237069
An efficient, versatile and scalable pattern growth approach to mine frequent patterns in unaligned protein sequences.
2007
17237070
SBaddon: high performance simulation for the Systems Biology Toolbox for MATLAB.
2007
17237071
Biskit--a software platform for structural bioinformatics.
2007
17237072
ProServer: a simple, extensible Perl DAS server.
2007
17237073
DataBiNS: a BioMoby-based data-mining workflow for biological pathways and non-synonymous SNPs.
2007
17237074
Phylogenetic reconstruction from non-genomic data.
2007
17237077
Inferring phylogeny from whole genomes.
2007
17237078
Learning probabilistic models of cis-regulatory modules that represent logical and spatial aspects.
2007
17237085
TOPP--the OpenMS proteomics pipeline.
2007
17237091
Difference detection in LC-MS data for protein biomarker discovery.
2007
17237092
Vorolign--fast structural alignment using Voronoi contacts.
2007
17237093
EBIMed--text crunching to gather facts for proteins from Medline.
2007
17237098
Multiple alignment by sequence annealing.
2007
17237099
Tandem repeats over the edit distance.
2007
17237101
A comparative genome approach to marker ordering.
2007
17237105
Merging microarray cell synchronization experiments through curve alignment.
2007
17237107
Family relationships: should consensus reign?--consensus clustering for protein families.
2007
17237108
SatDNA Analyzer: a computing tool for satellite-DNA evolutionary analysis.
2007
17242030
Molecular basis for specificity in the druggable kinome: sequence-based analysis.
2007
17255140
A simulation test bed for hypotheses of genome evolution.
2007
17267425
OMWSA: detection of DNA repeats using moving window spectral analysis.
2007
17267428
Gene expression network analysis and applications to immunology.
2007
17267429
SGN Sim, a stochastic genetic networks simulator.
2007
17267430
CGHcall: calling aberrations for array CGH tumor profiles.
2007
17267432
Ontology development for biological systems: immunology.
2007
17267433
COPYCAT: cophylogenetic analysis tool.
2007
17267434
De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures.
2007
17267435
SNPassoc: an R package to perform whole genome association studies.
2007
17267436
PROMALS: towards accurate multiple sequence alignments of distantly related proteins.
2007
17267437
An ensemble approach to microarray data-based gene prioritization after missing value imputation.
2007
17267438
SCOOP: a simple method for identification of novel protein superfamily relationships.
2007
17277330
NetMatch: a Cytoscape plugin for searching biological networks.
2007
17277332
Automatic correspondence of tags and genes (ACTG): a tool for the analysis of SAGE, MPSS and SBS data.
2007
17277333
DFprot: a webtool for predicting local chain deformability.
2007
17277334
NetPhosYeast: prediction of protein phosphorylation sites in yeast.
2007
17282998
Assessment of the probabilities for evolutionary structural changes in protein folds.
2007
17282999
Accurate automated clustering of two-dimensional data for single-nucleotide polymorphism genotyping by a combination of clustering methods: evaluation by large-scale real data.
2007
17301273
A new JAVA interface implementation of THESIAS: testing haplotype effects in association studies.
2007
17308338
Position dependencies in transcription factor binding sites.
2007
17308339
HomologMiner: looking for homologous genomic groups in whole genomes.
2007
17308341
ClusterDraw web server: a tool to identify and visualize clusters of binding motifs for transcription factors.
2007
17308342
Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation.
2007
17309895
Gepard: a rapid and sensitive tool for creating dotplots on genome scale.
2007
17309896
Gene symbol disambiguation using knowledge-based profiles.
2007
17314123
SwS: a solvation web service for nucleic acids.
2007
17324939
Enabling high-throughput data management for systems biology: the Bioinformatics Resource Manager.
2007
17324940
Multiple structural alignment and clustering of RNA sequences.
2007
17324941
rh_tsp_map 3.0: end-to-end radiation hybrid mapping with improved speed and quality control.
2007
17332018
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes.
2007
17332020
NucPred--predicting nuclear localization of proteins.
2007
17332022
Microarray blob-defect removal improves array analysis.
2007
17332024
PhyloGena--a user-friendly system for automated phylogenetic annotation of unknown sequences.
2007
17332025
GAPWM: a genetic algorithm method for optimizing a position weight matrix.
2007
17341493
AMPer: a database and an automated discovery tool for antimicrobial peptides.
2007
17341497
Simulating Epstein-Barr virus infection with C-ImmSim.
2007
17341499
Glycan classification with tree kernels.
2007
17344232
BioGuideSRS: querying multiple sources with a user-centric perspective.
2007
17344233
A new method to measure the semantic similarity of GO terms.
2007
17344234
ABCGrid: Application for Bioinformatics Computing Grid.
2007
17344235
EuSplice: a unified resource for the analysis of splice signals and alternative splicing in eukaryotic genes.
2007
17344236
Analyzing microarray data using CLANS.
2007
17344239
Codelink: an R package for analysis of GE healthcare gene expression bioarrays.
2007
17344240
pcaMethods--a bioconductor package providing PCA methods for incomplete data.
2007
17344241
MedicCyc: a biochemical pathway database for Medicago truncatula.
2007
17344243
iPTREE-STAB: interpretable decision tree based method for predicting protein stability changes upon mutations.
2007
17379687
UniRef: comprehensive and non-redundant UniProt reference clusters.
2007
17379688
IMEx: Imperfect Microsatellite Extractor.
2007
17379689
Domain-enhanced analysis of microarray data using GO annotations.
2007
17379692
Enhancements and modifications of primer design program Primer3.
2007
17379693
AutoSCOP: automated prediction of SCOP classifications using unique pattern-class mappings.
2007
17379694
GenABEL: an R library for genome-wide association analysis.
2007
17384015
Mediante: a web-based microarray data manager.
2007
17384016
SBML export interface for the systems biology toolbox for MATLAB.
2007
17384017
A mixture model approach to the tests of concordance and discordance between two large-scale experiments with two-sample groups.
2007
17384018
IlluminaGUI: graphical user interface for analyzing gene expression data generated on the Illumina platform.
2007
17384020
Unsupervised segmentation of continuous genomic data.
2007
17384021
SNPTools: a software tool for visualization and analysis of microarray data.
2007
17384422
Finding new structural and sequence attributes to predict possible disease association of single amino acid polymorphism (SAP).
2007
17384424
Enhancing the functional annotation of PDB structures in PDBsum using key figures extracted from the literature.
2007
17384425
GoSh: a web-based database for goat and sheep EST sequences.
2007
17384426
POPI: predicting immunogenicity of MHC class I binding peptides by mining informative physicochemical properties.
2007
17384427
Semantic Web Service provision: a realistic framework for Bioinformatics programmers.
2007
17384428
MPP: a microarray-to-phylogeny pipeline for analysis of gene and marker content datasets.
2007
17384430
Ngila: global pairwise alignments with logarithmic and affine gap costs.
2007
17387111
A sequential Monte Carlo EM approach to the transcription factor binding site identification problem.
2007
17387112
Assessing the need for sequence-based normalization in tiling microarray experiments.
2007
17387113
Classification based upon gene expression data: bias and precision of error rates.
2007
17392326
SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data.
2007
17392328
A fast and flexible approach to oligonucleotide probe design for genomes and gene families.
2007
17392329
DPTF: a database of poplar transcription factors.
2007
17392330
uBioRSS: tracking taxonomic literature using RSS.
2007
17392332
Cyclone: java-based querying and computing with Pathway/Genome databases.
2007
17392333
SCEPTRANS: an online tool for analyzing periodic transcription in yeast.
2007
17400726
PROTMAP2D: visualization, comparison and analysis of 2D maps of protein structure.
2007
17400727
Management, presentation and interpretation of genome scans using GSCANDB.
2007
17400728
TFmodeller: comparative modelling of protein-DNA complexes.
2007
17459960
Murlet: a practical multiple alignment tool for structural RNA sequences.
2007
17459961
Mapping the genetic architecture of complex traits in experimental populations.
2007
17459962
GENOME: a rapid coalescent-based whole genome simulator.
2007
17459963
CTX-BLAST: context sensitive version of protein BLAST.
2007
17459964
TOPD/FMTS: a new software to compare phylogenetic trees.
2007
17459965
Simultaneous and exact interval estimates for the contrast of two groups based on an extremely high dimensional variable: application to mass spec data.
2007
17459967
A quantitative model for linking two disparate sets of articles in MEDLINE.
2007
17463015
Faspad: fast signaling pathway detection.
2007
17463016
SciRoKo: a new tool for whole genome microsatellite search and investigation.
2007
17463017
The qualitative and time-dependent character of spatial relations in biomedical ontologies.
2007
17463018
SNP detection exploiting multiple sources of redundancy in large EST collections improves validation rates.
2007
17463019
OSLay: optimal syntenic layout of unfinished assemblies.
2007
17463020
Time-varying modeling of gene expression regulatory networks using the wavelet dynamic vector autoregressive method.
2007
17463021
iHMMune-align: hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences.
2007
17463026
Identifying the biologically relevant gene categories based on gene expression and biological data: an example on prostate cancer.
2007
17463028
Two-stage designs applying methods differing in costs.
2007
17463029
DITOP: drug-induced toxicity related protein database.
2007
17463030
Libaffy: software for processing Affymetrix GeneChip data.
2007
17463032
Alignment of molecular networks by integer quadratic programming.
2007
17468121
GAzer: gene set analyzer.
2007
17468122
SPACER: identification of cis-regulatory elements with non-contiguous critical residues.
2007
17470480
Weighted rank aggregation of cluster validation measures: a Monte Carlo cross-entropy approach.
2007
17483500
Genomix: a method for combining gene-finders' predictions, which uses evolutionary conservation of sequence and intron-exon structure.
2007
17483502
PQuad--a visual analysis platform for proteomic data exploration of microbial organisms.
2007
17483503
BioDownloader: bioinformatics downloads and updates in a few clicks.
2007
17483505
Automated Improvement of Domain ANnotations using context analysis of domain arrangements (AIDAN).
2007
17483506
Phenotypic clustering of yeast mutants based on kinetochore microtubule dynamics.
2007
17483508
CRCView: a web server for analyzing and visualizing microarray gene expression data using model-based clustering.
2007
17485426
Genetdes: automatic design of transcriptional networks.
2007
17485427
ChromatinDB: a database of genome-wide histone modification patterns for Saccharomyces cerevisiae.
2007
17485428
CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure.
2007
17485429
Comparing association network algorithms for reverse engineering of large-scale gene regulatory networks: synthetic versus real data.
2007
17485431
CALIB: a Bioconductor package for estimating absolute expression levels from two-color microarray data.
2007
17485432
AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes.
2007
17485433
SQUINT: a multiple alignment program and editor.
2007
17485434
Fast model-based protein homology detection without alignment.
2007
17488755
MODELER4SIMCOAL2: a user-friendly, extensible modeler of demography and linked loci for coalescent simulations.
2007
17488756
Madeline 2.0 PDE: a new program for local and web-based pedigree drawing.
2007
17488757
A phylogenetic Gibbs sampler that yields centroid solutions for cis-regulatory site prediction.
2007
17488758
Nucleotide composition string selection in HIV-1 subtyping using whole genomes.
2007
17495995
Biological network mapping and source signal deduction.
2007
17495996
PLMaddon: a power-law module for the Matlab SBToolbox.
2007
17495997
MutationFinder: a high-performance system for extracting point mutation mentions from text.
2007
17495998
WilcoxCV: an R package for fast variable selection in cross-validation.
2007
17495999
Data reduction of isotope-resolved LC-MS spectra.
2007
17496000
Rapid assessment of correlated amino acids from pair-to-pair (P2P) substitution matrices.
2007
17496318
DoriC: a database of oriC regions in bacterial genomes.
2007
17496319
BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations.
2007
17496321
The Cytochrome P450 Engineering Database: a navigation and prediction tool for the cytochrome P450 protein family.
2007
17510166
Probability-based pattern recognition and statistical framework for randomization: modeling tandem mass spectrum/peptide sequence false match frequencies.
2007
17510167
Computational identification of candidate loci for recessively inherited mutation using high-throughput SNP arrays.
2007
17510170
T-Pile--a package for thermodynamic calculations for biomolecules.
2007
17510173
Predicting functionally important residues from sequence conservation.
2007
17519246
The evolutionary forest algorithm.
2007
17519247
Recombination-filtered genomic datasets by information maximization.
2007
17519249
Discovering gene expression patterns in time course microarray experiments by ANOVA-SCA.
2007
17519250
StrBioLib: a Java library for development of custom computational structural biology applications.
2007
17537750
Computational methods for diffusion-influenced biochemical reactions.
2007
17537752
PALMA: mRNA to genome alignments using large margin algorithms.
2007
17537755
RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment.
2007
17537756
Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications.
2007
17540677
VISDA: an open-source caBIG analytical tool for data clustering and beyond.
2007
17540678
Logistic regression for disease classification using microarray data: model selection in a large p and small n case.
2007
17540680
Tree Gibbs Sampler: identifying conserved motifs without aligning orthologous sequences.
2007
17540681
Bayesian modelling of shared gene function.
2007
17540682
Simple and fast alignment of metabolic pathways by exploiting local diversity.
2007
17540683
POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions.
2007
17545177
BioText Search Engine: beyond abstract search.
2007
17545178
PIP: a database of potential intron polymorphism markers.
2007
17545179
OMA Browser--exploring orthologous relations across 352 complete genomes.
2007
17545180
VIPER: an advanced software package to support high-throughput LC-MS peptide identification.
2007
17545182
OBO-Edit--an ontology editor for biologists.
2007
17545183
Finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov models.
2007
17550911
Classification of small molecules by two- and three-dimensional decomposition kernels.
2007
17550912
Alvira: comparative genomics of viral strains.
2007
17550913
The commonality of protein interaction networks determined in neurodegenerative disorders (NDDs).
2007
17553855
Predicting survival from microarray data--a comparative study.
2007
17553857
The MiSink Plugin: Cytoscape as a graphical interface to the Database of Interacting Proteins.
2007
17553858
Boltzmann probability of RNA structural neighbors and riboswitch detection.
2007
17573364
ViroBLAST: a stand-alone BLAST web server for flexible queries of multiple databases and user's datasets.
2007
17586542
Multivariate correlation estimator for inferring functional relationships from replicated genome-wide data.
2007
17586543
Annotation-based distance measures for patient subgroup discovery in clinical microarray studies.
2007
17586546
MAnGO: an interactive R-based tool for two-colour microarray analysis.
2007
17586547
MareyMap: an R-based tool with graphical interface for estimating recombination rates.
2007
17586550
PowerCore: a program applying the advanced M strategy with a heuristic search for establishing core sets.
2007
17586551
Visualization-based cancer microarray data classification analysis.
2007
17586552
Stochastic simulation GUI for biochemical networks.
2007
17586553
BiVisu: software tool for bicluster detection and visualization.
2007
17586826
HaploBuild: an algorithm to construct non-contiguous associated haplotypes in family based genetic studies.
2007
17586827
beadarray: R classes and methods for Illumina bead-based data.
2007
17586828
Web-based GeneChip analysis system for large-scale collaborative projects.
2007
17586830
Penalized and weighted K-means for clustering with scattered objects and prior information in high-throughput biological data.
2007
17597097
Different packing of external residues can explain differences in the thermostability of proteins from thermophilic and mesophilic organisms.
2007
17599925
QPRIMER: a quick web-based application for designing conserved PCR primers from multigenome alignments.
2007
17599926
Detection of eQTL modules mediated by activity levels of transcription factors.
2007
17599927
Non-parametric quantification of protein lysate arrays.
2007
17599930
ChemDB update--full-text search and virtual chemical space.
2007
17599932
Identification of aberrant chromosomal regions from gene expression microarray studies applied to human breast cancer.
2007
17599933
Prediction of Ras-effector interactions using position energy matrices.
2007
17599936
CASVM: web server for SVM-based prediction of caspase substrates cleavage sites.
2007
17599937
Context-sensitive data integration and prediction of biological networks.
2007
17599939
POODLE-S: web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix.
2007
17599940
RefPlus: an R package extending the RMA Algorithm.
2007
17623700
EcoProDB: the Escherichia coli protein database.
2007
17623702
HMMoC--a compiler for hidden Markov models.
2007
17623703
Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood.
2008
17623705
Quantitative quality-assessment techniques to compare fractionation and depletion methods in SELDI-TOF mass spectrometry experiments.
2007
17626063
GSEA-P: a desktop application for Gene Set Enrichment Analysis.
2007
17644558
Analysis of array CGH data for cancer studies using fused quantile regression.
2007
17644559
APID2NET: unified interactome graphic analyzer.
2007
17644818
miniTUBA: medical inference by network integration of temporal data using Bayesian analysis.
2007
17644819
Haplotype inference for present-absent genotype data using previously identified haplotypes and haplotype patterns.
2007
17644820
Co-occurrence analysis of insertional mutagenesis data reveals cooperating oncogenes.
2007
17646289
Identification of functional modules from conserved ancestral protein-protein interactions.
2007
17646291
Computational prediction of host-pathogen protein-protein interactions.
2007
17646292
Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models.
2007
17646294
Efficient parameter estimation for RNA secondary structure prediction.
2007
17646296
Optimized design and assessment of whole genome tiling arrays.
2007
17646297
Systematic discovery of functional modules and context-specific functional annotation of human genome.
2007
17646300
A statistical method for alignment-free comparison of regulatory sequences.
2007
17646303
A geometric approach for the alignment of liquid chromatography-mass spectrometry data.
2007
17646306
Nested effects models for high-dimensional phenotyping screens.
2007
17646311
Using dynamic programming to create isotopic distribution maps from mass spectra.
2007
17646314
A Chado case study: an ontology-based modular schema for representing genome-associated biological information.
2007
17646315
Prediction of DNA-binding residues from sequence.
2007
17646316
SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments.
2007
17646318
Functional annotation of regulatory pathways.
2007
17646320
SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation.
2007
17646321
Locomotif: from graphical motif description to RNA motif search.
2007
17646322
Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows.
2007
17646323
Translation initiation site prediction on a genomic scale: beauty in simplicity.
2007
17646326
Nucleotide variation of regulatory motifs may lead to distinct expression patterns.
2007
17646329
Modeling recurrent DNA copy number alterations in array CGH data.
2007
17646330
Continuous hidden process model for time series expression experiments.
2007
17646331
Gene selection via the BAHSIC family of algorithms.
2007
17646335
From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis.
2007
17646338
Information theory applied to the sparse gene ontology annotation network to predict novel gene function.
2007
17646340
Kinetics analysis methods for approximate folding landscapes.
2007
17646341
Multiple alignment by aligning alignments.
2007
17646343
A graph-based approach to systematically reconstruct human transcriptional regulatory modules.
2007
17646346
Automated image analysis of protein localization in budding yeast.
2007
17646347
In search of lost introns.
2007
17646350
Homology search for genes.
2007
17646351
BLISS 2.0: a web-based tool for predicting conserved regulatory modules in distantly-related orthologous sequences.
2007
17660203
Quality estimation of multiple sequence alignments by Bayesian hypothesis testing.
2007
17660204
sMOL Explorer: an open source, web-enabled database and exploration tool for Small MOLecules datasets.
2007
17660205
Robust smooth segmentation approach for array CGH data analysis.
2007
17660206
Robustness analysis and tuning of synthetic gene networks.
