Diff for "Publications"

Please put any publications that use Cytoscape here. Periodically, we will edit the main cytoscape.org website to copy these over to make them more visible.

Gaggle: An open-source software system for integrating bioinformatics software and data sourcesBR Shannon PT,Reiss DJ,Bonneau R,Baliga NSBR BMC Bioinformatics, 7:(1), Mar, 2006 BR [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16569235 Abstract] [http://www.biomedcentral.com/content/pdf/1471-2105-7-176.pdf PDF]

Decomposing protein networks into domain-domain interactions BR Albrecht M,Huthmacher C,Tosatto SC,Lengauer TBR Bioinformatics, 21 Suppl 2, Sep, 2005BR [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16204107 Abstract] [http://bioinformatics.oxfordjournals.org/cgi/reprint/21/suppl_2/ii220.pdf PDF]

Pathway analysis of coronary atherosclerosisBR King JY, Ferrara R, Tabibiazar R, Spin JM, Chen MM, Kuchinsky A, Vailaya A, Kincaid R, Tsalenko A, Deng DX, Connolly A, Zhang P, Yang E, Watt C, Yakhini Z, Ben-Dor A, Adler A, Bruhn L, Tsao P, Quertermous T, Ashley EABR Physiol Genomics. 2005 Sep 21;23(1):103-18. Epub 2005 Jun 7BR [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=15942018&dopt=Abstract Abstract] [http://physiolgenomics.physiology.org/cgi/content/full/23/1/103 Full Text] [http://physiolgenomics.physiology.org/cgi/reprint/23/1/103 PDF]

BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks BR Maere S,Heymans K,Kuiper MBR Bioinformatics, 21:(16), Aug, 2005BR [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15972284 Abstract] [http://bioinformatics.oxfordjournals.org/cgi/reprint/21/16/3448.pdf PDF]

Proteins, 2005BR G Cavelier, D Anastassiou DBR Phenotype analysis using network motifs derived from changes in regulatory network dynamicsBR [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15971229 Abstract] [http://www3.interscience.wiley.com/cgi-bin/fulltext/110544754/HTMLSTART Full Text] [http://www3.interscience.wiley.com/cgi-bin/fulltext/110544754/PDFSTART PDF]

BMC Bioinformatics 2005, 6:154BR Tools enabling the elucidation of molecular pathways active in human disease: Application to Hepatitis C virus infectionBR David J Reiss , Iliana Avila-Campillo , Vesteinn Thorsson , Benno Schwikowski and Timothy GalitskiBR [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15967031 Abstract] [http://www.biomedcentral.com/1471-2105/6/154 Full Text] [http://www.biomedcentral.com/content/pdf/1471-2105-6-154.pdf PDF]

Genome Biology. March, 2005BR Becky L Drees, Vesteinn Thorsson, Gregory W Carter, Alexander W Rives, Marisa Z Raymond, Iliana Avila-Campillo, Paul Shannon and Timothy GalitskiBR Derivation of genetic networks from quantitative phenotype data. Genome BiologyBR [http://genomebiology.com/2005/6/4/R38/abstract Abstract] [http://genomebiology.com/2005/6/4/R38 Full Text] [http://genomebiology.com/content/pdf/gb-2005-6-4-r38.pdf PDF]

Proc Natl Acad Sci U S A. Feb 8, 2005BR Sharan R, Suthram S, Kelley RM, Kuhn T, McCuine S, Uetz P, Sittler T, Karp RM, Ideker TBR Conserved patterns of protein interaction in multiple speciesBR Proc Natl Acad Sci U S A. 2005 Feb 8;102(6):1974-9. Epub 2005 Feb 01BR [http://www.pnas.org/cgi/content/abstract/102/6/1974?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=ideker&searchid=1109093476283_4753&stored_search=&FIRSTINDEX=0&journalcode=pnas Abstract] [http://www.pnas.org/cgi/content/full/102/6/1974?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=ideker&searchid=1109093562510_4765&stored_search=&FIRSTINDEX=0&journalcode=pnas Full Text] [http://www.pnas.org/cgi/reprint/102/6/1974?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=ideker&searchid=1109093578097_4770&stored_search=&FIRSTINDEX=0&journalcode=pnas PDF]

T1DBase, a community web-based resource for type 1 diabetes research BR Smink LJ,Helton EM,Healy BC,Cavnor CC,Lam AC,Flamez D,Burren OS,Wang Y,Dolman GE,Burdick DB,Everett VH,Glusman G,Laneri D,Rowen L,Schuilenburg H,Walker NM,Mychaleckyj J,Wicker LS,Eizirik DL,Todd JA,Goodman NBR Nucleic Acids Res, 33:(Database issue), Jan, 2005BR [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15608258 Abstract] [http://nar.oxfordjournals.org/cgi/content/full/33/suppl_1/D544 FullText] [http://nar.oxfordjournals.org/cgi/reprint/33/suppl_1/D544.pdf PDF]

