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---- ----- Please put any publications that use Cytoscape here (it helps to keep Cytoscape funded!). 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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Krogan NJ, Cagney G, Yu HY, et al.[[BR]] Global landscape of protein complexes in the yeast Saccharomyces cerevisiae[[BR]] NATURE 440 (7084): 637-643 MAR 30 2006[[BR]] |
. 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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| 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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Gaggle: An open-source software system for integrating bioinformatics software and data sources[[BR]] Shannon PT,Reiss DJ,Bonneau R,Baliga NS[[BR]] 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] Junker BH, Klukas C, Schreiber F[[BR]] VANTED: A system for advanced data analysis and visualization in the context of biological networks[[BR]] BMC BIOINFORMATICS 7: Art. No. 109 MAR 6 2006[[BR]] Titz B, Thomas S, Rajagopala SV, et al.[[BR]] Transcriptional activators in yeast [[BR]] NUCLEIC ACIDS RESEARCH 34 (3): 955-967 2006[[BR]] Baitaluk M, Qian XF, Godbole S, et al.[[BR]] PathSys: integrating molecular interaction graphs for systems biology [[BR]] BMC BIOINFORMATICS 7: Art. No. 55 FEB 7 2006[[BR]] Yi M, Horton JD, Cohen JC, et al.[[BR]] WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data [[BR]] BMC BIOINFORMATICS 7: Art. No. 30 JAN 19 2006 [[BR]] Fentem JH[[BR]] Working together to respond to the challenges of EU policy to replace animal testing [[BR]] ATLA-ALTERNATIVES TO LABORATORY ANIMALS 34 (1): 11-18 FEB 2006[[BR]] Joyce AR, Palsson BO[[BR]] The model organism as a system: integrating 'omics' data sets [[BR]] NATURE REVIEWS MOLECULAR CELL BIOLOGY 7 (3): 198-210 MAR 2006[[BR]] Mookherjee N, Brown KL, Bowdish DME, et al.[[BR]] Modulation of the TLR-mediated inflammatory response by the endogenous human host defense peptide LL-37 [[BR]] JOURNAL OF IMMUNOLOGY 176 (4): 2455-2464 FEB 15 2006[[BR]] Baudot A, Martin D, Mouren P, et al.[[BR]] PRODISTIN Web Site: a tool for the functional classification of proteins from interaction networks [[BR]] BIOINFORMATICS 22 (2): 248-250 JAN 15 2006[[BR]] Sarai N, Matsuoka S, Noma A[[BR]] simBio: A Java package for the development of detailed cell models [[BR]] PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY 90 (1-3): 360-377 JAN-APR 2006[[BR]] Scott MS, Calafell SJ, Thomas DY, et al.[[BR]] Refining protein subcellular localization [[BR]] PLOS COMPUTATIONAL BIOLOGY 1 (6): 518-528 NOV 2005[[BR]] Kemmer D, Huang Y, Shah SP, et al.[[BR]] Ulysses - an application for the projection of molecular interactions across species [[BR]] GENOME BIOLOGY 6 (12): Art. No. R106 2005[[BR]] Suresh S, Mohan SS, Mishra G, et al.[[BR]] Proteomic resources: Integrating biomedical information in humans [[BR]] GENE 364: 13-18 DEC 30 2005[[BR]] Patwardhan AJ, Strittmatter EF, Camp DG, et al.[[BR]] Comparison of normal and breast cancer cell lines using proteome, genome, and interactome data [[BR]] JOURNAL OF PROTEOME RESEARCH 4 (6): 1952-1960 NOV-DEC 2005[[BR]] Ashburner M, Bergman CM[[BR]] Drosophila melanogaster: A case study of a model genomic sequence and its consequences [[BR]] GENOME RESEARCH 15 (12): 1661-1667 DEC 2005[[BR]] Hooper SD, Bork P[[BR]] Medusa: a simple tool for interaction graph analysis [[BR]] BIOINFORMATICS 21 (24): 4432-4433 DEC 15 2005[[BR]] Prill RJ, Iglesias PA, Levchenko A[[BR]] Dynamic properties of network motifs contribute to biological network organization [[BR]] PLOS BIOLOGY 3 (11): 1881-1892 NOV 2005[[BR]] Lacroix V, Fernandes CG, Sagot MF[[BR]] Reaction motifs in metabolic networks [[BR]] LECTURE NOTES IN COMPUTER SCIENCE 3692: 178-191 2005[[BR]] Polpitiya AD, Cobb JP, Ghosh BK[[BR]] Genetic regulatory networks and co-regulation of genes: A dynamic model based approach [[BR]] LECTURE NOTES IN CONTROL AND INFORMATION SCIENCES 321: 291-304 2005[[BR]] Lee D[[BR]] Component-based software architecture for biosystem reverse engineering [[BR]] BIOTECHNOLOGY AND BIOPROCESS ENGINEERING 10 (5): 400-407 SEP-OCT 2005 [[BR]] Tran N, Baral C, Nagaraj VJ, et al.