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| 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. |
== Publications about Cytoscape == Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T.[[BR]] Free Full Text Cytoscape: a software environment for integrated models of biomolecular interaction networks.[[BR]] Genome Res. 2003 Nov; 13(11):2498-504 |
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Proteins, 2005[[BR]] G Cavelier, D Anastassiou D[[BR]] Phenotype analysis using network motifs derived from changes in regulatory network dynamics[[BR]] [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] |
. Free full text at http://www.genome.org/cgi/content/full/13/11/2498 == Publications citing Cytoscape == Publications that use Cytoscape help to keep it funded. |
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BMC Bioinformatics 2005, 6:154[[BR]] Tools enabling the elucidation of molecular pathways active in human disease: Application to Hepatitis C virus infection[[BR]] David J Reiss , Iliana Avila-Campillo , Vesteinn Thorsson , Benno Schwikowski and Timothy Galitski[[BR]] [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] |
Link to a Google Scholar search for articles citing Shannon et al. (2003): http://scholar.google.com/scholar?hl=en&lr=&cites=3669641697993554798 (256 hits as of May 29, 2007) |
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Genome Biology. March, 2005[[BR]] Becky L Drees, Vesteinn Thorsson, Gregory W Carter, Alexander W Rives, Marisa Z Raymond, Iliana Avila-Campillo, Paul Shannon and Timothy Galitski[[BR]] Derivation of genetic networks from quantitative phenotype data. Genome Biology[[BR]] [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, 2005[[BR]] Sharan R, Suthram S, Kelley RM, Kuhn T, McCuine S, Uetz P, Sittler T, Karp RM, Ideker T[[BR]] Conserved patterns of protein interaction in multiple species[[BR]] Proc Natl Acad Sci U S A. 2005 Feb 8;102(6):1974-9. Epub 2005 Feb 01[[BR]] [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] 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 WV[[BR]] Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea[[BR]] Genome Res. 2004 Nov;14(11):2221-34[[BR]] [http://www.genome.org/cgi/content/abstract/14/11/2221 Abstract] [http://www.genome.org/cgi/reprint/14/11/2221 PDF] Bioinformatics August 2004[[BR]] Reiss David, Schwikowski Benno[[BR]] Predicting protein–peptide interactions via a network-based motif sampler[[BR]] Bioinformatics. 2004 Aug 4;20 Suppl 1:I274-I282[[BR]] [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 2004[[BR]] Bonneau, Richard, Baliga Nitin S, Deutsch, Eric W, Shannon Paul and Hood, Leroy[[BR]] Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1[[BR]] Genome Biology 2004, 5:R52[[BR]] [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, J[[BR]] Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1[[BR]] Genome Res. 2004 14: 1025-35[[BR]] [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 2004[[BR]] Prinz S, Avila-Campillo I, Aldridge C, Srinivasan A, Dimitrov K, Siegel AF, and Galitski T[[BR]] Control of Yeast Filamentous-Form Growth by Modules in an Integrated Molecular Network[[BR]] Genome Res. 2004 14: 380-390[[BR]] [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 2004[[BR]] Tong AH, et al., Global mapping of the yeast genetic interaction network[[BR]] Science. 2004 Feb 6;303(5659):808-13[[BR]] [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 2004[[BR]] A systems approach to dissecting immunity and inflammation[[BR]] Aderem A, Smith KD[[BR]] Semin Immunol. 2004 Feb;16(1):55-67[[BR]] [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%2F29%2F2004&_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 2003[[BR]] Kelley BP, Sharan R, Karp RM, Sittler T, Root DE, Stockwell BR, Ideker T[[BR]] Conserved pathways within bacteria and yeast as revealed by global protein network alignment[[BR]] Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11394-9[[BR]] [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 2003[[BR]] Yeang C-H, Jaakkola T[[BR]] Physical network models and multi-source data integration[[BR]] The Seventh Annual International Conference on Research in Computational Molecular Biology, 2003[[BR]] [http://www.ai.mit.edu/people/tommi/papers/YeaJaa-recomb03.pdf PDF] Molecular Cancer Research, 2002[[BR]] Begley TJ, Rosenbach AS, Ideker T, Samson LD[[BR]] Damage Recovery Pathways in Saccharomyces cerevisiae Revealed by Genomic Phenotyping and Interactome Mapping[[BR]] Mol Cancer Res. 2002 Dec;1(2):103-12[[BR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12496357&dopt=Abstract Abstract] ISMB 2002[[BR]] Ideker T, Ozier O, Schwikowski B, Siegel A[[BR]] Discovering regulatory and signaling circuits in molecular interaction networks[[BR]] [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] |
Link to a Pubmed Central search for (free full-text) articles citing Shannon et al. (2003): http://www.pubmedcentral.nih.gov/tocrender.fcgi?action=cited&artid=403769 (72 articles as of May 29, 2007) |
Publications about Cytoscape
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T.BR Free Full Text Cytoscape: a software environment for integrated models of biomolecular interaction networks.BR Genome Res. 2003 Nov; 13(11):2498-504
Free full text at http://www.genome.org/cgi/content/full/13/11/2498
Publications citing Cytoscape
Publications that use Cytoscape help to keep it funded.
Link to a Google Scholar search for articles citing Shannon et al. (2003): http://scholar.google.com/scholar?hl=en&lr=&cites=3669641697993554798 (256 hits as of May 29, 2007)
Link to a Pubmed Central search for (free full-text) articles citing Shannon et al. (2003): http://www.pubmedcentral.nih.gov/tocrender.fcgi?action=cited&artid=403769 (72 articles as of May 29, 2007)