2007
17660209
AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets.
2007
17660211
Expression ratio evaluation in two-colour microarray experiments is significantly improved by correcting image misalignment.
2007
17698492
Learning string similarity measures for gene/protein name dictionary look-up using logistic regression.
2007
17698493
Mining complex genotypic features for predicting HIV-1 drug resistance.
2007
17698858
Natively unstructured regions in proteins identified from contact predictions.
2007
17709338
A Laboratory Information Management System (LIMS) for a high throughput genetic platform aimed at candidate gene mutation screening.
2007
17709339
Con-Struct Map: a comparative contact map analysis tool.
2007
17709340
CTree: comparison of clusters between phylogenetic trees made easy.
2007
17717036
LICORN: learning cooperative regulation networks from gene expression data.
2007
17720703
A comparison of background correction methods for two-colour microarrays.
2007
17720982
Exploring the functional landscape of gene expression: directed search of large microarray compendia.
2007
17724061
TMpro web server and web service: transmembrane helix prediction through amino acid property analysis.
2007
17724062
AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics.
2008
17766271
An error model for protein quantification.
2007
17768165
MSQT for choosing SNP assays from multiple DNA alignments.
2007
17785349
A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts.
2007
17804435
Phylocomposer and phylodirector: analysis and visualization of transducer indel models.
2007
17804439
Medline search engine for finding genetic markers with biological significance.
2007
17823133
The global trace graph, a novel paradigm for searching protein sequence databases.
2007
17823134
Modeling protein loops with knowledge-based prediction of sequence-structure alignment.
2007
17827204
TAGster: efficient selection of LD tag SNPs in single or multiple populations.
2007
17827206
Clustal W and Clustal X version 2.0.
2007
17846036
RagPools: RNA-As-Graph-Pools--a web server for assisting the design of structured RNA pools for in vitro selection.
2007
17855416
Cyto-Sim: a formal language model and stochastic simulator of membrane-enclosed biochemical processes.
2007
17855418
AVIS: AJAX viewer of interactive signaling networks.
2007
17855420
EGEETomo: a user-friendly, fault-tolerant and grid-enabled application for 3D reconstruction in electron tomography.
2007
17872913
oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language.
2007
17875544
A parsimonious threshold-independent protein feature selection method through the area under receiver operating characteristic curve.
2007
17878205
Moderated statistical tests for assessing differences in tag abundance.
2007
17881408
The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees.
2007
17890735
Idiographica: a general-purpose web application to build idiograms on-demand for human, mouse and rat.
2007
17893084
TreeSnatcher: coding trees from images.
2007
17893085
Extending assembly of short DNA sequences to handle error.
2007
17893086
Construction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells.
2007
17893089
Fun&Co: identification of key functional differences in transcriptomes.
2007
17893090
CREx: inferring genomic rearrangements based on common intervals.
2007
17895271
SnoReport: computational identification of snoRNAs with unknown targets.
2008
17895272
TandTRAQ: an open-source tool for integrated protein identification and quantitation.
2007
17895273
meta-PPISP: a meta web server for protein-protein interaction site prediction.
2007
17895276
Minimizing the overlap problem in protein NMR: a computational framework for precision amino acid labeling.
2007
17895278
DIA-MCIS: an importance sampling network randomizer for network motif discovery and other topological observables in transcription networks.
2007
17901083
XtalPred: a web server for prediction of protein crystallizability.
2007
17921170
I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data.
2007
17921172
Identification and visualization of cage-shaped proteins.
2007
17921173
OSCAR: one-class SVM for accurate recognition of cis-elements.
2007
17921174
Biclustering as a method for RNA local multiple sequence alignment.
2007
17921494
CellLine, a stochastic cell lineage simulator.
2007
17928303
Conformational analysis of alternative protein structures.
2007
17933849
A congruence index for testing topological similarity between trees.
2007
17933852
Carbon-fate maps for metabolic reactions.
2007
17933853
Creating protein models from electron-density maps using particle-filtering methods.
2007
17933855
InterProSurf: a web server for predicting interacting sites on protein surfaces.
2007
17933856
Optimization of HAART with genetic algorithms and agent-based models of HIV infection.
2007
17942443
Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure.
2007
17942444
i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles.
2008
17947255
NAPROC-13: a database for the dereplication of natural product mixtures in bioassay-guided protocols.
2007
17956876
Boosting multiclass learning with repeating codes and weak detectors for protein subcellular localization.
2007
17956879
PfamAlyzer: domain-centric homology search.
2007
17977882
NPIDB: a database of nucleic acids-protein interactions.
2007
17977883
Graph sharpening plus graph integration: a synergy that improves protein functional classification.
2007
17977886
Accurate prediction of enzyme mutant activity based on a multibody statistical potential.
2007
17977887
Pepitope: epitope mapping from affinity-selected peptides.
2007
17977889
Synthetic microarray data generation with RANGE and NEMO.
2008
17982169
Hierarchical tree snipping: clustering guided by prior knowledge.
2007
17989094
Statistical methods to infer cooperative binding among transcription factors in Saccharomyces cerevisiae.
2008
17989095
Rintact: enabling computational analysis of molecular interaction data from the IntAct repository.
2008
17989096
MetaNetter: inference and visualization of high-resolution metabolomic networks.
2008
18003642
Vbmp: variational Bayesian Multinomial Probit Regression for multi-class classification in R.
2008
18003643
Kernel approaches for genic interaction extraction.
2008
18003645
Independent component analysis for the extraction of reliable protein signal profiles from MALDI-TOF mass spectra.
2008
18003646
Fast protein fold estimation from NMR-derived distance restraints.
2008
18003647
Text processing through Web services: calling Whatizit.
2008
18006544
Computing topological parameters of biological networks.
2008
18006545
GWAsimulator: a rapid whole-genome simulation program.
2008
18006546
TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins.
2008
18006547
Gene Set Expression Comparison kit for BRB-ArrayTools.
2008
18006549
GEIGER: investigating evolutionary radiations.
2008
18006550
MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing.
2007
18006551
Detecting high-order interactions of single nucleotide polymorphisms using genetic programming.
2007
18006552
Genome-wide co-expression based prediction of differential expressions.
2008
18006554
Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R.
2008
18024473
BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks.
2008
18024474
Algebraic stability indicators for ranked lists in molecular profiling.
2008
18024475
KUTE-BASE: storing, downloading and exporting MIAME-compliant microarray experiments in minutes rather than hours.
2008
18024967
Identification of linked regions using high-density SNP genotype data in linkage analysis.
2008
18024969
SNPtoGO: characterizing SNPs by enriched GO terms.
2008
18024970
A profile-based deterministic sequential Monte Carlo algorithm for motif discovery.
2008
18024972
Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment.
2008
18024973
Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting.
2008
18024975
GlobalANCOVA: exploration and assessment of gene group effects.
2008
18024976
MANTIS: a phylogenetic framework for multi-species genome comparisons.
2008
18025004
The SBML discrete stochastic models test suite.
2008
18025005
Estimating node degree in bait-prey graphs.
2008
18025006
PedVizApi: a Java API for the interactive, visual analysis of extended pedigrees.
2008
18033791
ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences.
2008
18033792
NET-SYNTHESIS: a software for synthesis, inference and simplification of signal transduction networks.
2008
18033793
Analysis of a Gibbs sampler method for model-based clustering of gene expression data.
2008
18033794
Improved recognition of figures containing fluorescence microscope images in online journal articles using graphical models.
2008
18033795
GEAR: genomic enrichment analysis of regional DNA copy number changes.
2008
18037611
Automatic synchronization and distribution of biological databases and software over low-bandwidth networks among developing countries.
2008
18037613
Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species.
2008
18037683
RReportGenerator: automatic reports from routine statistical analysis using R.
2008
18037684
Identification of differentially expressed gene categories in microarray studies using nonparametric multivariate analysis.
2008
18042553
An assessment of the uses of homologous interactions.
2008
18042554
Choosing BLAST options for better detection of orthologs as reciprocal best hits.
2008
18042555
Prediction of both conserved and nonconserved microRNA targets in animals.
2008
18048393
TOM: enhancement and extension of a tool suite for in silico approaches to multigenic hereditary disorders.
2008
18048394
MutaGeneSys: estimating individual disease susceptibility based on genome-wide SNP array data.
2008
18048395
Möbius: an integrated discrete-event modeling environment.
2007
18048397
DĂ©jĂ vu--a study of duplicate citations in Medline.
2008
18056062
Model-based deconvolution of genome-wide DNA binding.
2008
18056063
BAGET: a web server for the effortless retrieval of prokaryotic gene context and sequence.
2008
18056064
COMPARE, a multi-organism system for cross-species data comparison and transfer of information.
2008
18056065
OBO Explorer: an editor for Open Biomedical Ontologies in OWL.
2008
18056066
An integrated system for studying residue coevolution in proteins.
2008
18056067
KEGGanim: pathway animations for high-throughput data.
2008
18056068
Automated manipulation of systems biology models using libSBML within Taverna workflows.
2008
18056069
Rfold: an exact algorithm for computing local base pairing probabilities.
2008
18056736
Association studies for untyped markers with TUNA.
2008
18057020
Assembly reconciliation.
2008
18057021
TFBS identification based on genetic algorithm with combined representations and adaptive post-processing.
2008
18065426
TimeClust: a clustering tool for gene expression time series.
2008
18065427
ConoServer, a database for conopeptide sequences and structures.
2008
18065428
Co-evolving residues in membrane proteins.
2007
18065429
Efficient peptide-MHC-I binding prediction for alleles with few known binders.
2008
18083718
A new algorithm for cluster analysis of genomic methylation: the Helicobacter pylori case.
2008
18086685
affyGG: computational protocols for genetical genomics with Affymetrix arrays.
2008
18086686
ZFIQ: a software package for zebrafish biology.
2008
18089619
PRALINETM: a strategy for improved multiple alignment of transmembrane proteins.
2008
18174178
DECOMP--from interpreting Mass Spectrometry peaks to solving the Money Changing Problem.
2008
18174179
NetworkBLAST: comparative analysis of protein networks.
2008
18174180
Prediction of protein functional residues from sequence by probability density estimation.
2008
18174181
A note on difficult structure alignment problems.
2008
18174182
Natural similarity measures between position frequency matrices with an application to clustering.
2008
18174183
Beyond the 'best' match: machine learning annotation of protein sequences by integration of different sources of information.
2008
18174184
Automated programming for bioinformatics algorithm deployment.
2008
18174185
Structural search and retrieval using a tableau representation of protein folding patterns.
2008
18175768
Structural systems identification of genetic regulatory networks.
2008
18175769
Hybrid huberized support vector machines for microarray classification and gene selection.
2008
18175770
FAST: Fourier transform based algorithms for significance testing of ungapped multiple alignments.
2008
18180239
The ModFOLD server for the quality assessment of protein structural models.
2008
18184684
Reconstructing ancestral genome content based on symmetrical best alignments and Dollo parsimony.
2008
18184685
Interpool: interpreting smart-pooling results.
2008
18184686
A hybrid model for robust detection of transcription factor binding sites.
2008
18184687
Discovery of candidate KEN-box motifs using cell cycle keyword enrichment combined with native disorder prediction and motif conservation.
2008
18184688
Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction.
2008
18187439
OutlierD: an R package for outlier detection using quantile regression on mass spectrometry data.
2008
18187441
Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification.
2008
18187442
A feed-forward loop guarantees robust behavior in Escherichia coli carbohydrate uptake.
2008
18187443
Figaro: a novel statistical method for vector sequence removal.
2008
18202027
The SGN comparative map viewer.
2008
18202028
QTLNetwork: mapping and visualizing genetic architecture of complex traits in experimental populations.
2008
18202029
Sparse representation and Bayesian detection of genome copy number alterations from microarray data.
2008
18203770
Multiple testing on the directed acyclic graph of gene ontology.
2008
18203773
GENESIS: genome evolution scenarios.
2008
18204053
TreeMos: a high-throughput phylogenomic approach to find and visualize phylogenetic mosaicism.
2008
18204056
TagFinder for the quantitative analysis of gas chromatography--mass spectrometry (GC-MS)-based metabolite profiling experiments.
2008
18204057
DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein-protein interactions.
2008
18204058
HCGene: a software tool to support the hierarchical classification of genes.
2008
18204060
PGMapper: a web-based tool linking phenotype to genes.
2008
18204061
Precise score for the prediction of peptides cleaved by the proteasome.
2008
18216070
A discrete view on fold space.
2008
18218654
Flexible informatics for linking experimental data to mathematical models via DataRail.
2008
18218655
Using native and syntenically mapped cDNA alignments to improve de novo gene finding.
2008
18218656
Colorstock, SScolor, RatĂłn: RNA alignment visualization tools.
2008
18218657
Jenti: an efficient tool for mining complex inbred genealogies.
2008
18222918
SOAP: short oligonucleotide alignment program.
2008
18227114
Compressed indexing and local alignment of DNA.
2008
18227115
TaxonGap: a visualization tool for intra- and inter-species variation among individual biomarkers.
2008
18227116
Utility library for structural bioinformatics.
2008
18227118
Jane: suggesting journals, finding experts.
2008
18227119
Phyutility: a phyloinformatics tool for trees, alignments and molecular data.
2008
18227120
GenomeVx: simple web-based creation of editable circular chromosome maps.
2008
18227121
Prophinder: a computational tool for prophage prediction in prokaryotic genomes.
2008
18238785
ONTO-PERL: an API for supporting the development and analysis of bio-ontologies.
2008
18245124
De novo identification of highly diverged protein repeats by probabilistic consistency.
2008
18245125
Model-based Bayesian clustering (MBBC).
2008
18245126
SVM-HUSTLE--an iterative semi-supervised machine learning approach for pairwise protein remote homology detection.
2008
18245127
Using flowViz to visualize flow cytometry data.
2008
18245128
Prediction of zinc-binding sites in proteins from sequence.
2008
18245129
LibSBML: an API library for SBML.
2008
18252737
Statistical search on the Semantic Web.
2008
18263641
Interactive visualization software for exploring phylogenetic trees and clades.
2008
18263642
ConFunc--functional annotation in the twilight zone.
2008
18263643
Complexity reduction of biochemical rate expressions.
2008
18267948
Detecting hierarchical structure in molecular characteristics of disease using transitive approximations of directed graphs.
2008
18285370
ParCrys: a Parzen window density estimation approach to protein crystallization propensity prediction.
2008
18285371
GOTreePlus: an interactive gene ontology browser.
2008
18292113
MMG: a probabilistic tool to identify submodules of metabolic pathways.
2008
18292114
PCCA: a program for phylogenetic canonical correlation analysis.
2008
18292115
Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models.
2008
18292116
Tree-guided Bayesian inference of population structures.
2008
18296461
CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms.
2008
18296463
fdrMotif: identifying cis-elements by an EM algorithm coupled with false discovery rate control.
2008
18296465
Disease association tests by inferring ancestral haplotypes using a hidden markov model.
2008
18296746
The effect of sequence quality on sequence alignment.
2008
18296747
SubSeqer: a graph-based approach for the detection and identification of repetitive elements in low-complexity sequences.
2008
18304932
AIMIE: a web-based environment for detection and interpretation of significant sequence motifs in prokaryotic genomes.
2008
18304933
FTFD: an informatics pipeline supporting phylogenomic analysis of fungal transcription factors.
2008
18304934
DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra.
2008
18304935
Tracing evolutionary pressure.
2008
18304936
ISD: a software package for Bayesian NMR structure calculation.
2008
18310055
In silico Biochemical Reaction Network Analysis (IBRENA): a package for simulation and analysis of reaction networks.
2008
18310056
Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline.
2008
18310057
Reference descriptions of cellular electrophysiology models.
2008
18310619
Robustified MANOVA with applications in detecting differentially expressed genes from oligonucleotide arrays.
2008
18316342
PedMine--a simulated annealing algorithm to identify maximally unrelated individuals in population isolates.
2008
18321883
e-LiSe--an online tool for finding needles in the '(Medline) haystack'.
2008
18321884
BicOverlapper: a tool for bicluster visualization.
2008
18321885
Consensus generation and variant detection by Celera Assembler.
2008
18321888
W-AlignACE: an improved Gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/ChIP-chip data.
2008
18325926
Merging two gene-expression studies via cross-platform normalization.
2008
18325927
MiSearch adaptive pubMed search tool.
2009
18326507
3D-Garden: a system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm.
2008
18326508
A pattern recognition approach to infer time-lagged genetic interactions.
2008
18337258
Optimizing the size of the sequence profiles to increase the accuracy of protein sequence alignments generated by profile-profile algorithms.
2008
18337259
PlasmoGF: an integrated system for comparative genomics and phylogenetic analysis of Plasmodium gene families.
2008
18337260
The Taverna Interaction Service: enabling manual interaction in workflows.
2008
18337261
ChIPCodis: mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data.
2008
18339638
GlycoBase and autoGU: tools for HPLC-based glycan analysis.
2008
18344517
Unequal group variances in microarray data analyses.
2008
18344518
Integrating ARC grid middleware with Taverna workflows.
2008
18353787
Combining statistical alignment and phylogenetic footprinting to detect regulatory elements.
2008
18353788
A suite of Perl modules for handling microarray data.
2008
18353790
Linear time-varying models can reveal non-linear interactions of biomolecular regulatory networks using multiple time-series data.
2008
18367478
Visualization of unfavorable interactions in protein folds.
2008
18375963
CompariMotif: quick and easy comparisons of sequence motifs.
2008
18375965
An improved physico-chemical model of hybridization on high-density oligonucleotide microarrays.
2008
18378525
FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps.
2008
18381401
GeneTrack--a genomic data processing and visualization framework.
2008
18388141
MTMDAT: Automated analysis and visualization of mass spectrometry data for tertiary and quaternary structure probing of proteins.
2008
18388142
Prediction of the translocon-mediated membrane insertion free energies of protein sequences.
2008
18388143
ASPicDB: a database resource for alternative splicing analysis.
2008
18388144
siRNA specificity searching incorporating mismatch tolerance data.
2008
18397893
Domain annotation of trimeric autotransporter adhesins--daTAA.
2008
18397894
adegenet: a R package for the multivariate analysis of genetic markers.
2008
18397895
Fast network component analysis (FastNCA) for gene regulatory network reconstruction from microarray data.
2008
18400771
EPO-KB: a searchable knowledge base of biomarker to protein links.
2008
18400772
MedEvi: retrieving textual evidence of relations between biomedical concepts from Medline.
2008
18400773
A system for generating transcription regulatory networks with combinatorial control of transcription.
2008
18400774
Divisive Correlation Clustering Algorithm (DCCA) for grouping of genes: detecting varying patterns in expression profiles.
2008
18407922
Implementation of a regulatory gene network to simulate the TH1/2 differentiation in an agent-based model of hypersensitivity reactions.
2008
18413328
Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers.
2008
18413329
Forward-time simulations of non-random mating populations using simuPOP.
2008
18417488
IDMap: facilitating the detection of potential leads with therapeutic targets.
2008
18417489
OnD-CRF: predicting order and disorder in proteins using [corrected] conditional random fields.
2008
18430742
TOPDOM: database of domains and motifs with conservative location in transmembrane proteins.
2008
18434342
RNAplex: a fast tool for RNA-RNA interaction search.
2008
18434344
Annotation-Modules: a tool for finding significant combinations of multisource annotations for gene lists.