[[BR]] Knowledge-based integrative framework for hypothesis formation in biochemical networks [[BR]] LECTURE NOTES IN COMPUTER SCIENCE 3615: 121-136 2005[[BR]] Albrecht M, Huthmacher C, Tosatto SCE, et al.[[BR]] Decomposing protein networks into domain-domain interactions [[BR]] BIOINFORMATICS 21: 220-221 Suppl. 2 SEP 2005[[BR]] [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 atherosclerosis[[BR]] 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 EA[[BR]] Physiol Genomics. 2005 Sep 21;23(1):103-18. Epub 2005 Jun 7[[BR]] [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] Tran N, Baral C, Nagaraj VJ, et al.[[BR]] Knowledge-based integrative framework for hypothesis formation in biochemical networks [[BR]] LECTURE NOTES IN COMPUTER SCIENCE 3615: 121-136 2005[[BR]] Khatri P, Draghici S[[BR]] Ontological analysis of gene expression data: current tools, limitations, and open problems [[BR]] BIOINFORMATICS 21 (18): 3587-3595 SEP 15 2005[[BR]] Yu TW, Sun W, Yuan SS, et al.[[BR]] Study of coordinative gene expression at the biological process level [[BR]] BIOINFORMATICS 21 (18): 3651-3657 SEP 15 2005[[BR]] Yeang CH, Mak HC, McCuine S, et al.[[BR]] Validation and refinement of gene-regulatory pathways on a network of physical interactions [[BR]] GENOME BIOLOGY 6 (7): Art. No. R62 2005[[BR]] Gunsalus KC, Ge H, Schetter AJ, Goldberg DS, Han JD, Hao T, Berriz GF, Bertin N, Huang J, Chuang LS, Li N, Mani R, Hyman AA, Sonnichsen B, Echeverri CJ, Roth FP, Vidal M, Piano F.[[BR]] Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis.[[BR]] Nature. 2005 Aug 11;436(7052):861-5.[[BR]] Maere S, Heymans K, Kuiper M[[BR]] BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks [[BR]] BIOINFORMATICS 21 (16): 3448-3449 AUG 15 2005[[BR]] [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] Rhodes DR, Tomlins SA, Varambally S, et al.[[BR]] Probabilistic model of the human protein-protein interaction network [[BR]] NATURE BIOTECHNOLOGY 23 (8): 951-959 AUG 2005[[BR]] de Roos B, Rucklidge G, Reid M, et al.[[BR]] Divergent mechanisms of cis9, trans11-and trans10, cis12-conjugated linoleic acid affecting insulin resistance and inflammation in apolipoprotein E knockout mice: a proteomics approach [[BR]] FASEB JOURNAL 19 (9): doi:10.1096/fj.05-3953fje JUL 2005[[BR]] Longabaugh WJR, Davidson EH, Bolouri H[[BR]] Computational representation of developmental genetic regulatory networks [[BR]] DEVELOPMENTAL BIOLOGY 283 (1): 1-16 JUL 1 2005[[BR]] Cavelier G, Anastassiou D[[BR]] Phenotype analysis using network motifs derived from changes in regulatory network dynamics [[BR]] PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 60 (3): 525-546 AUG 15 2005[[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] Khalil IG, Hill C[[BR]] Systems biology for cancer [[BR]] CURRENT OPINION IN ONCOLOGY 17 (1): 44-48 JAN 2005[[BR]] Reiss DJ, Avila-Campillo I, Thorsson V, et al.[[BR]] Tools enabling the elucidation of molecular pathways active in human disease: Application to Hepatitis C virus infection [[BR]] BMC BIOINFORMATICS 6: Art. No. 154 JUN 20 2005[[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] Bing N, Hoeschele I[[BR]] Genetical genomics analysis of a yeast segregant population for transcription network inference [[BR]] GENETICS 170 (2): 533-542 JUN 2005[[BR]] Grijoriev A[[BR]] Understanding the yeast proteome: a bioinformatics perspective [[BR]] EXPERT REVIEW OF PROTEOMICS 1 (2): 193-205 AUG 2004[[BR]] Villas-Boas SG, Moxley JF, Akesson M, et al.[[BR]] High-throughput metabolic state analysis: the missing link in integrated functional genomics of yeasts [[BR]] BIOCHEMICAL JOURNAL 388: 669-677 Part 2 JUN 1 2005[[BR]] Gutierrez RA, Shasha DE, Coruzzi GM[[BR]] Systems biology for the virtual plant [[BR]] PLANT PHYSIOLOGY 138 (2): 550-554 JUN 2005[[BR]] Kelley R, Ideker T[[BR]] Systematic interpretation of genetic interactions using protein networks [[BR]] NATURE BIOTECHNOLOGY 23 (5): 561-566 MAY 2005[[BR]] Scott MS, Perkins T, Bunnell S, et al.