System-based proteomic analysis of the interferon response in human liver cells BR Yan W,Lee H,Yi EC,Reiss D,Shannon P,Kwieciszewski BK,Coito C,Li XJ,Keller A,Eng J,Galitski T,Goodlett DR,Aebersold R,Katze MGBR Genome Biol, 5:(8), 2004BR [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=15942018&dopt=Abstract Abstract] [http://physiolgenomics.physiology.org/cgi/content/full/23/1/103 FullText] [http://physiolgenomics.physiology.org/cgi/reprint/23/1/103 PDF]

Genome Research, November 2004 (cover article)BR Baliga NS, Bonneau R, Facciotti MT, Pan M, Glusman G, Deutsch EW, Shannon P, Chiu Y, Weng RS, Gan RR, Hung P, Date SV, Marcotte E, Hood L, Ng WVBR Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead SeaBR Genome Res. 2004 Nov;14(11):2221-34BR [http://www.genome.org/cgi/content/abstract/14/11/2221 Abstract] [http://www.genome.org/cgi/reprint/14/11/2221 PDF]

Bioinformatics August 2004BR Reiss David, Schwikowski BennoBR Predicting protein–peptide interactions via a network-based motif samplerBR Bioinformatics. 2004 Aug 4;20 Suppl 1:I274-I282BR [http://bioinformatics.oupjournals.org/cgi/content/abstract/20/suppl_1/i274 Abstract] [http://bioinformatics.oupjournals.org/cgi/reprint/20/suppl_1/i274 PDF]

Genome Biology, July 2004BR Bonneau, Richard, Baliga Nitin S, Deutsch, Eric W, Shannon Paul and Hood, LeroyBR Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1BR Genome Biology 2004, 5:R52BR [http://genomebiology.com/2004/5/8/r52/abstract Abstract] [http://genomebiology.com/2004/5/8/r52 Full Text] [http://genomebiology.com/content/pdf/gb-2004-5-8-r52.pdf PDF]

Genome Research, June 2004 (cover article)BR Baliga, NS, Bjork, SJ, Bonneau, R, Pan, M, Iloanusi, C, Kottemann, MCH, Hood, L, and DiRuggiero, JBR Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1BR Genome Res. 2004 14: 1025-35BR [http://www.genome.org/cgi/content/abstract/14/6/1025 Abstract] [http://www.genome.org/cgi/reprint/14/6/1025.pdf PDF] [http://www.genome.org/cgi/content/full/1993504/DC1 Supplemental Research Data]

Genome Research, March 2004BR Prinz S, Avila-Campillo I, Aldridge C, Srinivasan A, Dimitrov K, Siegel AF, and Galitski TBR Control of Yeast Filamentous-Form Growth by Modules in an Integrated Molecular NetworkBR Genome Res. 2004 14: 380-390BR [http://www.genome.org/cgi/content/abstract/14/3/380" Abstract][http://www.genome.org/cgi/reprint/14/3/380.pdf" PDF] [http://www.genome.org/cgi/content/full/14/3/380/DC1" Supplemental Research Data]

Science, Feb 2004BR Tong AH, et al., Global mapping of the yeast genetic interaction networkBR Science. 2004 Feb 6;303(5659):808-13BR [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14764870 Abstract] [http://www.sciencemag.org/cgi/content/full/303/5659/808 Full Text]

Seminars in Immunology, January 2004BR A systems approach to dissecting immunity and inflammationBR Aderem A, Smith KDBR Semin Immunol. 2004 Feb;16(1):55-67BR [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14751764 Abstract] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WX3-4BHSYWW-9&_coverDate=02/29/2004&_alid=188374479&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=7147&_sort=d&view=c&_acct=C000016018&_version=1&_urlVersion=0&_userid=281587&md5=110a35c81c74edf330477297c5d59184 Full Text]

PNAS, Septemer 2003BR Kelley BP, Sharan R, Karp RM, Sittler T, Root DE, Stockwell BR, Ideker TBR Conserved pathways within bacteria and yeast as revealed by global protein network alignmentBR Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11394-9BR [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14504397 Abstract] [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=14504397 Full Text]

RECOMB 2003BR Yeang C-H, Jaakkola TBR Physical network models and multi-source data integrationBR The Seventh Annual International Conference on Research in Computational Molecular Biology, 2003BR [http://www.ai.mit.edu/people/tommi/papers/YeaJaa-recomb03.pdf PDF]

Molecular Cancer Research, 2002BR Begley TJ, Rosenbach AS, Ideker T, Samson LDBR Damage Recovery Pathways in Saccharomyces cerevisiae Revealed by Genomic Phenotyping and Interactome MappingBR Mol Cancer Res. 2002 Dec;1(2):103-12BR [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12496357&dopt=Abstract Abstract]

ISMB 2002BR Ideker T, Ozier O, Schwikowski B, Siegel ABR Discovering regulatory and signaling circuits in molecular interaction networksBR [http://bioinformatics.oupjournals.org/ Bioinformatics] 18, S233 (2002)BR [http://bioinformatics.oupjournals.org/cgi/content/abstract/18/suppl_1/S233 Abstract] [http://bioinformatics.oupjournals.org/cgi/reprint/18/suppl_1/S233.pdf PDF] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12169552&dopt=Abstract Abstract] [http://cytoscape.org/ISMB2002/index.html Supplementary Material]