2008
18434345
swissPIT: a novel approach for pipelined analysis of mass spectrometry data.
2008
18436540
MAMOT: hidden Markov modeling tool.
2008
18440999
fdrtool: a versatile R package for estimating local and tail area-based false discovery rates.
2008
18441000
gpDB: a database of GPCRs, G-proteins, effectors and their interactions.
2008
18441001
PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure.
2008
18443018
Cytoscape ESP: simple search of complex biological networks.
2008
18445605
jSquid: a Java applet for graphical on-line network exploration.
2008
18445606
nuScore: a web-interface for nucleosome positioning predictions.
2008
18445607
quantiNemo: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation.
2008
18450810
Characterization and prediction of residues determining protein functional specificity.
2008
18450811
A correction for estimating error when using the Local Pooled Error Statistical Test.
2008
18450812
A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics.
2008
18453551
DAnTE: a statistical tool for quantitative analysis of -omics data.
2008
18453552
Mireval: a web tool for simple microRNA prediction in genome sequences.
2008
18453555
SYCAMORE--a systems biology computational analysis and modeling research environment.
2008
18463116
Identification of OBO nonalignments and its implications for OBO enrichment.
2008
18463117
PatMaN: rapid alignment of short sequences to large databases.
2008
18467344
lumi: a pipeline for processing Illumina microarray.
2008
18467348
HSEpred: predict half-sphere exposure from protein sequences.
2008
18467349
FunSiP: a modular and extensible classifier for the prediction of functional sites in DNA.
2008
18474505
Malin: maximum likelihood analysis of intron evolution in eukaryotes.
2008
18474506
OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar.
2008
18474507
DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony.
2008
18474508
ProBias: a web-server for the identification of user-specified types of compositionally biased segments in protein sequences.
2008
18480099
Computing chemical organizations in biological networks.
2008
18480100
An overview of the wcd EST clustering tool.
2008
18480101
qpcR: an R package for sigmoidal model selection in quantitative real-time polymerase chain reaction analysis.
2008
18482995
Penalized estimation of haplotype frequencies.
2008
18487240
PhyloWidget: web-based visualizations for the tree of life.
2008
18487241
Swelfe: a detector of internal repeats in sequences and structures.
2008
18487242
MOCSphaser: a haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data.
2008
18492685
EM-random forest and new measures of variable importance for multi-locus quantitative trait linkage analysis.
2008
18499695
The Sleipnir library for computational functional genomics.
2008
18499696
A Bayesian estimator of protein-protein association probabilities.
2008
18499697
InteroPORC: automated inference of highly conserved protein interaction networks.
2008
18508856
Using inferred residue contacts to distinguish between correct and incorrect protein models.
2008
18511466
Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration.
2008
18511468
CellTrack: an open-source software for cell tracking and motility analysis.
2008
18511469
Sparse kernel methods for high-dimensional survival data.
2008
18515276
Web-based design and evaluation of T-cell vaccine candidates.
2008
18515277
SNP analysis to results (SNPator): a web-based environment oriented to statistical genomics analyses upon SNP data.
2008
18515823
LOT: a tool for linkage analysis of ordinal traits for pedigree data.
2008
18535081
Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification.
2008
18535082
Modeling promoter grammars with evolving hidden Markov models.
2008
18535083
Optimal vaccination schedules using simulated annealing.
2008
18535084
Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data.
2008
18544546
Microarray-based classification and clinical predictors: on combined classifiers and additional predictive value.
2008
18544547
DNAlive: a tool for the physical analysis of DNA at the genomic scale.
2008
18544548
MINS2: revisiting the molecular code for transmembrane-helix recognition by the Sec61 translocon.
2008
18544549
MPIDB: the microbial protein interaction database.
2008
18556668
Modeling immune system control of atherogenesis.
2008
18556669
Predicting functional regulatory polymorphisms.
2008
18562267
Biomarker selection and sample prediction for multi-category disease on MALDI-TOF data.
2008
18562269
Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models.
2008
18562270
Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence.
2008
18565990
iFoldRNA: three-dimensional RNA structure prediction and folding.
2008
18579566
Intrinsic disorder prediction from the analysis of multiple protein fold recognition models.
2008
18579567
PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation patterns of CpG islands.
2008
18579568
Comparing simulation results of SBML capable simulators.
2008
18579569
Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors.
2008
18586699
FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space.
2008
18586700
Estimating true evolutionary distances under the DCJ model.
2008
18586703
Efficient inference of bacterial strain trees from genome-scale multilocus data.
2008
18586704
Alignment and classification of time series gene expression in clinical studies.
2008
18586707
Inferring differentiation pathways from gene expression.
2008
18586709
Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences.
2008
18586710
Predicting protein thermostability changes from sequence upon multiple mutations.
2008
18586713
Identifying functional modules in protein-protein interaction networks: an integrated exact approach.
2008
18586718
Prediction of drug-target interaction networks from the integration of chemical and genomic spaces.
2008
18586719
Protein complex identification by supervised graph local clustering.
2008
18586722
Identifying gene-disease associations using centrality on a literature mined gene-interaction network.
2008
18586725
Integrating high dimensional bi-directional parsing models for gene mention tagging.
2008
18586726
The EXACT description of biomedical protocols.
2008
18586727
Towards the use of argumentation in bioinformatics: a gene expression case study.
2008
18586728
The ontology of biological taxa.
2008
18586729
GenoQuery: a new querying module for functional annotation in a genomic warehouse.
2008
18586731
Matching isotopic distributions from metabolically labeled samples.
2008
18586733
Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification.
2008
18586734
BLASTing small molecules--statistics and extreme statistics of chemical similarity scores.
2008
18586735
Selecting anti-HIV therapies based on a variety of genomic and clinical factors.
2008
18586740
A robust framework for detecting structural variations in a genome.
2008
18586745
POIMs: positional oligomer importance matrices--understanding support vector machine-based signal detectors.
2008
18586746
A max-margin model for efficient simultaneous alignment and folding of RNA sequences.
2008
18586747
MACHOS: Markov clusters of homologous subsequences.
2008
18586748
Classification and feature selection algorithms for multi-class CGH data.
2008
18586749
Predicting protein function from domain content.
2008
18591194
PuReD-MCL: a graph-based PubMed document clustering methodology.
2008
18593717
BioMAJ: a flexible framework for databanks synchronization and processing.
2008
18593718
ChemmineR: a compound mining framework for R.
2008
18596077
Watermarking sexually reproducing diploid organisms.
2008
18599517
FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology.
2008
18599518
TRITON: a graphical tool for ligand-binding protein engineering.
2008
18603567
A probe-density-based analysis method for array CGH data: simulation, normalization and centralization.
2008
18603568
ProteoWizard: open source software for rapid proteomics tools development.
2008
18606607
Discovering regulatory motifs in the Plasmodium genome using comparative genomics.
2008
18611947
Dynamical modeling and multi-experiment fitting with PottersWheel.
2008
18614583
Yale Image Finder (YIF): a new search engine for retrieving biomedical images.
2008
18614584
Synchronous versus asynchronous modeling of gene regulatory networks.
2008
18614585
Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli.
2008
18621757
Classification with reject option in gene expression data.
2008
18621758
Semantic reclassification of the UMLS concepts.
2008
18625612
PathCluster: a framework for gene set-based hierarchical clustering.
2008
18628289
Artificial neural network for prediction of antigenic activity for a major conformational epitope in the hepatitis C virus NS3 protein.
2008
18628290
Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis.
2008
18632749
ProCope--protein complex prediction and evaluation.
2008
18635566
A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all?
2008
18635567
Development of a two-dimensional agent-based model for chronic chagasic cardiomyopathy after stem cell transplantation.
2008
18635568
Sircah: a tool for the detection and visualization of alternative transcripts.
2008
18635569
mlegp: statistical analysis for computer models of biological systems using R.
2008
18635570
MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence.
2008
18635571
The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data.
2008
18635572
MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization.
2008
18635573
Data-driven extraction of relative reasoning rules to limit combinatorial explosion in biodegradation pathway prediction.
2008
18641402
PIGS: automatic prediction of antibody structures.
2008
18641403
GenoSNP: a variational Bayes within-sample SNP genotyping algorithm that does not require a reference population.
2008
18653518
An integrated approach for automating validation of extracted ion chromatographic peaks.
2008
18653519
Cytoprophet: a Cytoscape plug-in for protein and domain interaction networks inference.
2008
18653520
Robust and efficient identification of biomarkers by classifying features on graphs.
2008
18653521
hapConstructor: automatic construction and testing of haplotypes in a Monte Carlo framework.
2008
18653522
DrugViz: a Cytoscape plugin for visualizing and analyzing small molecule drugs in biological networks.
2008
18658180
The CellML Model Repository.
2008
18658182
Site-specific evolutionary rates in proteins are better modeled as non-independent and strictly relative.
2008
18662926
HELIQUEST: a web server to screen sequences with specific alpha-helical properties.
2008
18662927
Modelling non-stationary gene regulatory processes with a non-homogeneous Bayesian network and the allocation sampler.
2008
18664467
Efficient whole-genome association mapping using local phylogenies for unphased genotype data.
2008
18667442
Large-scale computation of elementary flux modes with bit pattern trees.
2008
18676417
Model-based prediction of sequence alignment quality.
2008
18678587
Powerful fusion: PSI-BLAST and consensus sequences.
2008
18678588
VistaClara: an expression browser plug-in for Cytoscape.
2008
18678589
Phylocom: software for the analysis of phylogenetic community structure and trait evolution.
2008
18678590
BLogo: a tool for visualization of bias in biological sequences.
2008
18682425
ZOOM! Zillions of oligos mapped.
2008
18684737
PK/DB: database for pharmacokinetic properties and predictive in silico ADME models.
2008
18684738
Peptide Finder: mapping measured molecular masses to peptides and proteins.
2008
18687695
BioJava: an open-source framework for bioinformatics.
2008
18689808
RNA structure alignment by a unit-vector approach.
2008
18689811
Inter-species normalization of gene mentions with GNAT.
2008
18689813
A fast and flexible method for the segmentation of aCGH data.
2008
18689815
PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database.
2008
18689816
Efficient representation and P-value computation for high-order Markov motifs.
2008
18689819
Optimal spliced alignments of short sequence reads.
2008
18689821
ChIPmix: mixture model of regressions for two-color ChIP-chip analysis.
2008
18689822
Segment-based multiple sequence alignment.
2008
18689823
Connect the dots: exposing hidden protein family connections from the entire sequence tree.
2008
18689824
Comprehensive in silico mutagenesis highlights functionally important residues in proteins.
2008
18689826
Organization and integration of biomedical knowledge with concept maps for key peroxisomal pathways.
2008
18689827
Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules.
2008
18689828
Temporal logic patterns for querying dynamic models of cellular interaction networks.
2008
18689830
Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc.
2008
18689831
Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry.
2008
18689838
Towards de novo identification of metabolites by analyzing tandem mass spectra.
2008
18689839
Fusing time series expression data through hybrid aggregation and hierarchical merge.
2008
18689841
Gaussian process modelling of latent chemical species: applications to inferring transcription factor activities.
2008
18689843
SIRENE: supervised inference of regulatory networks.
2008
18689844
PhyloDetect: a likelihood-based strategy for detecting microorganisms with diagnostic microarrays.
2008
18689845
Clinically driven semi-supervised class discovery in gene expression data.
2008
18689846
Protein structure alignment considering phenotypic plasticity.
2008
18689847
Arabidopsis thaliana regulatory element analyzer.
2008
18694893
Dasty2, an Ajax protein DAS client.
2008
18694895
The Synergizer service for translating gene, protein and other biological identifiers.
2008
18697767
Computational prediction of human proteins that can be secreted into the bloodstream.
2008
18697770
Detection of stoichiometric inconsistencies in biomolecular models.
2008
18697772
High-performance signal peptide prediction based on sequence alignment techniques.
2008
18697773
Cancer outlier detection based on likelihood ratio test.
2008
18697774
PRODECOMPv3: decompositions of NMR projections for protein backbone and side-chain assignments and structural studies.
2008
18701530
GIMSAN: a Gibbs motif finder with significance analysis.
2008
18703586
Inference of structure in subdivided populations at low levels of genetic differentiation--the correlated allele frequencies model revisited.
2008
18710873
Integrating expression data with domain interaction networks.
2008
18710874
A toolkit for analysing large-scale plant small RNA datasets.
2008
18713789
Analyzing gene perturbation screens with nested effects models in R and bioconductor.
2008
18718939
Eigen-R2 for dissecting variation in high-dimensional studies.
2008
18718946
Direct mapping and alignment of protein sequences onto genomic sequence.
2008
18728043
PathCase: pathways database system.
2008
18728044
GOfetcher: a database with complex searching facility for gene ontology.
2008
18728045
SynBioSS: the synthetic biology modeling suite.
2008
18757873
PREDICT-2ND: a tool for generalized protein local structure prediction.
2008
18757875
Bosque: integrated phylogenetic analysis software.
2008
18762483
MeltDB: a software platform for the analysis and integration of metabolomics experiment data.
2008
18765459
FACTA: a text search engine for finding associated biomedical concepts.
2008
18772154
Identification of the idiosyncratic bacterial protein tyrosine kinase (BY-kinase) family signature.
2008
18772155
varDB: a pathogen-specific sequence database of protein families involved in antigenic variation.
2008
18776192
INTREPID--INformation-theoretic TREe traversal for Protein functional site IDentification.
2008
18776193
STREAM: Static Thermodynamic REgulAtory Model of transcription.
2008
18776194
DESHARKY: automatic design of metabolic pathways for optimal cell growth.
2008
18776195
ADZE: a rarefaction approach for counting alleles private to combinations of populations.
2008
18779233
OmicsViz: Cytoscape plug-in for visualizing omics data across species.
2008
18779234
Predicting gene targets of perturbations via network-based filtering of mRNA expression compendia.
2008
18779235
F-Seq: a feature density estimator for high-throughput sequence tags.
2008
18784119
MPI-LIT: a literature-curated dataset of microbial binary protein--protein interactions.
2008
18786976
Specific alignment of structured RNA: stochastic grammars and sequence annealing.
2008
18796475
MonkeySNP: a web portal for non-human primate single nucleotide polymorphisms.
2008
18796476
tCal: transcriptional probability calculator using thermodynamic model.
2008
18796477
TESE: generating specific protein structure test set ensembles.
2008
18796478
GOSLING: a rule-based protein annotator using BLAST and GO.
2008
18796479
FunNet: an integrative tool for exploring transcriptional interactions.
2008
18799481
GenMiner: mining non-redundant association rules from integrated gene expression data and annotations.
2008
18799482
BEST: Bayesian estimation of species trees under the coalescent model.
2008
18799483
A toolkit for capturing and sharing FuGE experiments.
2008
18801749
Functional modules integrating essential cellular functions are predictive of the response of leukaemia cells to DNA damage.
2008
18801750
MS-BID: a Java package for label-free LC-MS-based comparative proteomic analysis.
2008
18805798
Integrating and annotating the interactome using the MiMI plugin for cytoscape.
2009
18812364
DOCKGROUND protein-protein docking decoy set.
2008
18812365
A new rule-based algorithm for identifying metabolic markers in prostate cancer using tandem mass spectrometry.
2008
18815183
Searching protein structure databases with DaliLite v.3.
2008
18818215
Bayesian learning of biological pathways on genomic data assimilation.
2008
18818216
Identifying differentially expressed subnetworks with MMG.
2008
18819939
Databases, data tombs and dust in the wind.
2008
18819940
MSX-3D: a tool to validate 3D protein models using mass spectrometry.
2008
18826958
Smarter clustering methods for SNP genotype calling.
2008
18826959
Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation.
2008
18842597
Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications.
2008
18842598
GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus.
2008
18842599
The Burkholderia Genome Database: facilitating flexible queries and comparative analyses.
2008
18842600
A flexible forward simulator for populations subject to selection and demography.
2008
18842601
A novel method for comparing topological models of protein structures enhanced with ligand information.
2008
18842602
CNVDetector: locating copy number variations using array CGH data.
2008
18842603
Systems-level modeling of cellular glycosylation reaction networks: O-linked glycan formation on natural selectin ligands.
2008
18842604
IPEP: an in silico tool to examine proteolytic peptides for mass spectrometry.
2008
18842605
Impact of dimeric organization of enzyme on its function: the case of photosynthetic water splitting.
2008
18845578
FABSIM: a software for generating FST distributions with various ascertainment biases.
2008
18845580
Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database.
2008
18845581
A better block partition and ligation strategy for individual haplotyping.
2008
18845583
Profile Comparer: a program for scoring and aligning profile hidden Markov models.
2008
18845584
A bioinformatics analysis of the cell line nomenclature.
2008
18849319
POPE--a tool to aid high-throughput phylogenetic analysis.
2008
18849569
Osiris: an integrated promoter database for Oryza sativa L.
2008
18922805
BioCaster: detecting public health rumors with a Web-based text mining system.
2008
18922806
Reconstructing tumor-wise protein expression in tissue microarray studies using a Bayesian cell mixture model.
2008
18922808
mspire: mass spectrometry proteomics in Ruby.
2008
18930952
WAVECLOCK: wavelet analysis of circadian oscillation.
2008
18931366
The Protein Feature Ontology: a tool for the unification of protein feature annotations.
2008
18936051
REJECTOR: software for population history inference from genetic data via a rejection algorithm.
2008
18936052
IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions.
2008
18940824
Predicting small ligand binding sites in proteins using backbone structure.
2008
18940825
QGene 4.0, an extensible Java QTL-analysis platform.
2008
18940826
Effective cluster-based seed design for cross-species sequence comparisons.
2008
18940827
Prediction of kinase-specific phosphorylation sites using conditional random fields.
2008
18940828
SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology.
2008
18945683
Integrated search and alignment of protein structures.
2008
18945684
CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data.
2008
18945685
Aggressive assembly of pyrosequencing reads with mates.
2008
18952627
BASH: a tool for managing BeadArray spatial artefacts.
2008
18953044
AUGIST: inferring species trees while accommodating gene tree uncertainty.
2008
18953045
Poisson approximation for significance in genome-wide ChIP-chip tiling arrays.
2008
18953047
Identifying molecular markers associated with classification of genotypes by External Logistic Biplots.
2008
18974073
Protease substrate site predictors derived from machine learning on multilevel substrate phage display data.
2008
18974075
iMapper: a web application for the automated analysis and mapping of insertional mutagenesis sequence data against Ensembl genomes.
2008
18974167
SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap.
2008
18974171
Model-based analysis of non-specific binding for background correction of high-density oligonucleotide microarrays.
2009
18977779
PConPy--a Python module for generating 2D protein maps.
2008
18977780
Cross-hybridization modeling on Affymetrix exon arrays.
2008
18984598
TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops.
2009
18984599
DNAPlotter: circular and linear interactive genome visualization.
2009
18990721
A novel signaling pathway impact analysis.
2009
18990722
RANKPROP: a web server for protein remote homology detection.
2009
18990723
ProtorP: a protein-protein interaction analysis server.
2009
19001476
Predicting DNA recognition by Cys2His2 zinc finger proteins.
2009
19008249
MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context.
2009
19008250
Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature.
2009
19008251
Genetic algorithms for simultaneous variable and sample selection in metabonomics.
2009
19010803
CRONOS: the cross-reference navigation server.