[[BR]] Identifying regulatory subnetworks for a set of genes [[BR]] MOLECULAR & CELLULAR PROTEOMICS 4 (5): 683-692 MAY 2005[[BR]] Irwin B, Aye M, Baldi P, et al.[[BR]] Retroviruses and yeast retrotransposons use overlapping sets of host genes [[BR]] GENOME RESEARCH 15 (5): 641-654 MAY 2005[[BR]] Cavalieri D, De Filippo C[[BR]] Bioinformatic methods for integrating whole-genome expression results into cellular networks [[BR]] DRUG DISCOVERY TODAY 10 (10): 727-734 MAY 15 2005[[BR]] Li WJ, Kurata H[[BR]] A grid layout algorithm for automatic drawing of biochemical networks [[BR]] BIOINFORMATICS 21 (9): 2036-2042 MAY 1 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 interaction networks from quantitative phenotype data [[BR]] GENOME BIOLOGY 6 (4): Art. No. R38 2005[[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] Lefebvre C, Aude JC, Glemet E, et al.[[BR]] Balancing protein similarity and gene co-expression reveals new links between genetic conservation and developmental diversity in invertebrates [[BR]] BIOINFORMATICS 21 (8): 1550-1558 APR 15 2005[[BR]] de Roos B, Duivenvoorden I, Rucklidge G, et al.[[BR]] Response of apolipoprotein E*3-Leiden transgenic mice to dietary fatty acids: combining liver proteomics with physiological data [[BR]] FASEB JOURNAL 19 (3): doi:10.1096/fj.04-2974fje MAR 2005 Uetz P, Finley RL[[BR]] From protein networks to biological systems [[BR]] FEBS LETTERS 579 (8): 1821-1827 Sp. Iss. SI MAR 21 2005[[BR]] Aksenov SV, Church B, Dhiman A, et al.[[BR]] An integrated approach for inference and mechanistic modeling for advancing drug development [[BR]] FEBS LETTERS 579 (8): 1878-1883 Sp. Iss. SI MAR 21 2005[[BR]] Loeillet S, Palancade B, Cartron M, et al.[[BR]] Genetic network interactions among replication, repair and nuclear pore deficiencies in yeast [[BR]] DNA REPAIR 4 (4): 459-468 APR 4 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]] PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102 (6): 1974-1979 FEB 8 2005 [[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] Alfarano C, Andrade CE, Anthony K, et al.[[BR]] The Biomolecular Interaction Network Database and related tools 2005 update [[BR]] NUCLEIC ACIDS RESEARCH 33: D418-D424 Sp. Iss. SI JAN 1 2005[[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 N[[BR]] T1DBase, a community web-based resource for type 1 diabetes research [[BR]] NUCLEIC ACIDS RESEARCH 33: D544-D549 Sp. Iss. SI JAN 1 2005[[BR]] [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] Symeonidis A, Tollis IG[[BR]] Visualization of biological information with circular drawings [[BR]] LECTURE NOTES IN COMPUTER SCIENCE 3337: 468-478 2004[[BR]] Iragne F, Nikolski M, Mathieu B, et al.[[BR]] ProViz: protein interaction visualization and exploration [[BR]] BIOINFORMATICS 21 (2): 272-274 JAN 15 2005[[BR]] Said MR, Begley TJ, Oppenheim AV, et al.[[BR]] Global network analysis of phenotypic effects: Protein networks and toxicity modulation in Saccharomyces cerevisiae [[BR]] PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 101 (52): 18006-18011 DEC 28 2004[[BR]] Hurban P[[BR]] Toward an integrative systems toxicology [[BR]] PHARMACOGENOMICS 5 (8): 1163-1166 DEC 2004[[BR]] de la Fuente A, Bing N, Hoeschele I, et al.[[BR]] Discovery of meaningful associations in genomic data using partial correlation coefficients [[BR]] BIOINFORMATICS 20 (18): 3565-3574 DEC 12 2004[[BR]] Wu CC, Huang HC, Juan HF, et al.[[BR]] GeneNetwork: an interactive tool for reconstruction of genetic networks using microarray data [[BR]] BIOINFORMATICS 20 (18): 3691-3693 DEC 12 2004[[BR]] Grotkjaer T, Nielsen J[[BR]] Enhancing yeast transcription analysis through integration of heterogeneous data [[BR]] CURRENT GENOMICS 5 (8): 673-686 DEC 2004[[BR]] Haugen AC, Kelley R, Collins JB, et al.[[BR]] Integrating phenotypic and expression profiles to map arsenic-response networks [[BR]] GENOME BIOLOGY 5 (12): Art. No. R95 2004[[BR]] Facciotti MT, Bonneau R, Hood L, et al.