2009
19010804
Align human interactome with phenome to identify causative genes and networks underlying disease families.
2009
19010805
Selection of oligonucleotides for whole-genome microarrays with semi-automatic update.
2009
19015129
Prediction of translation initiation site for microbial genomes with TriTISA.
2009
19015130
Genetic association analysis with FAMHAP: a major program update.
2009
19015131
Power enhancement via multivariate outlier testing with gene expression arrays.
2009
19015138
Motif Tool Manager: a web-based framework for motif discovery.
2008
19017656
CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets.
2009
19017659
Gene expression trends and protein features effectively complement each other in gene function prediction.
2009
19050035
Computationally feasible estimation of haplotype frequencies from pooled DNA with and without Hardy-Weinberg equilibrium.
2009
19050036
Reference alignment of SNP microarray signals for copy number analysis of tumors.
2009
19052058
Estimation of errors introduced by confocal imaging into the data on segmentation gene expression in Drosophila.
2009
19052059
Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment.
2009
19056777
Structural profiles of human miRNA families from pairwise clustering.
2009
19059941
Matrix correlations for high-dimensional data: the modified RV-coefficient.
2009
19073588
SIMoNe: Statistical Inference for MOdular NEtworks.
2009
19073589
PASTAA: identifying transcription factors associated with sets of co-regulated genes.
2009
19073590
Evaluating contributions of natural language parsers to protein-protein interaction extraction.
2009
19073593
NOEnet--use of NOE networks for NMR resonance assignment of proteins with known 3D structure.
2009
19074506
rHVDM: an R package to predict the activity and targets of a transcription factor.
2009
19074958
FastMap: fast eQTL mapping in homozygous populations.
2009
19091771
Precision and recall estimates for two-hybrid screens.
2009
19091773
Probabilistic assignment of formulas to mass peaks in metabolomics experiments.
2009
19095699
Prediction of RNA secondary structure using generalized centroid estimators.
2009
19095700
Matching methods for observational microarray studies.
2009
19098026
SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms.
2009
19098027
PuMA: Bayesian analysis of partitioned (and unpartitioned) model adequacy.
2009
19098028
SNPHarvester: a filtering-based approach for detecting epistatic interactions in genome-wide association studies.
2009
19098029
SAFEGUI: resampling-based tests of categorical significance in gene expression data made easy.
2009
19098030
The analysis of inconsistencies between cytogenetic annotations and sequence mapping by defining the imprecision zones of cytogenetic banding.
2009
19098301
AnnotationSketch: a genome annotation drawing library.
2009
19106120
arrayQualityMetrics--a bioconductor package for quality assessment of microarray data.
2009
19106121
Differential dependency network analysis to identify condition-specific topological changes in biological networks.
2009
19112081
The Flannotator--a gene and protein expression annotation tool for Drosophila melanogaster.
2009
19126575
BioCichlid: central dogma-based 3D visualization system of time-course microarray data on a hierarchical biological network.
2009
19126577
DichroCalc--circular and linear dichroism online.
2009
19129206
A novel method for large tree visualization.
2009
19129207
bioDBnet: the biological database network.
2009
19129209
Biodiversity informatics: automated approaches for documenting global biodiversity patterns and processes.
2009
19129210
SCARF: maximizing next-generation EST assemblies for evolutionary and population genomic analyses.
2009
19129211
Prequips--an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data.
2009
19129212
Non-negative matrix factorization of gene expression profiles: a plug-in for BRB-ArrayTools.
2009
19131367
Correcting for ascertainment bias in the inference of population structure.
2009
19136550
Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies.
2009
19136551
Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery.
2009
19136552
Module networks revisited: computational assessment and prioritization of model predictions.
2009
19136553
DTA: dihedral transition analysis for characterization of the effects of large main-chain dihedral changes in proteins.
2009
19147660
Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics.
2009
19147661
A hierarchical model for incomplete alignments in phylogenetic inference.
2009
19147663
MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions.
2009
19147664
PROMOT: modular modeling for systems biology.
2009
19147665
MSMAD: a computationally efficient method for the analysis of noisy array CGH data.
2009
19147666
IslandViewer: an integrated interface for computational identification and visualization of genomic islands.
2009
19151094
Jalview Version 2--a multiple sequence alignment editor and analysis workbench.
2009
19151095
CPSP-web-tools: a server for 3D lattice protein studies.
2009
19151096
FrameDP: sensitive peptide detection on noisy matured sequences.
2009
19153134
The protein-small-molecule database, a non-redundant structural resource for the analysis of protein-ligand binding.
2009
19153135
Sequence-based prediction of protein interaction sites with an integrative method.
2009
19153136
Gclust: trans-kingdom classification of proteins using automatic individual threshold setting.
2009
19158159
DSSTox chemical-index files for exposure-related experiments in ArrayExpress and Gene Expression Omnibus: enabling toxico-chemogenomics data linkages.
2009
19158160
Detecting gene clusters under evolutionary constraint in a large number of genomes.
2009
19158161
Disperse--a software system for design of selector probes for exon resequencing applications.
2009
19158162
RNAither, an automated pipeline for the statistical analysis of high-throughput RNAi screens.
2009
19168909
MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data.
2009
19168910
Sparse linear discriminant analysis for simultaneous testing for the significance of a gene set/pathway and gene selection.
2009
19168911
KEA: kinase enrichment analysis.
2009
19176546
A novel meta-analysis method exploiting consistency of high-throughput experiments.
2009
19176547
Benchmarks for identification of ordinary differential equations from time series data.
2009
19176548
Automated procedure for candidate compound selection in GC-MS metabolomics based on prediction of Kovats retention index.
2009
19176550
QMSim: a large-scale genome simulator for livestock.
2009
19176551
Serial dilution curve: a new method for analysis of reverse phase protein array data.
2009
19176552
Testing significance relative to a fold-change threshold is a TREAT.
2009
19176553
Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques.
2009
19176554
A flexible rank-based framework for detecting copy number aberrations from array data.
2009
19176555
Parallelized prediction error estimation for evaluation of high-dimensional models.
2009
19176556
The DICS repository: module-assisted analysis of disease-related gene lists.
2009
19176557
Retention time alignment algorithms for LC/MS data must consider non-linear shifts.
2009
19176558
A novel comprehensive wave-form MS data processing method.
2009
19176559
'Double water exclusion': a hypothesis refining the O-ring theory for the hot spots at protein interfaces.
2009
19179356
SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements.
2009
19179357
CORNA: testing gene lists for regulation by microRNAs.
2009
19181683
NOBLAST and JAMBLAST: New Options for BLAST and a Java Application Manager for BLAST results.
2009
19181685
Benchmarking regulatory network reconstruction with GRENDEL.
2009
19188190
SciMiner: web-based literature mining tool for target identification and functional enrichment analysis.
2009
19188191
Accurate identification of orthologous segments among multiple genomes.
2009
19188192
High-performance gene name normalization with GeNo.
2009
19188193
Meta-analysis of age-related gene expression profiles identifies common signatures of aging.
2009
19189975
Systems biology metabolic modeling assistant: an ontology-based tool for the integration of metabolic data in kinetic modeling.
2009
19189977
Lightweight comparison of RNAs based on exact sequence-structure matches.
2009
19189979
QVALITY: non-parametric estimation of q-values and posterior error probabilities.
2009
19193729
CoCAS: a ChIP-on-chip analysis suite.
2009
19193731
Radié: visualizing taxon properties and parsimonious mappings using a radial phylogenetic tree.
2009
19193733
FRANz: reconstruction of wild multi-generation pedigrees.
2009
19202194
A web-based software system for dynamic gene cluster comparison across multiple genomes.
2009
19208612
STEM: species tree estimation using maximum likelihood for gene trees under coalescence.
2009
19211573
Enumeration of condition-dependent dense modules in protein interaction networks.
2009
19213739
Simulation of large-scale rule-based models.
2009
19213740
Allergen Atlas: a comprehensive knowledge center and analysis resource for allergen information.
2009
19213741
PASS: a program to align short sequences.
2009
19218350
Gene network reconstruction from transcriptional dynamics under kinetic model uncertainty: a case for the second derivative.
2009
19218351
CGAS: comparative genomic analysis server.
2009
19218352
OnTheFly: a tool for automated document-based text annotation, data linking and network generation.
2009
19223449
RAMI: a tool for identification and characterization of phylogenetic clusters in microbial communities.
2009
19223450
Homogeneous decomposition of protein interaction networks: refining the description of intra-modular interactions.
2009
19223451
A new ensemble-based algorithm for identifying breath gas marker candidates in liver disease using ion molecule reaction mass spectrometry.
2009
19223453
MOM: maximum oligonucleotide mapping.
2009
19228804
Seevolution: visualizing chromosome evolution.
2009
19233896
PLATINUM: a web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes.
2009
19244385
Biomarker discovery in MALDI-TOF serum protein profiles using discrete wavelet transformation.
2009
19244390
A robust peak detection method for RNA structure inference by high-throughput contact mapping.
2009
19246511
Textual data compression in computational biology: a synopsis.
2009
19251772
GeNGe: systematic generation of gene regulatory networks.
2009
19251773
WSsas: a web service for the annotation of functional residues through structural homologues.
2009
19251774
DIYA: a bacterial annotation pipeline for any genomics lab.
2009
19254921
Multivariate analysis of variance test for gene set analysis.
2009
19254923
Illoura: a software tool for analysis, visualization and semantic querying of cellular and other spatial biological data.
2009
19258351
SpliceAid: a database of experimental RNA target motifs bound by splicing proteins in humans.
2009
19261717
A web server for inferring the human N-acetyltransferase-2 (NAT2) enzymatic phenotype from NAT2 genotype.
2009
19261719
A modified hyperplane clustering algorithm allows for efficient and accurate clustering of extremely large datasets.
2009
19261720
LOCP--locating pilus operons in gram-positive bacteria.
2009
19261721
PADRE: a package for analyzing and displaying reticulate evolution.
2009
19269989
A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads.
2009
19269990
Smoothing waves in array CGH tumor profiles.
2009
19276148
DV-Curve: a novel intuitive tool for visualizing and analyzing DNA sequences.
2009
19276149
The tspair package for finding top scoring pair classifiers in R.
2009
19276151
Joint estimation of copy number variation and reference intensities on multiple DNA arrays using GADA.
2009
19276152
Switching regulatory models of cellular stress response.
2009
19279066
CodonExplorer: an online tool for analyzing codon usage and sequence composition, scaling from genes to genomes.
2009
19279067
Site of metabolism prediction for six biotransformations mediated by cytochromes P450.
2009
19286831
A novel parallel approach to the likelihood-based estimation of admixture in population genetics.
2009
19286832
Statistical detection of cooperative transcription factors with similarity adjustment.
2009
19286833
SimMLST: simulation of multi-locus sequence typing data under a neutral model.
2009
19286834
A method and program for estimating graphical models for linkage disequilibrium that scale linearly with the number of loci, and their application to gene drop simulation.
2009
19289443
GS2: an efficiently computable measure of GO-based similarity of gene sets.
2009
19289444
TopHat: discovering splice junctions with RNA-Seq.
2009
19289445
Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts.
2009
19289446
Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data.
2009
19289448
Synergy Disequilibrium Plots: graphical visualization of pairwise synergies and redundancies of SNPs with respect to a phenotype.
2009
19297347
Visualization of genomic data with the Hilbert curve.
2009
19297348
DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System.
2009
19297349
Artefacts and biases affecting the evaluation of scoring functions on decoy sets for protein structure prediction.
2009
19297350
Identifying functional modules using expression profiles and confidence-scored protein interactions.
2009
19297352
Automated diagnosis of LC-MS/MS performance.
2009
19304874
Local RNA structure alignment with incomplete sequence.
2009
19304875
The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance.
2009
19304876
GNU MCSim: Bayesian statistical inference for SBML-coded systems biology models.
2009
19304877
Biopython: freely available Python tools for computational molecular biology and bioinformatics.
2009
19304878
Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates.
2009
19307237
KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor.
2009
19307239
SBML2L(A)T(E)X: conversion of SBML files into human-readable reports.
2009
19307240
BioconductorBuntu: a Linux distribution that implements a web-based DNA microarray analysis server.
2009
19307241
Infernal 1.0: inference of RNA alignments.
2009
19307242
A web application to perform linkage disequilibrium and linkage analyses on a computational grid.
2009
19318423
Integrating shotgun proteomics and mRNA expression data to improve protein identification.
2009
19318424
dCAS: a desktop application for cDNA sequence annotation.
2009
19318425
Structure similarity measure with penalty for close non-equivalent residues.
2009
19321733
GetBonNie for building, analyzing and sharing rule-based models.
2009
19321734
CNVVdb: a database of copy number variations across vertebrate genomes.
2009
19321736
StatQuant: a post-quantification analysis toolbox for improving quantitative mass spectrometry.
2009
19336442
Hooke: an open software platform for force spectroscopy.
2009
19336443
KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways.
2009
19336445
Variable slope normalization of reverse phase protein arrays.
2009
19336447
IGG3: a tool to rapidly integrate large genotype datasets for whole-genome imputation and individual-level meta-analysis.
2009
19346322
Identification of ribosomal RNA genes in metagenomic fragments.
2009
19346323
Globally optimal stitching of tiled 3D microscopic image acquisitions.
2009
19346324
DnaSP v5: a software for comprehensive analysis of DNA polymorphism data.
2009
19346325
ELISA-BASE: an integrated bioinformatics tool for analyzing and tracking ELISA microarray data.
2009
19346326
TEclass--a tool for automated classification of unknown eukaryotic transposable elements.
2009
19349283
Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x.
2009
19349284
Enrichment constrained time-dependent clustering analysis for finding meaningful temporal transcription modules.
2009
19351618
ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches.
2009
19351619
Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment.
2009
19351620
WebGBrowse--a web server for GBrowse.
2009
19357095
Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy.
2009
19357097
BIPA: a database for protein-nucleic acid interaction in 3D structures.
2009
19357098
CloudBurst: highly sensitive read mapping with MapReduce.
2009
19357099
ModLink+: improving fold recognition by using protein-protein interactions.
2009
19357100
Automatic identification of species-specific repetitive DNA sequences and their utilization for detecting microbial organisms.
2009
19357101
A graphical algorithm for fast computation of identity coefficients and generalized kinship coefficients.
2009
19359355
MICAlign: a sequence-to-structure alignment tool integrating multiple sources of information in conditional random fields.
2009
19359356
LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures.
2009
19369493
ProtVirDB: a database of protozoan virulent proteins.
2009
19369494
Bayesian inference of protein-protein interactions from biological literature.
2009
19369495
Many-core algorithms for statistical phylogenetics.
2009
19369496
MapView: visualization of short reads alignment on a desktop computer.
2009
19369497
ViaComplex: software for landscape analysis of gene expression networks in genomic context.
2009
19369498
pySolo: a complete suite for sleep analysis in Drosophila.
2009
19369499
PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots.
2009
19369500
BEsTRF: a tool for optimal resolution of terminal-restriction fragment length polymorphism analysis based on user-defined primer-enzyme-sequence databases.
2009
19369501
Fluctuation analysis CalculatOR: a web tool for the determination of mutation rate using Luria-Delbruck fluctuation analysis.
2009
19369502
Metal-MACiE: a database of metals involved in biological catalysis.
2009
19369503
CATMAID: collaborative annotation toolkit for massive amounts of image data.
2009
19376822
A local multiple alignment method for detection of non-coding RNA sequences.
2009
19376823
FDR made easy in differential feature discovery and correlation analyses.
2009
19376824
Application and evaluation of automated semantic annotation of gene expression experiments.
2009
19376825
A stochastic model for the evolution of metabolic networks with neighbor dependence.
2009
19376826
KIRMES: kernel-based identification of regulatory modules in euchromatic sequences.
2009
19389732
Protein function annotation from sequence: prediction of residues interacting with RNA.
2009
19389733
MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction.
2009
19389734
A Bayesian segmentation approach to ascertain copy number variations at the population level.
2009
19389735
A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays.
2009
19389736
CROC: finding chromosomal clusters in eukaryotic genomes.
2009
19389737
GeneRegionScan: a Bioconductor package for probe-level analysis of specific, small regions of the genome.
2009
19398447
VARNA: Interactive drawing and editing of the RNA secondary structure.
2009
19398448
Rahnuma: hypergraph-based tool for metabolic pathway prediction and network comparison.
2009
19398450
penalizedSVM: a R-package for feature selection SVM classification.
2009
19398451
Affinity Density: a novel genomic approach to the identification of transcription factor regulatory targets.
2009
19401399
baobabLUNA: the solution space of sorting by reversals.
2009
19401401
Utilizing gene pair orientations for HMM-based analysis of promoter array ChIP-chip data.
2009
19401402
apLCMS--adaptive processing of high-resolution LC/MS data.
2009
19414529
A tool for identification of genes expressed in patterns of interest using the Allen Brain Atlas.
2009
19414530
PESTAS: a web server for EST analysis and sequence mining.
2009
19414531
Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner.
2009
19414532
MetNetAligner: a web service tool for metabolic network alignments.
2009
19414533
U-Compare: share and compare text mining tools with UIMA.
2009
19414535
Flexible structural protein alignment by a sequence of local transformations.
2009
19417057
Ulla: a program for calculating environment-specific amino acid substitution tables.
2009
19417059
RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions.
2009
19420051
A toolbox for validation of mass spectrometry peptides identification and generation of database: IRMa.
2009
19420053
CycSim--an online tool for exploring and experimenting with genome-scale metabolic models.
2009
19420054
TANDEM: integrating automated allele binning into genetics and genomics workflows.
2009
19420055
Estimating the posterior probability that genome-wide association findings are true or false.
2009
19420056
DASMI: exchanging, annotating and assessing molecular interaction data.
2009
19420069
FlexServ: an integrated tool for the analysis of protein flexibility.
2009
19429600
MaHCO: an ontology of the major histocompatibility complex for immunoinformatic applications and text mining.
2009
19429601
Robust synthetic biology design: stochastic game theory approach.
2009
19435742
ESG: extended similarity group method for automated protein function prediction.
2009
19435743
Generating linkage mapping files from Affymetrix SNP chip data.
2009
19435744
DIANA-mirPath: Integrating human and mouse microRNAs in pathways.
2009
19435746
Apollo: a community resource for genome annotation editing.
2009
19439563
Figure mining for biomedical research.
2009
19439564
SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences.
2009
19439565
Data structures and compression algorithms for genomic sequence data.
2009
19447783
Gradient lasso for Cox proportional hazards model.
2009
19447787
Highly accelerated feature detection in proteomics data sets using modern graphics processing units.
2009
19447788
Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data.
2009
19447789
Fast and accurate short read alignment with Burrows-Wheeler transform.
2009
19451168
Efficient computation of all perfect repeats in genomic sequences of up to half a gigabyte, with a case study on the human genome.
2009
19451169
jClust: a clustering and visualization toolbox.
2009
19454618
An active registry for bioinformatics web services.
2009
19460889
Using chemical organization theory for model checking.
2009
19468053
rtracklayer: an R package for interfacing with genome browsers.
2009
19468054
NTAP: for NimbleGen tiling array ChIP-chip data analysis.
2009
19468055
Genetic modification of flux for flux prediction of mutants.
2009
19468056
CORAL: aligning conserved core regions across domain families.
2009
19470584
Treevolution: visual analysis of phylogenetic trees.
2009
19470585
Modeling stochasticity and robustness in gene regulatory networks.
2009
19477975
Clustered alignments of gene-expression time series data.
2009
19477977
KELLER: estimating time-varying interactions between genes.
2009
19477978
Probabilistic retrieval and visualization of biologically relevant microarray experiments.
2009
19477980
A general computational method for robustness analysis with applications to synthetic gene networks.
2009
19477984
E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs.
2009
19477985
Multi-locus match probability in a finite population: a fundamental difference between the Moran and Wright-Fisher models.
2009
19477986
A multivariate regression approach to association analysis of a quantitative trait network.
2009
19477989
Inference of locus-specific ancestry in closely related populations.
2009
19477991
A geometric approach for classification and comparison of structural variants.
2009
19477992
Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data.
2009
19477993
Domain-oriented edge-based alignment of protein interaction networks.
2009
19477994
IsoRankN: spectral methods for global alignment of multiple protein networks.
2009
19477996
REPETITA: detection and discrimination of the periodicity of protein solenoid repeats by discrete Fourier transform.
2009
19478001
Model-based clustering of array CGH data.
2009
19478003
DISCOVER: a feature-based discriminative method for motif search in complex genomes.
2009
19478006
Predictions of RNA secondary structure by combining homologous sequence information.
2009
19478007
Efficient exact motif discovery.
2009
19478010
A partition function algorithm for interacting nucleic acid strands.
2009
19478011
Predicting and understanding the stability of G-quadruplexes.
2009
19478012
Identifying novel constrained elements by exploiting biased substitution patterns.
2009
19478016
Constrained mixture estimation for analysis and robust classification of clinical time series.
2009
19478017
From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations.
2009
19478018
Alignment of the UMLS semantic network with BioTop: methodology and assessment.
2009
19478019
Ontology quality assurance through analysis of term transformations.
2009
19478020
Computing galled networks from real data.
2009
19478021
PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy.
2009
19497931
SOAP2: an improved ultrafast tool for short read alignment.
2009
19497933
PROCAIN server for remote protein sequence similarity search.
2009
19497935
ABACAS: algorithm-based automatic contiguation of assembled sequences.
2009
19497936
UTGB toolkit for personalized genome browsers.
2009
19497937
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data.
2009
19505939
Identifying the topology of protein complexes from affinity purification assays.
2009
19505940
ChromA: signal-based retention time alignment for chromatography-mass spectrometry data.
2009
19505941
Importing ArrayExpress datasets into R/Bioconductor.
2009
19505942
The Sequence Alignment/Map format and SAMtools.
2009
19505943
Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood.
2009
19505944
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
2009
19505945
Rapid detection, classification and accurate alignment of up to a million or more related protein sequences.
2009
19505947
Reordering contigs of draft genomes using the Mauve aligner.
2009
19515959
Visual and statistical comparison of metagenomes.
2009
19515961
A pattern-based nearest neighbor search approach for promoter prediction using DNA structural profiles.
2009
19515962
De novo transcriptome assembly with ABySS.
2009
19528083
PROMISE: a tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables.
2009
19528086
InterMap3D: predicting and visualizing co-evolving protein residues.
2009
19528088
A statistical framework for protein quantitation in bottom-up MS-based proteomics.
2009
19535538
ISOLATE: a computational strategy for identifying the primary origin of cancers using high-throughput sequencing.
2009
19542156
The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction.
2009
19561015
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.
2009
19561018
Comparative study on ChIP-seq data: normalization and binding pattern characterization.
2009
19561022
ITM Probe: analyzing information flow in protein networks.
2009
19561335
HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome.
2009
19561337
High-throughput minor histocompatibility antigen prediction.
2009
19570803
Affy exon tissues: exon levels in normal tissues in human, mouse and rat.
2009
19570805
k-link EST clustering: evaluating error introduced by chimeric sequences under different degrees of linkage.
2009
19570806
SNP-o-matic.
2009
19574284
TTA Lynx: a web-based service for analysis of actinomycete genes containing rare TTA codon.
2009
19574286
Statistical lower bounds on protein copy number from fluorescence expression images.
2009
19574287
On the inference of spatial structure from population genetics data.
2009
19574291
Antimony: a modular model definition language.
2009
19578039
TreeTime: an extensible C++ software package for Bayesian phylogeny reconstruction with time-calibration.
2009
19578040
FBA-SimVis: interactive visualization of constraint-based metabolic models.
2009
19578041
FRED--a framework for T-cell epitope detection.
2009
19578173
Identification of distant family relationships.
2009
19584067
ViTraM: visualization of transcriptional modules.
2009
19587224
TileProbe: modeling tiling array probe effects using publicly available data.
2009
19592393
aGEM: an integrative system for analyzing spatial-temporal gene-expression information.
2009
19592395
Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition.
2009
19602524
PIQA: pipeline for Illumina G1 genome analyzer data quality assessment.
2009
19602525
WebArrayDB: cross-platform microarray data analysis and public data repository.
2009
19602526
A multi-dimensional evidence-based candidate gene prioritization approach for complex diseases-schizophrenia as a case.
2009
19602527
Expertomica metabolite profiling: getting more information from LC-MS using the stochastic systems approach.
2009
19602528
ADAN: a database for prediction of protein-protein interaction of modular domains mediated by linear motifs.
2009
19602529
DiProGB: the dinucleotide properties genome browser.
2009
19605418
Motif discovery and motif finding from genome-mapped DNase footprint data.
2009
19605419
Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite.
2009
19605420
Supervised prediction of drug-target interactions using bipartite local models.
2009
19605421
Reconstructing spatiotemporal gene expression data from partial observations.
2009
19608707
An algorithm for learning maximum entropy probability models of disease risk that efficiently searches and sparingly encodes multilocus genomic interactions.
2009
19608708
Caleydo: connecting pathways and gene expression.
2009
19620095
Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis.
2009
19620096
The SNP ratio test: pathway analysis of genome-wide association datasets.
2009
19620097
Benchmarking homology detection procedures with low complexity filters.
2009
19620098
FRODOCK: a new approach for fast rotational protein-protein docking.
2009
19620099
A new method for revealing correlated mutations under the structural and functional constraints in proteins.
2009
19628501
Modified variational Bayes EM estimation of hidden Markov tree model of cell lineages.
2009
19628503
PathBuilder--open source software for annotating and developing pathway resources.
2009
19628504
A modified LOESS normalization applied to microRNA arrays: a comparative evaluation.
2009
19628505
Enhancement of beta-sheet assembly by cooperative hydrogen bonds potential.
2009
19628506
iBioSim: a tool for the analysis and design of genetic circuits.
2009
19628507
Path: a tool to facilitate pathway-based genetic association analysis.
2009
19628508
A System for Information Management in BioMedical Studies--SIMBioMS.
2009
19633095
PhyloDet: a scalable visualization tool for mapping multiple traits to large evolutionary trees.
2009
19633096
Mining gene functional networks to improve mass-spectrometry-based protein identification.
2009
19633097
Accessible methods for the dynamic time-scale decomposition of biochemical systems.
2009
19633098
Gene ranking and biomarker discovery under correlation.
2009
19648135
Methyl side-chain dynamics prediction based on protein structure.
2009
19648137
RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data.
2009
19648138
A hypergraph-based learning algorithm for classifying gene expression and arrayCGH data with prior knowledge.
2009
19648139
metahdep: meta-analysis of hierarchically dependent gene expression studies.
2009
19648140
CMap 1.01: a comparative mapping application for the Internet.
2009
19648141
The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets.
2009
19654113
PubMed-EX: a web browser extension to enhance PubMed search with text mining features.
2009
19654114
Multiple testing in genome-wide association studies via hidden Markov models.
2009
19654115
Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks.
2009
19654116
A phylogenetic and Markov model approach for the reconstruction of mutational pathways of drug resistance.
2009
19654117
Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0.
2009
19654118
Flynet: a genomic resource for Drosophila melanogaster transcriptional regulatory networks.
2009
19656951
R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips.
2009
19661241
Methods for labeling error detection in microarrays based on the effect of data perturbation on the regression model.
2009
19661242
Efficient SCOP-fold classification and retrieval using index-based protein substructure alignments.
2009
19667079
Knowledge-guided inference of domain-domain interactions from incomplete protein-protein interaction networks.
2009
19667081
PineSAP--sequence alignment and SNP identification pipeline.
2009
19667082
T-REKS: identification of Tandem REpeats in sequences with a K-meanS based algorithm.
2009
19671691
Partition function and base pairing probabilities for RNA-RNA interaction prediction.
2009
19671692
Testing the hypothesis of tissue selectivity: the intersection-union test and a Bayesian approach.
2009
19671693
PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds.
2009
19675096
PopABC: a program to infer historical demographic parameters.
2009
19679678
YADA: a tool for taking the most out of high-resolution spectra.
2009
19684088
SnoopCGH: software for visualizing comparative genomic hybridization data.
2009
19687029
Statistical methods for gene set co-expression analysis.
2009
19689953
Improving peptide identification with single-stage mass spectrum peaks.
2009
19689954
info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling.
2009
19689955
CEAS: cis-regulatory element annotation system.
2009
19689956
Mobyle: a new full web bioinformatics framework.
2009
19689959
WEbcoli: an interactive and asynchronous web application for in silico design and analysis of genome-scale E.coli model.
2009
19689960
CoCoa: a software tool for estimating the coefficient of coancestry from multilocus genotype data.
2009
19689961
Simultaneous inference of biological networks of multiple species from genome-wide data and evolutionary information: a semi-supervised approach.
2009
19689962
MISTRAL: a tool for energy-based multiple structural alignment of proteins.
2009
19692555
TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples.
2009
19692556
Metabolite and reaction inference based on enzyme specificities.
2009
19696044
ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes.
2009
19696045
PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains.
2009
19696046
A boosting approach to structure learning of graphs with and without prior knowledge.
2009
19696047
Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics.
2009
19706742
digeR: a graphical user interface R package for analyzing 2D-DIGE data.
2009
19706743
A new taxonomy-based protein fold recognition approach based on autocross-covariance transformation.
2009
19706744
integrOmics: an R package to unravel relationships between two omics datasets.
2009
19706745
Using a mutual information-based site transition network to map the genetic evolution of influenza A/H3N2 virus.
2009
19706746
ERNEST: a toolbox for chemical reaction network theory.
2009
19713415
A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis.
2009
19713416
UniMaP: finding unique mass and peptide signatures in the human proteome.
2009
19713417
Next generation software for functional trend analysis.
2009
19717575
ANCHOR: web server for predicting protein binding regions in disordered proteins.
2009
19717576
Comparative analysis and unification of domain-domain interaction networks.
2009
19720675
Identification of genes involved in the same pathways using a Hidden Markov Model-based approach.
2009
19720676
Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl.
2009
19720677
CellClassifier: supervised learning of cellular phenotypes.
2009
19729371
Analyzing biological network parameters with CentiScaPe.
2009
19729372
Saint: a lightweight integration environment for model annotation.
2009
19734151
Bi-correlation clustering algorithm for determining a set of co-regulated genes.
2009
19734153
Automated inference of molecular mechanisms of disease from amino acid substitutions.
2009
19734154
Identifying related journals through log analysis.
2009
19734155
Updates to the RMAP short-read mapping software.
2009
19736251
Efficiently finding genome-wide three-way gene interactions from transcript- and genotype-data.
2009
19736252
Predicting homologous signaling pathways using machine learning.
2009
19736253
TagDust--a program to eliminate artifacts from next generation sequencing data.
2009
19737799
massXpert 2: a cross-platform software environment for polymer chemistry modelling and simulation/analysis of mass spectrometric data.
2009
19740912
QuickGO: a web-based tool for Gene Ontology searching.
2009
19744993
CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information.
2009
19744995
De novo computational prediction of non-coding RNA genes in prokaryotic genomes.
2009
19744996
3D-SURFER: software for high-throughput protein surface comparison and analysis.
2009
19759195
A dictionary to identify small molecules and drugs in free text.
2009
19759196
Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis.
2009
19759197
Characterization of 1H NMR spectroscopic data and the generation of synthetic validation sets.
2009
19759199
COMPASS: a program for generating serial samples under an infinite sites model.
2009
19762347
PoreLogo: a new tool to analyse, visualize and compare channels in transmembrane proteins.
2009
19762348
Understanding hydrogen-bond patterns in proteins using network motifs.
2009
19767299
Client-side integration of life science literature resources.
2009
19767300
Reproducing the manual annotation of multiple sequence alignments using a SVM classifier.
2009
19770262
MOODS: fast search for position weight matrix matches in DNA sequences.
2009
19773334
HHsvm: fast and accurate classification of profile-profile matches identified by HHsearch.
2009
19773335
Bayesian detection of non-sinusoidal periodic patterns in circadian expression data.
2009
19773336
SimCT: a generic tool to visualize ontology-based relationships for biological objects.
2009
19776214
Automatically classifying sentences in full-text biomedical articles into Introduction, Methods, Results and Discussion.
2009
19783830
LIBRUS: combined machine learning and homology information for sequence-based ligand-binding residue prediction.
2009
19786483
Detection of new protein domains using co-occurrence: application to Plasmodium falciparum.
2009
19786484
VDNA: the virtual DNA plug-in for VMD.
2009
19789266
EasyMIFS and SiteHound: a toolkit for the identification of ligand-binding sites in protein structures.
2009
19789268
The interwinding nature of protein-protein interfaces and its implication for protein complex formation.
2009
19789269
Processing and population genetic analysis of multigenic datasets with ProSeq3 software.
2009
19797407
W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data.
2009
19797408
Functionally guided alignment of protein interaction networks for module detection.
2009
19797409
Qupe--a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments.
2009
19808875
CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score.
2009
19808876
Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.
2009
19808877
Quantitative measurement of aging using image texture entropy.
2009
19808878
Exon Array Analyzer: a web interface for Affymetrix exon array analysis.
2009
19808879
HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in R.
2009
19808880
ncRNAppi--a tool for identifying disease-related miRNA and siRNA targeting pathways.
2009
19808883
Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models.
2009
19812110
Inferring relative proportions of DNA variants from sequencing electropherograms.
2009
19819885
Predicting citation count of Bioinformatics papers within four years of publication.
2009
19819886
Efficient estimation of pairwise distances between genomes.
2009
19825795
Detailing regulatory networks through large scale data integration.
2009
19825796
Significant speedup of database searches with HMMs by search space reduction with PSSM family models.
2009
19828575
Integrated analysis of copy number alterations and gene expression: a bivariate assessment of equally directed abnormalities.
2009
19828576
ABWGAT: anchor-based whole genome analysis tool.
2009
19828577
NAViGaTOR: Network Analysis, Visualization and Graphing Toronto.
2009
19837718
INTERSNP: genome-wide interaction analysis guided by a priori information.
2009
19837719
GeneE: gene and protein query expansion with disambiguation.
2010
19837720
CRISPI: a CRISPR interactive database.
2009
19846435
Reporting bias when using real data sets to analyze classification performance.
2010
19846436
Accurate confidence aware clustering of array CGH tumor profiles.
2010
19846437
Targeted interrogation of copy number variation using SCIMMkit.
2010
19846438
G-compass: a web-based comparative genome browser between human and other vertebrate genomes.
2009
19846439
Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere.
2010
19846440
Evaluation of linguistic features useful in extraction of interactions from PubMed; application to annotating known, high-throughput and predicted interactions in I2D.
2010
19850753
The gputools package enables GPU computing in R.
2010
19850754
Ancestors 1.0: a web server for ancestral sequence reconstruction.
2010
19850756
Annotation confidence score for genome annotation: a genome comparison approach.
2010
19855104
DEGseq: an R package for identifying differentially expressed genes from RNA-seq data.
2010
19855105
NGSView: an extensible open source editor for next-generation sequencing data.
2010
19855106
Computational protein profile similarity screening for quantitative mass spectrometry experiments.
2010
19861354
The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing.
2010
19861355
Estimating population haplotype frequencies from pooled SNP data using incomplete database information.
2009
19861356
Phenopedia and Genopedia: disease-centered and gene-centered views of the evolving knowledge of human genetic associations.
2010
19864262
Predictive rule inference for epistatic interaction detection in genome-wide association studies.
2010
19880365
inGAP: an integrated next-generation genome analysis pipeline.
2010
19880367
MATICCE: mapping transitions in continuous character evolution.
2010
19880368
MicroRazerS: rapid alignment of small RNA reads.
2010
19880369
Model aggregation: a building-block approach to creating large macromolecular regulatory networks.
2009
19880372
SimBoolNet--a Cytoscape plugin for dynamic simulation of signaling networks.
2010
19887508
Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure.
2010
19889798
GATE: software for the analysis and visualization of high-dimensional time series expression data.
2010
19892805
Identification of microRNA activity by Targets' Reverse EXpression.
2010
19897564
Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments.
2010
19897565
hPDI: a database of experimental human protein-DNA interactions.
2010
19900953
Target prediction and a statistical sampling algorithm for RNA-RNA interaction.
2010
19910305
Automatic clustering of docking poses in virtual screening process using self-organizing map.
2010
19910307
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
2010
19910308
PyNAST: a flexible tool for aligning sequences to a template alignment.
2010
19914921
PerturbationAnalyzer: a tool for investigating the effects of concentration perturbation on protein interaction networks.
2010
19914922
AQUA: automated quality improvement for multiple sequence alignments.
2010
19926669
Pathway analysis using random forests with bivariate node-split for survival outcomes.
2010
19933158
LegumeTFDB: an integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors.
2010
19933159
MADS+: discovery of differential splicing events from Affymetrix exon junction array data.
2010
19933160
Annotation and merging of SBML models with semanticSBML.
2010
19933161
SCAN: SNP and copy number annotation.
2010
19933162
Bayesian variable selection for disease classification using gene expression data.
2010
19933163
VIBE 2.0: visual integration for bayesian evaluation.
2010
19933164
MAVEN: a tool for visualization and functional analysis of genome-wide association results.
2010
19933166
mimiRNA: a microRNA expression profiler and classification resource designed to identify functional correlations between microRNAs and their targets.
2010
19933167
Joint estimation of DNA copy number from multiple platforms.
2010
19933593
MIRAGAA--a methodology for finding coordinated effects of microRNA expression changes and genome aberrations in cancer.
2010
19933823
A personalized microRNA microarray normalization method using a logistic regression model.
2010
19933824
EGAN: exploratory gene association networks.
2010
19933825
Expertomica Cells: analysis of cell monolayer development.
2010
19939831
CMap3D: a 3D visualization tool for comparative genetic maps.
2010
19942584
Extraction and comparison of gene expression patterns from 2D RNA in situ hybridization images.
2010
19942587
Ceres: software for the integrated analysis of transcription factor binding sites and nucleosome positions in Saccharomyces cerevisiae.
2010
19959498
The Gene Interaction Miner: a new tool for data mining contextual information for protein-protein interaction analysis.
2010
19965878
DataPflex: a MATLAB-based tool for the manipulation and visualization of multidimensional datasets.
2010
19965880
Tablet--next generation sequence assembly visualization.
2010
19965881
PathGen: a transitive gene pathway generator.
2010
19965882
Biomarker detection in the integration of multiple multi-class genomic studies.
2010
19965884
Protein complex prediction based on simultaneous protein interaction network.
2010
19965885
A new gene selection procedure based on the covariance distance.