[[BR]] Systems biology experimental design - Considerations for building predictive gene regulatory network models for prokaryotic systems [[BR]] CURRENT GENOMICS 5 (7): 527-544 NOV 2004[[BR]] Smith KD, Thorsson V[[BR]] Exploring toll-like receptor regulation of innate immunity with the tools of systems biology [[BR]] CURRENT GENOMICS 5 (7): 545-557 NOV 2004[[BR]] Ludemann A, Weicht D, Selbig J, et al.[[BR]] PaVESy: Pathway visualization and editing system [[BR]] BIOINFORMATICS 20 (16): 2841-2844 NOV 1 2004[[BR]] Pedrioli PGA, Eng JK, Hubley R, et al.[[BR]] A common open representation of mass spectrometry data and its application to proteomics research [[BR]] NATURE BIOTECHNOLOGY 22 (11): 1459-1466 NOV 2004[[BR]] Paek E, Park J, Lee KJ[[BR]] Multi-layered representation for cell signaling pathways [[BR]] MOLECULAR & CELLULAR PROTEOMICS 3 (10): 1009-1022 OCT 2004[[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 RESEARCH 14 (11): 2221-2234 NOV 2004[[BR]] [http://www.genome.org/cgi/content/abstract/14/11/2221 Abstract] [http://www.genome.org/cgi/reprint/14/11/2221 PDF] Galitski T[[BR]] Molecular networks in model systems [[BR]] ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS 5: 177-187 2004[[BR]] de Hoog CL, Mann M[[BR]] Proteomics [[BR]] ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS 5: 267-293 2004[[BR]] Begley TJ, Rosenbach AS, Ideker T, et al.[[BR]] Hot spots for modulating toxicity identified by genomic phenotyping and localization mapping [[BR]] MOLECULAR CELL 16 (1): 117-125 OCT 8 2004[[BR]] Blanchard JL[[BR]] Bioinformatics and Systems Biology, rapidly evolving tools for interpreting plant response to global change [[BR]] FIELD CROPS RESEARCH 90 (1): 117-131 NOV 8 2004[[BR]] Hood L, Heath JR, Phelps ME, et al.[[BR]] Systems biology and new technologies enable predictive and preventative medicine [[BR]] SCIENCE 306 (5696): 640-643 OCT 22 2004[[BR]] Stephanopoulos G, Alper H, Moxley J[[BR]] Exploiting biological complexity for strain improvement through systems biology [[BR]] NATURE BIOTECHNOLOGY 22 (10): 1261-1267 OCT 2004[[BR]] Mischel PS, Cloughesy TF, Nelson SF[[BR]] DNA-microarray analysis of brain cancer: Molecular classification for therapy [[BR]] NATURE REVIEWS NEUROSCIENCE 5 (10): 782-792 OCT 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 5 (8): Art. No. R52 2004[[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] 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] 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 MG[[BR]] System-based proteomic analysis of the interferon response in human liver cells [[BR]] GENOME BIOLOGY 5 (8): Art. No. R54 2004[[BR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15287976 Abstract] [http://genomebiology.com/2004/5/8/R54 FullText] [http://genomebiology.com/content/pdf/gb-2004-5-8-r54.pdf PDF] Wei GH, Liu DP, Liang CC[[BR]] Charting gene regulatory networks: strategies, challenges and perspectives [[BR]] BIOCHEMICAL JOURNAL 381: 1-12 Part 1 JUL 1 2004[[BR]] Kelley BP, Yuan BB, Lewitter F, et al.[[BR]] PathBLAST: a tool for alignment of protein interaction networks [[BR]] NUCLEIC ACIDS RESEARCH 32: W83-W88 Suppl. 2 JUL 1 2004[[BR]] Han KS, Ju BH, Jung HM[[BR]] WebInterViewer: visualizing and analyzing molecular interaction networks [[BR]] NUCLEIC ACIDS RESEARCH 32: W89-W95 Suppl. 2 JUL 1 2004[[BR]] Chung HJ, Kim M, Park CH, et al.[[BR]] ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics [[BR]] NUCLEIC ACIDS RESEARCH 32: W460-W464 Suppl. 2 JUL 1 2004[[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 RESEARCH 14 (6): 1025-1035 JUN 2004[[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] Prinz S, Avila-Campillo I, Aldridge C, et al.[[BR]] Control of yeast filamentous-form growth by modules in an integrated molecular network [[BR]] GENOME RESEARCH 14 (3): 380-390 MAR 2004[[BR]] 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=02/29/2004&_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] '''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'''[[BR]] 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)