2010
19996162
HIGEDA: a hierarchical gene-set genetics based algorithm for finding subtle motifs in biological sequences.
2010
19996163
Validation of double digest selective label database for sequenced prokaryotic genomes.
2010
19996164
Temporal clustering by affinity propagation reveals transcriptional modules in Arabidopsis thaliana.
2010
19996165
CellMC--a multiplatform model compiler for the Cell Broadband Engine and x86.
2010
19996166
ChiBE: interactive visualization and manipulation of BioPAX pathway models.
2010
20007251
PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approaches.
2010
20007253
On the beta-binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics.
2010
20007255
Tmod: toolbox of motif discovery.
2010
20007740
QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects.
2010
20007741
sORF finder: a program package to identify small open reading frames with high coding potential.
2010
20008477
RNAsnoop: efficient target prediction for H/ACA snoRNAs.
2010
20015949
FoldAmyloid: a method of prediction of amyloidogenic regions from protein sequence.
2010
20019059
webMGR: an online tool for the multiple genome rearrangement problem.
2010
20022974
DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data.
2010
20031972
Mixtures of regression models for time course gene expression data: evaluation of initialization and random effects.
2010
20040587
Disambiguating the species of biomedical named entities using natural language parsers.
2010
20053840
Xper2: introducing e-taxonomy.
2010
20053842
dbTEU: a protein database of trace element utilization.
2010
20053843
CD-HIT Suite: a web server for clustering and comparing biological sequences.
2010
20053844
PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta.
2010
20061306
BamView: viewing mapped read alignment data in the context of the reference sequence.
2010
20071372
Fast and accurate long-read alignment with Burrows-Wheeler transform.
2010
20080505
A censored beta mixture model for the estimation of the proportion of non-differentially expressed genes.
2010
20080506
MSMSpdbb: providing protein databases of closely related organisms to improve proteomic characterization of prokaryotic microbes.
2010
20080508
pegas: an R package for population genetics with an integrated-modular approach.
2010
20080509
NEMO: a tool for analyzing gene and chromosome territory distributions from 3D-FISH experiments.
2010
20080510
Faster computation of exact RNA shape probabilities.
2010
20080511
PSiFR: an integrated resource for prediction of protein structure and function.
2010
20080513
Next-generation bioinformatics: using many-core processor architecture to develop a web service for sequence alignment.
2010
20081221
Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS.
2010
20081222
rMAT--an R/Bioconductor package for analyzing ChIP-chip experiments.
2010
20089513
iDBPs: a web server for the identification of DNA binding proteins.
2010
20089514
ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes.
2010
20089515
Computational quantification of metabolic fluxes from a single isotope snapshot: application to an animal biopsy.
2010
20097912
Correcting population stratification in genetic association studies using a phylogenetic approach.
2010
20097913
Exploring classification strategies with the CoEPrA 2006 contest.
2010
20097914
WellReader: a MATLAB program for the analysis of fluorescence and luminescence reporter gene data.
2010
20097915
iMotifs: an integrated sequence motif visualization and analysis environment.
2010
20106815
FineStr: a web server for single-base-resolution nucleosome positioning.
2010
20106816
XDIA: improving on the label-free data-independent analysis.
2010
20106817
Easy retrieval of single amino-acid polymorphisms and phenotype information using SwissVar.
2010
20106818
invertFREGENE: software for simulating inversions in population genetic data.
2010
20106819
Predicting biodegradation products and pathways: a hybrid knowledge- and machine learning-based approach.
2010
20106820
A hidden Ising model for ChIP-chip data analysis.
2010
20110277
BEDTools: a flexible suite of utilities for comparing genomic features.
2010
20110278
A fast and automated solution for accurately resolving protein domain architectures.
2010
20118117
The Locus Lookup tool at MaizeGDB: identification of genomic regions in maize by integrating sequence information with physical and genetic maps.
2010
20124413
A visual framework for sequence analysis using n-grams and spectral rearrangement.
2010
20130028
Small-sample precision of ROC-related estimates.
2010
20130029
Identifying biologically relevant differences between metagenomic communities.
2010
20130030
Six Rossmannoid folds, including the Class I aminoacyl-tRNA synthetases, share a partial core with the anti-codon-binding domain of a Class II aminoacyl-tRNA synthetase.
2010
20130031
Cascleave: towards more accurate prediction of caspase substrate cleavage sites.
2010
20130033
Improving protein secondary structure prediction using a simple k-mer model.
2010
20130034
SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.
2010
20130035
Non-linear classification for on-the-fly fractional mass filtering and targeted precursor fragmentation in mass spectrometry experiments.
2010
20134030
Modeling macro-molecular interfaces with Intervor.
2010
20139468
Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks.
2010
20139469
Snoopy--a unifying Petri net framework to investigate biomolecular networks.
2010
20139470
Fast and SNP-tolerant detection of complex variants and splicing in short reads.
2010
20147302
SoDA2: a Hidden Markov Model approach for identification of immunoglobulin rearrangements.
2010
20147303
Estimating replicate time shifts using Gaussian process regression.
2010
20147305
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments.
2010
20147306
Assigning roles to DNA regulatory motifs using comparative genomics.
2010
20147307
MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8.
2010
20150411
Phybase: an R package for species tree analysis.
2010
20156990
iPHACE: integrative navigation in pharmacological space.
2010
20156991
Standard virtual biological parts: a repository of modular modeling components for synthetic biology.
2010
20160009
Treephyler: fast taxonomic profiling of metagenomes.
2010
20172941
CandiSNPer: a web tool for the identification of candidate SNPs for causal variants.
2010
20172942
A meta-analysis of two-dimensional electrophoresis pattern of the Parkinson's disease-related protein DJ-1.
2010
20172943
A principal skeleton algorithm for standardizing confocal images of fruit fly nervous systems.
2010
20172944
DASS-GUI: a user interface for identification and analysis of significant patterns in non-sequential data.
2010
20172945
An optimal experimental design approach to model discrimination in dynamic biochemical systems.
2010
20176580
SBRML: a markup language for associating systems biology data with models.
2010
20176582
Domain adaptation for semantic role labeling in the biomedical domain.
2010
20179074
GOSemSim: an R package for measuring semantic similarity among GO terms and gene products.
2010
20179076
The power of protein interaction networks for associating genes with diseases.
2010
20185403
Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes.
2010
20185404
SPICi: a fast clustering algorithm for large biological networks.
2010
20185405
ESBTL: efficient PDB parser and data structure for the structural and geometric analysis of biological macromolecules.
2010
20185407
Exploiting sequence similarity to validate the sensitivity of SNP arrays in detecting fine-scaled copy number variations.
2010
20189937
Post hoc power estimation in large-scale multiple testing problems.
2010
20189938
BioNet: an R-Package for the functional analysis of biological networks.
2010
20189939
CPFP: a central proteomics facilities pipeline.
2010
20189941
SDOP-DB: a comparative standardized-protocol database for mouse phenotypic analyses.
2010
20194625
An Ergatis-based prokaryotic genome annotation web server.
2010
20194626
ScripTree: scripting phylogenetic graphics.
2010
20194627
Inferring dynamic gene networks under varying conditions for transcriptomic network comparison.
2010
20197286
Modeling sample variables with an Experimental Factor Ontology.
2010
20200009
PaperMaker: validation of biomedical scientific publications.
2010
20200010
Cross-species common regulatory network inference without requirement for prior gene affiliation.
2010
20200011
Statistical expression deconvolution from mixed tissue samples.
2010
20202973
Filtering error from SOLiD Output.
2010
20207696
Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq.
2010
20208068
Genome-wide synteny through highly sensitive sequence alignment: Satsuma.
2010
20208069
Genome-wide inferring gene-phenotype relationship by walking on the heterogeneous network.
2010
20215462
PanCGHweb: a web tool for genotype calling in pangenome CGH data.
2010
20219865
Integrative mixture of experts to combine clinical factors and gene markers.
2010
20223834
Localized motif discovery in gene regulatory sequences.
2010
20223835
TiSGeD: a database for tissue-specific genes.
2010
20223836
Inferring cluster-based networks from differently stimulated multiple time-course gene expression data.
2010
20223837
DensiTree: making sense of sets of phylogenetic trees.
2010
20228129
SeSAW: balancing sequence and structural information in protein functional mapping.
2010
20299324
Going from where to why--interpretable prediction of protein subcellular localization.
2010
20299325
HALO--a Java framework for precise transcript half-life determination.
2010
20299326
ArchSchema: a tool for interactive graphing of related Pfam domain architectures.
2010
20299327
ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment.
2010
20305268
CoP: a database for characterizing co-expressed gene modules with biological information in plants.
2010
20305269
varLD: a program for quantifying variation in linkage disequilibrium patterns between populations.
2010
20308177
PathWave: discovering patterns of differentially regulated enzymes in metabolic pathways.
2010
20335275
PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations.
2010
20335276
TopoGSA: network topological gene set analysis.
2010
20335277
EBImage--an R package for image processing with applications to cellular phenotypes.
2010
20338898
Multi-threaded vectorized distance matrix computation on the CELL/BE and x86/SSE2 architectures.
2010
20348545
SICAGO: Semi-supervised cluster analysis using semantic distance between gene pairs in Gene Ontology.
2010
20348546
DistanceScan: a tool for promoter modeling.
2010
20360058
Building a high-quality sense inventory for improved abbreviation disambiguation.
2010
20360059
Supervised normalization of microarrays.
2010
20363728
Studying the co-evolution of protein families with the Mirrortree web server.
2010
20363731
Streamlining the construction of large-scale dynamic models using generic kinetic equations.
2010
20363732
Modular analysis of gene expression data with R.
2010
20371495
A signal-noise model for significance analysis of ChIP-seq with negative control.
2010
20371496
Payao: a community platform for SBML pathway model curation.
2010
20371497
Alignment-free local structural search by writhe decomposition.
2010
20371498
partDSA: deletion/substitution/addition algorithm for partitioning the covariate space in prediction.
2010
20375111
Multilevel support vector regression analysis to identify condition-specific regulatory networks.
2010
20375112
FastEpistasis: a high performance computing solution for quantitative trait epistasis.
2010
20375113
Correction of sequencing errors in a mixed set of reads.
2010
20378555
VSDocker: a tool for parallel high-throughput virtual screening using AutoDock on Windows-based computer clusters.
2010
20378556
A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval.
2010
20378557
BoolNet--an R package for generation, reconstruction and analysis of Boolean networks.
2010
20378558
Detection and characterization of novel sequence insertions using paired-end next-generation sequencing.
2010
20385726
Permutation importance: a corrected feature importance measure.
2010
20385727
Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation.
2010
20385728
Multi-objective tag SNPs selection using evolutionary algorithms.
2010
20385729
Quality assessment of protein model-structures using evolutionary conservation.
2010
20385730
Picante: R tools for integrating phylogenies and ecology.
2010
20395285
A hidden Markov support vector machine framework incorporating profile geometry learning for identifying microbial RNA in tiling array data.
2010
20395286
HIV classification using the coalescent theory.
2010
20400454
ParaSAM: a parallelized version of the significance analysis of microarrays algorithm.
2010
20400455
EuGène-maize: a web site for maize gene prediction.
2010
20400755
Novel statistical framework to identify differentially expressed genes allowing transcriptomic background differences.
2010
20400756
CNAnova: a new approach for finding recurrent copy number abnormalities in cancer SNP microarray data.
2010
20403815
Inferring combined CNV/SNP haplotypes from genotype data.
2010
20406911
Supersplat--spliced RNA-seq alignment.
2010
20410051
Inference of combinatorial Boolean rules of synergistic gene sets from cancer microarray datasets.
2010
20410052
Meta-analysis for pathway enrichment analysis when combining multiple genomic studies.
2010
20410053
Ergatis: a web interface and scalable software system for bioinformatics workflows.
2010
20413634
HangOut: generating clean PSI-BLAST profiles for domains with long insertions.
2010
20413635
PepC: proteomics software for identifying differentially expressed proteins based on spectral counting.
2010
20413636
FABIA: factor analysis for bicluster acquisition.
2010
20418340
CGHnormaliter: a Bioconductor package for normalization of array CGH data with many CNAs.
2010
20418341
A CoD-based reduction algorithm for designing stationary control policies on Boolean networks.
2010
20421196
Finding metabolic pathways using atom tracking.
2010
20421197
DendroPy: a Python library for phylogenetic computing.
2010
20421198
Parallelization of the MAFFT multiple sequence alignment program.
2010
20427515
Modeling RNA loops using sequence homology and geometric constraints.
2010
20427516
Semantic integration of data on transcriptional regulation.
2010
20427517
ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking.
2010
20427518
TAPIR, a web server for the prediction of plant microRNA targets, including target mimics.
2010
20430753
The Genomedata format for storing large-scale functional genomics data.
2010
20435580
Inferring the human microRNA functional similarity and functional network based on microRNA-associated diseases.
2010
20439255
Deuteration distribution estimation with improved sequence coverage for HX/MS experiments.
2010
20439256
Learning combinatorial transcriptional dynamics from gene expression data.
2010
20444835
CHOYCE: a web server for constrained homology modelling with cryoEM maps.
2010
20444836
SensSB: a software toolbox for the development and sensitivity analysis of systems biology models.
2010
20444837
LCE: a link-based cluster ensemble method for improved gene expression data analysis.
2010
20444838
Computing biological functions using BioPsi, a formal description of biological processes based on elementary bricks of actions.
2010
20448138
Arcadia: a visualization tool for metabolic pathways.
2010
20453003
Discover regulatory DNA elements using chromatin signatures and artificial neural network.
2010
20453004
Repitools: an R package for the analysis of enrichment-based epigenomic data.
2010
20457667
Classification of DNA sequences using Bloom filters.
2010
20472541
The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell.
2010
20472542
PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes.
2010
20472543
Identifying duplicate content using statistically improbable phrases.
2010
20472545
Ligand-binding site prediction of proteins based on known fragment-fragment interactions.
2010
20472546
Prediction of protein-RNA binding sites by a random forest method with combined features.
2010
20483814
Pathgroups, a dynamic data structure for genome reconstruction problems.
2010
20483815
A new data mining approach for profiling and categorizing kinetic patterns of metabolic biomarkers after myocardial injury.
2010
20483816
Automated analysis of protein subcellular location in time series images.
2010
20484328
FuncBase: a resource for quantitative gene function annotation.
2010
20495000
GPCR-OKB: the G Protein Coupled Receptor Oligomer Knowledge Base.
2010
20501551
A parallel algorithm to compute chemical organizations in biological networks.
2010
20501552
COMPASSS (COMplex PAttern of Sequence Search Software), a simple and effective tool for mining complex motifs in whole genomes.
2010
20501554
A quality control algorithm for filtering SNPs in genome-wide association studies.
2010
20501555
DA 1.0: parameter estimation of biological pathways using data assimilation approach.
2010
20505000
Predicting post-translational lysine acetylation using support vector machines.
2010
20505001
Threshold Average Precision (TAP-k): a measure of retrieval designed for bioinformatics.
2010
20505002
Prediction of protease substrates using sequence and structure features.
2010
20505003
On safari to Random Jungle: a fast implementation of Random Forests for high-dimensional data.
2010
20505004
A UIMA wrapper for the NCBO annotator.
2010
20505005
Evoker: a visualization tool for genotype intensity data.
2010
20507892
MODEVO: exploring modularity and evolution of protein interaction networks.
2010
20507893
Integrative platform to translate gene sets to networks.
2010
20507894
Fast integration of heterogeneous data sources for predicting gene function with limited annotation.
2010
20507895
geWorkbench: an open source platform for integrative genomics.
2010
20511363
Global analysis of microarray data reveals intrinsic properties in gene expression and tissue selectivity.
2010
20511364
FastMEDUSA: a parallelized tool to infer gene regulatory networks.
2010
20513661
Gap5--editing the billion fragment sequence assembly.
2010
20513662
DETECT--a density estimation tool for enzyme classification and its application to Plasmodium falciparum.
2010
20513663
CisGenome Browser: a flexible tool for genomic data visualization.
2010
20513664
SLIMS--a user-friendly sample operations and inventory management system for genotyping labs.
2010
20513665
Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy.
2010
20519284
A computational genomics pipeline for prokaryotic sequencing projects.
2010
20519285
Structure-based variable selection for survival data.
2010
20519286
Learning transcriptional networks from the integration of ChIP-chip and expression data in a non-parametric model.
2010
20525821
Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function.
2010
20525822
adephylo: new tools for investigating the phylogenetic signal in biological traits.
2010
20525823
COMA server for protein distant homology search.
2010
20529888
ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays.
2010
20529889
Applying the NaĂŻve Bayes classifier with kernel density estimation to the prediction of protein-protein interaction sites.
2010
20529890
Efficient learning of microbial genotype-phenotype association rules.
2010
20529891
MiRror: a combinatorial analysis web tool for ensembles of microRNAs and their targets.
2010
20529892
SuperTriplets: a triplet-based supertree approach to phylogenomics.
2010
20529895
Automated tracking and analysis of centrosomes in early Caenorhabditis elegans embryos.
2010
20529897
Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data.
2010
20529898
Close lower and upper bounds for the minimum reticulate network of multiple phylogenetic trees.
2010
20529899
Inferring combinatorial association logic networks in multimodal genome-wide screens.
2010
20529900
Analyzing circadian expression data by harmonic regression based on autoregressive spectral estimation.
2010
20529902
Estimating genome-wide IBD sharing from SNP data via an efficient hidden Markov model of LD with application to gene mapping.
2010
20529903
Multi-population GWA mapping via multi-task regularized regression.
2010
20529908
Modularity and directionality in genetic interaction maps.
2010
20529911
Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM.
2010
20529912
Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework.
2010
20529913
Thermodynamics of RNA structures by Wang-Landau sampling.
2010
20529917
Recognition of beta-structural motifs using hidden Markov models trained with simulated evolution.
2010
20529918
A spectral graph theoretic approach to quantification and calibration of collective morphological differences in cell images.
2010
20529919
A statistical method for the detection of variants from next-generation resequencing of DNA pools.
2010
20529923
VARiD: a variation detection framework for color-space and letter-space platforms.
2010
20529926
Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery.
2010
20529927
Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model.
2010
20529931
Complex event extraction at PubMed scale.
2010
20529932
Multivariate multi-way analysis of multi-source data.
2010
20529933
Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate.
2010
20529934
SPEX2: automated concise extraction of spatial gene expression patterns from Fly embryo ISH images.
2010
20529936
As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets.
2010
20529937
Reconstruction of the neuromuscular junction connectome.
2010
20529938
Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing.
2010
20529939
Using semantic web rules to reason on an ontology of pseudogenes.
2010
20529940
Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph.
2010
20529941
Semi-automated ontology generation within OBO-Edit.
2010
20529942
Testing multiple gene interactions by the ordered combinatorial partitioning method in case-control studies.
2010
20538724
cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data.
2010
20538725
A highly accurate statistical approach for the prediction of transmembrane beta-barrels.
2010
20538726
PESDserv: a server for high-throughput comparison of protein binding site surfaces.
2010
20538727
LOX: inferring Level Of eXpression from diverse methods of census sequencing.
2010
20538728
Large-scale benchmark of Endeavour using MetaCore maps.
2010
20538729
Uniformly curated signaling pathways reveal tissue-specific cross-talks and support drug target discovery.
2010
20542890
DARNED: a DAtabase of RNa EDiting in humans.
2010
20547637
ViewDock TDW: high-throughput visualization of virtual screening results.
2010
20551133
Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood.
2010
20551134
JAMIE: joint analysis of multiple ChIP-chip experiments.
2010
20551135
Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease.
2010
20551136
Molecular signatures-based prediction of enzyme promiscuity.
2010
20551137
A Bayesian approach using covariance of single nucleotide polymorphism data to detect differences in linkage disequilibrium patterns between groups of individuals.
2010
20554688
A Poisson model for random multigraphs.
2010
20554690
Causal relationship inference for a large-scale cellular network.
2010
20554691
Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor.
2010
20562413
Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels.
2010
20562414
Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology.
2010
20562415
Manipulation of FASTQ data with Galaxy.
2010
20562416
An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System.
2010
20562417
Phenoclustering: online mining of cross-species phenotypes.
2010
20562418
CplexA: a Mathematica package to study macromolecular-assembly control of gene expression.
2010
20562419
MISS: a non-linear methodology based on mutual information for genetic association studies in both population and sib-pairs analysis.
2010
20562420
Savant: genome browser for high-throughput sequencing data.
2010
20562449
A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics.
2010
20568665
Cassis: detection of genomic rearrangement breakpoints.
2010
20576622
Chromaligner: a web server for chromatogram alignment.
2010
20576623
EpiTOP--a proteochemometric tool for MHC class II binding prediction.
2010
20576624
A probabilistic framework for aligning paired-end RNA-seq data.
2010
20576625
Single feature polymorphism detection using recombinant inbred line microarray expression data.
2010
20576626
MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities.
2010
20576627
EGM: encapsulated gene-by-gene matching to identify gene orthologs and homologous segments in genomes.
2010
20581400
Over-optimism in bioinformatics: an illustration.
2010
20581402
Mining metabolic pathways through gene expression.
2010
20587705
MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data.
2010
20591903
MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus.
2010
20591904
Biological knowledge bases using Wikis: combining the flexibility of Wikis with the structure of databases.
2010
20591906
ABC-SysBio--approximate Bayesian computation in Python with GPU support.
2010
20591907
mbmdr: an R package for exploring gene-gene interactions associated with binary or quantitative traits.
2010
20595460
ExTopoDB: a database of experimentally derived topological models of transmembrane proteins.
2010
20601677
G-SQZ: compact encoding of genomic sequence and quality data.
2010
20605925
PERMORY: an LD-exploiting permutation test algorithm for powerful genome-wide association testing.
2010
20605926
MamPhEA: a web tool for mammalian phenotype enrichment analysis.
2010
20605928
Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud.
2010
20605929
CNVineta: a data mining tool for large case-control copy number variation datasets.
2010
20605930
Genome-wide functional element detection using pairwise statistical alignment outperforms multiple genome footprinting techniques.
2010
20610610
ROAST: rotation gene set tests for complex microarray experiments.
2010
20610611
Fast overlapping of protein contact maps by alignment of eigenvectors.
2010
20610612
METAL: fast and efficient meta-analysis of genomewide association scans.
2010
20616382
Ontogenomic study of the relationship between number of gene splice variants and GO categorization.
2010
20616384
First insight into the prediction of protein folding rate change upon point mutation.
2010
20616385
Computational analysis of tissue-specific gene networks: application to murine retinal functional studies.
2010
20616386
Analyzing taxonomic classification using extensible Markov models.
2010
20624777
Interactive and fuzzy search: a dynamic way to explore MEDLINE.
2010
20624778
Dealing with sparse data in predicting outcomes of HIV combination therapies.
2010
20624779
An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes.
2010
20624780
A comparison of several algorithms for the single individual SNP haplotyping reconstruction problem.
2010
20624781
iAlign: a method for the structural comparison of protein-protein interfaces.
2010
20624782
genoPlotR: comparative gene and genome visualization in R.
2010
20624783
Logic Forest: an ensemble classifier for discovering logical combinations of binary markers.
2010
20628070
C-It: a knowledge database for tissue-enriched genes.
2010
20628071
A dynamic wavelet-based algorithm for pre-processing tandem mass spectrometry data.
2010
20628072
BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks.
2010
20628073
Editing, validating and translating of SBGN maps.
2010
20628075
PriorsEditor: a tool for the creation and use of positional priors in motif discovery.
2010
20628076
MetPA: a web-based metabolomics tool for pathway analysis and visualization.
2010
20628077
ANAIS: analysis of NimbleGen arrays interface.
2010
20631159
Probabilistic analysis of gene expression measurements from heterogeneous tissues.
2010
20631160
LocusZoom: regional visualization of genome-wide association scan results.
2010
20634204
RPPanalyzer: Analysis of reverse-phase protein array data.
2010
20634205
On reverse engineering of gene interaction networks using time course data with repeated measurements.
2010
20639410
BigWig and BigBed: enabling browsing of large distributed datasets.
2010
20639541
Towards optimal alignment of protein structure distance matrices.
2010
20639543
SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data.
2010
20639544
Ontology for medicinal materials based on traditional Korean medicine.
2010
20647520
PathwayAccess: CellDesigner plugins for pathway databases.
2010
20647521
Prophossi: automating expert validation of phosphopeptide-spectrum matches from tandem mass spectrometry.
2010
20651112
Cytoscape Web: an interactive web-based network browser.
2010
20656902
A fast and robust statistical test based on likelihood ratio with Bartlett correction to identify Granger causality between gene sets.
2010
20660295
Integrative classification and analysis of multiple arrayCGH datasets with probe alignment.
2010
20660296
Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites.
2010
20663846
proTF: a comprehensive data and phylogenomics resource for prokaryotic transcription factors.
2010
20663847
RepMaestro: scalable repeat detection on disk-based genome sequences.
2010
20663848
MetNetMaker: a free and open-source tool for the creation of novel metabolic networks in SBML format.
2010
20671147
Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data.
2010
20671148
ExpressionView--an interactive viewer for modules identified in gene expression data.
2010
20671149
TreesimJ: a flexible, forward time population genetic simulator.
2010
20671150
Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology.
2010
20671151
Multi-objective pairwise RNA sequence alignment.
2010
20679330
The CoFactor database: organic cofactors in enzyme catalysis.
2010
20679331
Multi-netclust: an efficient tool for finding connected clusters in multi-parametric networks.
2010
20679333
ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level.
2010
20679334
PSExplorer: whole parameter space exploration for molecular signaling pathway dynamics.
2010
20679335
DMDM: domain mapping of disease mutations.
2010
20685956
SPRINT: side-chain prediction inference toolbox for multistate protein design.
2010
20685957
Ultra-fast FFT protein docking on graphics processors.
2010
20685958
A framework for oligonucleotide microarray preprocessing.
2010
20688976
Gene function prediction using semantic similarity clustering and enrichment analysis in the malaria parasite Plasmodium falciparum.
2010
20693320
Association screening of common and rare genetic variants by penalized regression.
2010
20693321
RefProtDom: a protein database with improved domain boundaries and homology relationships.
2010
20693322
MASiVE: Mapping and Analysis of Sirevirus Elements in plant genome sequences.
2010
20696734
An alignment-free model for comparison of regulatory sequences.
2010
20696736
RBSDesigner: software for designing synthetic ribosome binding sites that yields a desired level of protein expression.
2010
20702394
BDVal: reproducible large-scale predictive model development and validation in high-throughput datasets.
2010
20702395
Cross-species queries of large gene expression databases.
2010
20702396
A Bayesian method for 3D macromolecular structure inference using class average images from single particle electron microscopy.
2010
20702397
NoiseMaker: simulated screens for statistical assessment.
2010
20702398
Automated analysis of time-lapse fluorescence microscopy images: from live cell images to intracellular foci.
2010
20702399
Identifying informative subsets of the Gene Ontology with information bottleneck methods.
2010
20702400
MetDAT: a modular and workflow-based free online pipeline for mass spectrometry data processing, analysis and interpretation.
2010
20702401
Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies.
2010
20702402
QuantProReloaded: quantitative analysis of microspot immunoassays.
2010
20709689
Text mining meets workflow: linking U-Compare with Taverna.
2010
20709690
Search and clustering orders of magnitude faster than BLAST.
2010
20709691
A cell-based simulation software for multi-cellular systems.
2010
20709692
ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments.
2010
20709693
Module-based prediction approach for robust inter-study predictions in microarray data.
2010
20719761
A discriminatory function for prediction of protein-DNA interactions based on alpha shape modeling.
2010
20733060
GolgiP: prediction of Golgi-resident proteins in plants.
2010
20733061
Annotare--a tool for annotating high-throughput biomedical investigations and resulting data.
2010
20733062
OpenStructure: a flexible software framework for computational structural biology.
2010
20733063
Improving performances of suboptimal greedy iterative biclustering heuristics via localization.
2010
20733064
Circoletto: visualizing sequence similarity with Circos.
2010
20736339
Deep and wide digging for binding motifs in ChIP-Seq data.
2010
20736340
Obtaining better quality final clustering by merging a collection of clusterings.
2010
20736341
ICPS: an integrative cancer profiler system.
2010
20736342
Detecting two-locus associations allowing for interactions in genome-wide association studies.
2010
20736343
BioRuby: bioinformatics software for the Ruby programming language.
2010
20739307
2Struc: the secondary structure server.
2010
20739308
Structural genomics of histone tail recognition.
2010
20739309
GASSST: global alignment short sequence search tool.
2010
20739310
TFInfer: a tool for probabilistic inference of transcription factor activities.
2010
20739311
METAREP: JCVI metagenomics reports--an open source tool for high-performance comparative metagenomics.
2010
20798169
RDP3: a flexible and fast computer program for analyzing recombination.
2010
20798170
A study of the efficiency of pooling in haplotype estimation.
2010
20801910
miRNAkey: a software for microRNA deep sequencing analysis.
2010
20801911
Ontology- and graph-based similarity assessment in biological networks.
2010
20801912
Simple sequence-based kernels do not predict protein-protein interactions.
2010
20801913
XMSF: Structure-preserving noise reduction and pre-segmentation in microscope tomography.
2010
20802209
Model-based clustering of microarray expression data via latent Gaussian mixture models.
2010
20802251
A sample storage management system for biobanks.
2010
20807837
Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes.
2010
20807838
CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data.
2010
20810601
Global modeling of transcriptional responses in interaction networks.
2010
20813878
Using manifold embedding for assessing and predicting protein interactions from high-throughput experimental data.
2010
20817744
Temporal waves of coherent gene expression during Drosophila embryogenesis.
2010
20819957
Identification of protein binding surfaces using surface triplet propensities.
2010
20819959
Automated construction and analysis of the design space for biochemical systems.
2010
20823298
Characteristics of 454 pyrosequencing data--enabling realistic simulation with flowsim.
2010
20823302
Classification of ncRNAs using position and size information in deep sequencing data.
2010
20823303
Integrating genome assemblies with MAIA.
2010
20823304
Parsimony and likelihood reconstruction of human segmental duplications.
2010
20823306
Discriminatory power of RNA family models.
2010
20823307
RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming.
2010
20823308
Solenoid and non-solenoid protein recognition using stationary wavelet packet transform.
2010
20823309
A predictor for toxin-like proteins exposes cell modulator candidates within viral genomes.
2010
20823311
Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources.
2010
20823312
A varying threshold method for ChIP peak-calling using multiple sources of information.
2010
20823314
Discovering graphical Granger causality using the truncating lasso penalty.
2010
20823316
is-rSNP: a novel technique for in silico regulatory SNP detection.
2010
20823317
Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes.
2010
20823318
BioXSD: the common data-exchange format for everyday bioinformatics web services.
2010
20823319
Discriminative and informative features for biomolecular text mining with ensemble feature selection.
2010
20823321
Improving disease gene prioritization using the semantic similarity of Gene Ontology terms.
2010
20823322
Utopia documents: linking scholarly literature with research data.
2010
20823323
A graphical method for reducing and relating models in systems biology.
2010
20823324
Bayesian experts in exploring reaction kinetics of transcription circuits.
2010
20823326
Dynamic deterministic effects propagation networks: learning signalling pathways from longitudinal protein array data.
2010
20823327
Efficient parameter search for qualitative models of regulatory networks using symbolic model checking.
2010
20823328
Prediction of a gene regulatory network linked to prostate cancer from gene expression, microRNA and clinical data.
2010
20823333
Semi-supervised multi-task learning for predicting interactions between HIV-1 and human proteins.
2010
20823334
Mass spectrometry data processing using zero-crossing lines in multi-scale of Gaussian derivative wavelet.
2010
20823336
Robust and accurate data enrichment statistics via distribution function of sum of weights.
2010
20826881
ODES: an overlapping dense sub-graph algorithm.
2010
20829442
SBML2TikZ: supporting the SBML render extension in LaTeX.
2010
20829443
The Chemical Translation Service--a web-based tool to improve standardization of metabolomic reports.
2010
20829444
PubDNA Finder: a web database linking full-text articles to sequences of nucleic acids.
2010
20829445
Reptile: representative tiling for short read error correction.
2010
20834037
Semi-supervised recursively partitioned mixture models for identifying cancer subtypes.
2010
20834038
A unified index of sequence quality and contig overlap for DNA barcoding.
2010
20837570
SynBioWave--a real-time communication platform for molecular and synthetic biology.
2010
20841324
PedMerge: merging pedigrees to facilitate family-based genetic statistical analyses.
2010
20843958
Characterizing molecular adaptation: a hierarchical approach to assess the selective influence of amino acid properties.
2010
20847216
Ruffus: a lightweight Python library for computational pipelines.
2010
20847218
Combined prediction of Tat and Sec signal peptides with hidden Markov models.
2010
20847219
Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape.
2010
20847220
The binding site distance test score: a robust method for the assessment of predicted protein binding sites.
2010
20861025
Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes.
2010
20861026
SeqEM: an adaptive genotype-calling approach for next-generation sequencing studies.
2010
20861027
BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis.
2010
20861028
FastPval: a fast and memory efficient program to calculate very low P-values from empirical distribution.
2010
20861029
Girafe--an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads.
2010
20861030
MOBI: a web server to define and visualize structural mobility in NMR protein ensembles.
2010
20861031
DisGeNET: a Cytoscape plugin to visualize, integrate, search and analyze gene-disease networks.
2010
20861032
SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks.
2010
20861033
Metric learning for enzyme active-site search.
2010
20870642
PAR: a PARallel and distributed job crusher.
2010
20870644
Identification of context-dependent motifs by contrasting ChIP binding data.
2010
20870645
SimiCon: a web tool for protein-ligand model comparison through calculation of equivalent atomic contacts.
2010
20871105
A Gibbs sampling strategy applied to the mapping of ambiguous short-sequence tags.
2010
20871106
RAPID detection of gene-gene interactions in genome-wide association studies.
2010
20871107
SylArray: a web server for automated detection of miRNA effects from expression data.
2010
20871108
HybridNET: a tool for constructing hybridization networks.
2010
20871109
GLOOME: gain loss mapping engine.
2010
20876605
SLOPE: a quick and accurate method for locating non-SNP structural variation from targeted next-generation sequence data.
2010
20876606
Spial: analysis of subtype-specific features in multiple sequence alignments of proteins.
2010
20880955
A statistical framework for Illumina DNA methylation arrays.
2010
20880956
Network-based comparison of temporal gene expression patterns.
2010
20889495
Chembench: a cheminformatics workbench.
2010
20889496
CopyMap: localization and calling of copy number variation by joint analysis of hybridization data from multiple individuals.
2010
20926418
GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop.
2010
20926419
ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations.
2010
20926420
MEDELLER: homology-based coordinate generation for membrane proteins.
2010
20926421
TURNIP: tracking unresolved nucleotide polymorphisms in large hard-to-assemble regions of repetitive DNA sequence.
2010
20926422
GPCRRD: G protein-coupled receptor spatial restraint database for 3D structure modeling and function annotation.
2010
20926423
Robust relationship inference in genome-wide association studies.
2010
20926424
PyETV: a PyMOL evolutionary trace viewer to analyze functional site predictions in protein complexes.
2010
20929911
Pathway Activity Profiling (PAPi): from the metabolite profile to the metabolic pathway activity.
2010
20929912
R3D Align: global pairwise alignment of RNA 3D structures using local superpositions.
2010
20929913
High-throughput prediction of protein antigenicity using protein microarray data.
2010
20934990
Graph-based word sense disambiguation of biomedical documents.
2010
20934991
Target-align: a tool for plant microRNA target identification.
2010
20934992
Pre-calculated protein structure alignments at the RCSB PDB website.
2010
20937596
A classification model for G-to-A hypermutation in hepatitis B virus ultra-deep pyrosequencing reads.
2010
20937597
PICMI: mapping point mutations on genomes.
2010
20940168
The SMARTCyp cytochrome P450 metabolism prediction server.
2010
20947523
OmicsAnalyzer: a Cytoscape plug-in suite for modeling omics data.
2010
20947524
CellPublisher: a web platform for the intuitive visualization and sharing of metabolic, signalling and regulatory pathways.
2010
20947526
Flapjack--graphical genotype visualization.
2010
20956241
FILTREST3D: discrimination of structural models using restraints from experimental data.
2010
20956242
SPLATCHE2: a spatially explicit simulation framework for complex demography, genetic admixture and recombination.
2010
20956243
Interactive microbial genome visualization with GView.
2010
20956244
High-quality annotation of promoter regions for 913 bacterial genomes.
2010
20956245
VEGA: variational segmentation for copy number detection.
2010
20959380
SmashCommunity: a metagenomic annotation and analysis tool.
2010
20959381
MiRonTop: mining microRNAs targets across large scale gene expression studies.
2010
20959382
Interactional and functional centrality in transcriptional co-expression networks.
2010
20959383
CNAseg--a novel framework for identification of copy number changes in cancer from second-generation sequencing data.
2010
20966003
R/qtl: high-throughput multiple QTL mapping.
2010
20966004
SmashCell: a software framework for the analysis of single-cell amplified genome sequences.
2010
20966005
Discovering homotypic binding events at high spatial resolution.
2010
20966006
Generalized random set framework for functional enrichment analysis using primary genomics datasets.
2011
20971985
GAMES identifies and annotates mutations in next-generation sequencing projects.
2011
20971986
Interoperability between phenotype and anatomy ontologies.
2010
20971987
The GMOD Drupal bioinformatic server framework.
2010
20971988
Optimized data fusion for K-means Laplacian clustering.
2011
20980271
Identification of subfamily-specific sites based on active sites modeling and clustering.
2010
20980272
PPO: predictor for prokaryotic operons.
2010
21030461
SPHINX--an algorithm for taxonomic binning of metagenomic sequences.
2011
21030462
A variable selection method for genome-wide association studies.
2011
21036813
Benchmarking the performance of human antibody gene alignment utilities using a 454 sequence dataset.
2010
21036814
Bayesian sampling of genomic rearrangement scenarios via double cut and join.
2010
21037244
A stochastic expectation and maximization algorithm for detecting quantitative trait-associated genes.
2011
21037246
dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks.
2011
21045073
Accelerating reaction-diffusion simulations with general-purpose graphics processing units.
2011
21062761
Inverse perturbation for optimal intervention in gene regulatory networks.
2011
21062762
NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads.
2011
21062764
A hybrid approach to extract protein-protein interactions.
2011
21062765
Generation of a consensus protein domain dictionary.
2011
21068000
PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes.
2011
21068001
The uniqueome: a mappability resource for short-tag sequencing.
2011
21075741
Inference of gene networks--application to Bifidobacterium.
2011
21075742
Analyzing marginal cases in differential shotgun proteomics.
2011
21075743
Protein Peeling 3D: new tools for analyzing protein structures.
2011
21075745
QuACN: an R package for analyzing complex biological networks quantitatively.
2011
21075747
Differential effects of chromatin regulators and transcription factors on gene regulation: a nucleosomal perspective.
2011
21075748
TE Displayer for post-genomic analysis of transposable elements.
2011
21075749
PLEXY: efficient target prediction for box C/D snoRNAs.
2011
21076148
Statistical confidence measures for genome maps: application to the validation of genome assemblies.
2010
21076149
Automated construction and testing of multi-locus gene-gene associations.
2011
21076150
Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization.
2011
21081509
iMAT: an integrative metabolic analysis tool.
2010
21081510
GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments.
2011
21081511
SESAME (SEquence Sorter & AMplicon Explorer): genotyping based on high-throughput multiplex amplicon sequencing.
2011
21084284
PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences.
2011
21088024
SAMStat: monitoring biases in next generation sequencing data.
2011
21088025
Scoring-and-unfolding trimmed tree assembler: concepts, constructs and comparisons.
2011
21088026
GPU-BLAST: using graphics processors to accelerate protein sequence alignment.
2011
21088027
GSearcher: agile attribute querying for biological networks.
2010
21088028
Efficient change point detection for genomic sequences of continuous measurements.
2011
21088029
Anatomy of a hash-based long read sequence mapping algorithm for next generation DNA sequencing.
2011
21088030
SLIM: a sliding linear model for estimating the proportion of true null hypotheses in datasets with dependence structures.
2011
21098430
Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data.
2011
21098431
Improving structure alignment-based prediction of SCOP families using Vorolign kernels.
2011
21098432
Prognostic transcriptional association networks: a new supervised approach based on regression trees.
2011
21098433
von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models.
2011
21115436
HiTEC: accurate error correction in high-throughput sequencing data.
2011
21115437
Real-world comparison of CPU and GPU implementations of SNPrank: a network analysis tool for GWAS.
2011
21115438
Identification of protein complexes from co-immunoprecipitation data.
2011
21115439
A dynamic data structure for flexible molecular maintenance and informatics.
2011
21115440
A performance enhanced PSI-BLAST based on hybrid alignment.
2011
21115441
Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution.
2011
21118823
maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences.
2011
21123221
Open source platform for the execution and analysis of mechanical refolding experiments.
2011
21123222
GLay: community structure analysis of biological networks.
2010
21123224
MTR: taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks.
2011
21127032
New approach for segmentation and quantification of two-dimensional gel electrophoresis images.
2011
21127033
A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain-peptide interaction from primary sequence.
2011
21127034
RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries.
2011
21134889
Predicting in vitro drug sensitivity using Random Forests.
2011
21134890
Toward the estimation of the absolute quality of individual protein structure models.
2011
21134891
Rseg--an R package to optimize segmentation of SNP array data.
2011
21134892
MASISH: a database for gene expression in maize seeds.
2011
21134893
MSPocket: an orientation-independent algorithm for the detection of ligand binding pockets.
2011
21134896
Toward an automatic method for extracting cancer- and other disease-related point mutations from the biomedical literature.
2011
21138947
W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data.
2011
21138948
Bayesian ensemble methods for survival prediction in gene expression data.
2011
21148161
SlideSort: all pairs similarity search for short reads.
2011
21148542
Mugsy: fast multiple alignment of closely related whole genomes.
2011
21148543
SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks.
2011
21148545
Improved predictions by Pcons.net using multiple templates.
2011
21149277
MU2A--reconciling the genome and transcriptome to determine the effects of base substitutions.
2011
21149339
Cytoscape 2.8: new features for data integration and network visualization.
2011
21149340
Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array.
2011
21149341
When the Web meets the cell: using personalized PageRank for analyzing protein interaction networks.
2011
21149343
A Bayesian approach for estimating calibration curves and unknown concentrations in immunoassays.
2011
21149344
PE-Assembler: de novo assembler using short paired-end reads.
2011
21149345
The Bayesian lasso for genome-wide association studies.
2011
21156729
Automated analysis of information processing, kinetic independence and modular architecture in biochemical networks using MIDIA.
2011
21159624
Identifying cancer driver genes in tumor genome sequencing studies.
2011
21169372
SAIL--a software system for sample and phenotype availability across biobanks and cohorts.
2011
21169373
Multi-level mixed effects models for bead arrays.
2011
21169374
ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping.
2011
21169377
phangorn: phylogenetic analysis in R.
2011
21169378
Lipid Data Analyzer: unattended identification and quantitation of lipids in LC-MS data.
2011
21169379
Functional integration of a metabolic network model and expression data without arbitrary thresholding.
2011
21172910
Improvements in the reconstruction of time-varying gene regulatory networks: dynamic programming and regularization by information sharing among genes.
2011
21177328
ASSIMILATOR: a new tool to inform selection of associated genetic variants for functional studies.
2011
21177990
DiNAMIC: a method to identify recurrent DNA copy number aberrations in tumors.
2011
21183584
CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments.
2011
21183585
Ct3d: tracking microglia motility in 3D using a novel cosegmentation approach.
2011
21186244
PUGSVM: a caBIG™ analytical tool for multiclass gene selection and predictive classification.
2011
21186245
A computationally efficient modular optimal discovery procedure.
2011
21186247
Voroprot: an interactive tool for the analysis and visualization of complex geometric features of protein structure.
2011
21186248
Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences.
2011
21193521
Principal network analysis: identification of subnetworks representing major dynamics using gene expression data.
2011
21193522
Tabix: fast retrieval of sequence features from generic TAB-delimited files.
2011
21208982
Wave-spec: a preprocessing package for mass spectrometry data.
2011
21208983
Model selection in Bayesian segmentation of multiple DNA alignments.
2011
21208984
MBRole: enrichment analysis of metabolomic data.
2011
21208985
MIRACH: efficient model checker for quantitative biological pathway models.
2011
21208986
flowPhyto: enabling automated analysis of microscopic algae from continuous flow cytometric data.
2011
21208987
The CCPN Metabolomics Project: a fast protocol for metabolite identification by 2D-NMR.
2011
21216771
Improved side-chain modeling by coupling clash-detection guided iterative search with rotamer relaxation.
2011
21216772
A method for identifying haplotypes carrying the causative allele in positive natural selection and genome-wide association studies.
2011
21216773
The Physiome Model Repository 2.
2011
21216774
A greedy, graph-based algorithm for the alignment of multiple homologous gene lists.
2011
21216775
MADGene: retrieval and processing of gene identifier lists for the analysis of heterogeneous microarray datasets.
2011
21216776
HiSpOD: probe design for functional DNA microarrays.
2011
21216777
X-MATE: a flexible system for mapping short read data.
2011
21216778
A Java API for working with PubChem datasets.
2011
21216779
A novel hybrid gene prediction method employing protein multiple sequence alignments.
2011
21216780
R/mpMap: a computational platform for the genetic analysis of multiparent recombinant inbred lines.
2011
21217121
A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.
2011
21217122
GPU accelerated biochemical network simulation.
2011
21224286
A k-mer scheme to predict piRNAs and characterize locust piRNAs.
2011
21224287
CNAmet: an R package for integrating copy number, methylation and expression data.
2011
21228048
ESS++: a C++ objected-oriented algorithm for Bayesian stochastic search model exploration.
2011
21233165
A pipeline for RNA-seq data processing and quality assessment.
2011
21233166
AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision.
2011
21233167
High-accuracy prediction of bacterial type III secreted effectors based on position-specific amino acid composition profiles.
2011
21233168
Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering.
2011
21233169
Automated bond order assignment as an optimization problem.
2011
21245051
Identifying viral integration sites using SeqMap 2.0.
2011
21245052
BayesPeak--an R package for analysing ChIP-seq data.
2011
21245054
Compression of DNA sequence reads in FASTQ format.
2011
21252073
PhyloPro: a web-based tool for the generation and visualization of phylogenetic profiles across Eukarya.
2011
21252074
Dalliance: interactive genome viewing on the web.
2011
21252075
Length bias correction for RNA-seq data in gene set analyses.
2011
21252076
Biological assessment of robust noise models in microarray data analysis.
2011
21252077
Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup.
2011
21257608
OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms.
2011
21257609
WIST: toolkit for rapid, customized LIMS development.
2011
21258060
HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens.
2011
21258062
Automated validation of genetic variants from large databases: ensuring that variant references refer to the same genomic locations.
2011
21258063
Computational inference of grammars for larger-than-gene structures from annotated gene sequences.
2011
21258064
Computational refinement of post-translational modifications predicted from tandem mass spectrometry.
2011
21258065
An efficient hierarchical generalized linear mixed model for pathway analysis of genome-wide association studies.
2011
21266443
Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions.
2011
21266444
Quality control and preprocessing of metagenomic datasets.
2011
21278185
Modeling and comparing the organization of circular genomes.
2011
21278186
Identity-by-descent filtering of exome sequence data for disease-gene identification in autosomal recessive disorders.
2011
21278187
PiNGO: a Cytoscape plugin to find candidate genes in biological networks.
2011
21278188
Conveyor: a workflow engine for bioinformatic analyses.
2011
21278189
Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format.
2011
21278191
SHRiMP2: Sensitive yet Practical Short Read Mapping.
2011
21278192
Easyfig: a genome comparison visualizer.
2011
21278367
Gobe: an interactive, web-based tool for comparative genomic visualization.
2011
21296748
LSPR: an integrated periodicity detection algorithm for unevenly sampled temporal microarray data.
2011
21296749
SIMA: Simultaneous Multiple Alignment of LC/MS Peak Lists.
2011
21296750
GOSSIP: a method for fast and accurate global alignment of protein structures.
2011
21296751
DDN: a caBIG(R) analytical tool for differential network analysis.
2011
21296752
Model annotation for synthetic biology: automating model to nucleotide sequence conversion.
2011
21296753
SpaCEM3: a software for biological module detection when data is incomplete, high dimensional and dependent.
2011
21296754
uMELT: prediction of high-resolution melting curves and dynamic melting profiles of PCR products in a rich web application.
2011
21300699
BioGRID REST Service, BiogridPlugin2 and BioGRID WebGraph: new tools for access to interaction data at BioGRID.
2011
21300700
HLA*IMP--an integrated framework for imputing classical HLA alleles from SNP genotypes.
2011
21300701
tigre: Transcription factor inference through gaussian process reconstruction of expression for bioconductor.
2011
21300702
SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based models.
2011
21303862
GeneTUKit: a software for document-level gene normalization.
2011
21303863
GeneReporter--sequence-based document retrieval and annotation.
2011
21310745
FISH Finder: a high-throughput tool for analyzing FISH images.
2011
21310746
Entropy-accelerated exact clustering of protein decoys.
2011
21310747
Automated analysis of biological oscillator models using mode decomposition.
2011
21317138
eGOB: eukaryotic Gene Order Browser.
2011
21317139
SiGN-SSM: open source parallel software for estimating gene networks with state space models.
2011
21317140
Topological entropy of DNA sequences.
2011
21317142
Cross-platform comparison of microarray data using order restricted inference.
2011
21317143
Improving SNP discovery by base alignment quality.
2011
21320865
Identifying dispersed epigenomic domains from ChIP-Seq data.
2011
21325299
Automated workflows for accurate mass-based putative metabolite identification in LC/MS-derived metabolomic datasets.
2011
21325300
Annotating genes and genomes with DNA sequences extracted from biomedical articles.
2011
21325301
Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows.
2011
21325302
Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.
2011
21330288
Defining an informativeness metric for clustering gene expression data.
2011
21330289
FIMO: scanning for occurrences of a given motif.
2011
21330290
libfbi: a C++ implementation for fast box intersection and application to sparse mass spectrometry data.
2011
21330291
Topology and prediction of RNA pseudoknots.
2011
21335320
ProtTest 3: fast selection of best-fit models of protein evolution.
2011
21335321
B2G-FAR, a species-centered GO annotation repository.
2011
21335611
fconv: format conversion, manipulation and feature computation of molecular data.
2011
21335612
A common layer of interoperability for biomedical ontologies based on OWL EL.
2011
21343142
BiC: a web server for calculating bimodality of coexpression between gene and protein networks.
2011
21345871
Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software.
2011
21349861
PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers.
2011
21349862
ACT: aggregation and correlation toolbox for analyses of genome tracks.
2011
21349863
All-atom knowledge-based potential for RNA structure prediction and assessment.
2011
21349865
A high-throughput processing service for retention time alignment of complex proteomics and metabolomics LC-MS data.
2011
21349866
Interactive, multiscale navigation of large and complicated biological networks.
2011
21349867
Gene List significance at-a-glance with GeneValorization.
2011
21349868
R453Plus1Toolbox: an R/Bioconductor package for analyzing Roche 454 Sequencing data.
2011
21349869
MPID-T2: a database for sequence-structure-function analyses of pMHC and TR/pMHC structures.
2011
21349870
FNV: light-weight flash-based network and pathway viewer.
2011
21349871
The MEMPACK alpha-helical transmembrane protein structure prediction server.
2011
21349872
AGRA: analysis of gene ranking algorithms.
2011
21349873
STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB.
2011
21357575
Automatically identifying and annotating mouse embryo gene expression patterns.
2011
21357576
eCEO: an efficient Cloud Epistasis cOmputing model in genome-wide association study.
2011
21367868
MemLoci: predicting subcellular localization of membrane proteins in Eukaryotes.
2011
21367869
Large scale learning of combinatorial transcriptional dynamics from gene expression.
2011
21367870
Connectedness of PPI network neighborhoods identifies regulatory hub proteins.
2011
21367871
Human variation database: an open-source database template for genomic discovery.
2011
21367872
SurvJamda: an R package to predict patients' survival and risk assessment using joint analysis of microarray gene expression data.
2011
21367873
Mixtures of common t-factor analyzers for clustering high-dimensional microarray data.
2011
21372081
ncIDP-assign: a SPARKY extension for the effective NMR assignment of intrinsically disordered proteins.
2011
21372082
A probabilistic model of nuclear import of proteins.
2011
21372083
SC2ATmd: A tool for integration of the figure of merit with cluster analysis for gene expression data.
2011
21372084
Comparative Visualization of Genetic and Physical Maps with Strudel.
2011
21372085
Identifying Discriminative Classification Based Motifs in Biological Sequences.
2011
21372086
GBOOST : A GPU-based tool for detecting gene-gene interactions in genome-wide case control studies.
2011
21372087
Agos - a universal web tool for GW Argonaute-binding domain prediction.
2011
21385787
Baking a mass-spectrometry data PIE with McMC and simulated annealing: predicting protein post-translational modifications from integrated top-down and bottom-up data.
2011
21389073
birgHPC: Creating Instant Computing Clusters for Bioinformatics and Molecular Dynamics.
2011
21398666
GeCo++: a C++ library for genomic features computation and annotation in the presence of variants.
2011
21398667
sc-PDB: a database for identifying variations and multiplicity of "druggable" binding sites in proteins.
2011
21398668
UniCarb-DB: A Database Resource for Glycomic Discovery.
2011
21398669
Identification and Quantification of Metabolites in 1H NMR Spectra by Bayesian Model Selection.
2011
21398670
Histogram-Based DNA Analysis for the Visualization of Chromosome, Genome and Species Information.
2011
21398672
PRIMe: A Method for Characterization and Evaluation of Pleiotropic Regions from Multiple Genome-wide Association Studies.
2011
21398673
TEQC: an R-package for quality control in target capture experiments.
2011
21398674
ogaraK: A population genetics simulator for malaria.
2011
21414984
A wholly-defined Agilent microarray spike-in dataset.
2011
21414985
MrBayes on a Graphics Processing Unit.
2011
21414986
COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method.
2011
21414987
Compounds In Literature (CIL): Screening for Compounds and Relatives in PubMed.
2011
21414988
Structure-based de novo prediction of zinc-binding sites in proteins of unknown function.
2011
21414989
AStream: An R package for annotating LC/MS metabolomic data.
2011
21414990
Customisable views on semantically integrated networks for systems biology.
2011
21414991
Integrative Network Alignment Reveals Large Regions of Global Network Similarity in Yeast and Human.
2011
21414992
SplamiR - Prediction of spliced miRNAs in plants.
2011
21421552
GO-Module: functional synthesis and improved interpretation of Gene Ontology patterns.
2011
21421553
anota: analysis of differential translation in genome wide studies.
2011
21422072
Prediction of microRNA targets in Caenorhabditis elegans using a Self-Organizing Map.
2011
21422073
ExpEdit: a web server to explore human RNA editing in RNA-Seq experiments.
2011
21427194
Prediction of Novel Pre-microRNAs with High Accuracy through Boosting and SVM.
2011
21436129
PlantMiRNAPred: efficient classification of real and pseudo plant pre-miRNAs.
2011
21441575
Comparison of Global Tests for Functional Gene Sets in Two-Group Designs and Selection of Potentially Effect-causing Genes.
2011
21441576
Faster Exact Maximum Parsimony Search with XMP.
2011
21444294
The caBIG(R) Life Science Business Architecture Model.
2011
21450709
hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data.
2011
21450710
pathClass: An R-Package for Integration of Pathway Knowledge into Support Vector Machines for Biomarker Discovery.
2011
21450711
Exact and complete short read alignment to microbial genomes using GPU programming.
2011
21450712
Inference of transcriptional regulatory network by bootstrapping patterns.
2011
21450714
A novel network-based method for measuring the functional relationship between gene sets.
2011
21450716
A qualitative continuous model of cellular auxin and brassinosteroid signaling and their crosstalk.
2011
21450717
Rigid substructure search.
2011
21460026
EpiGPU: Exhaustive pairwise epistasis scans parallelised on consumer level graphics cards.
2011
21471009
Independent Surrogate Variable Analysis to deconvolve confounding factors in large-scale microarray profiling studies.
2011
21471010
Alignment-free detection of local similarity among viral and bacterial genomes.
2011
21471011
ProDy: Protein Dynamics Inferred from Theory and Experiments.
2011
21471012
Correcting Errors in Short Reads by Multiple Alignments.
2011
21471014
DIME: R-package for Identifying Differential ChIP-seq Based on an Ensemble of Mixture Models.
2011
21471015
CMView: Interactive contact map visualization and analysis.
2011
21471016
Comprehensive and relaxed search for oligonucleotide signatures in hierarchically-clustered sequence datasets.
2011
21471017
Multi-platform Segmentation for Joint Detection of Copy Number Variants.
2011
21471018
Reasoning with bio-ontologies: using relational closure rules to enable practical querying.
2011
21471019
Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds.
2011
21478194
CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks.
2011
21478195
Performance assessment of copy number microarray platforms using a spike-in experiment.
2011
21478196
A comprehensive protein-centric ID mapping service for molecular data integration.
2011
21478197
Comrad: a novel algorithmic framework for the integrated analysis of RNA-Seq and WGSS data.
2011
21478487
Reliability Oriented Bioinformatic Networks Visualization.
2011
21478488
MEME-ChIP: motif analysis of large DNA datasets.
2011
21486936
Cobweb: a Java applet for network exploration and visualisation.
2011
21486937