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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. |
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. 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]] 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]] King JY, Ferrara R, Tabibiazar R, et al.[[BR]] Pathway analysis of coronary atherosclerosis [[BR]] PHYSIOLOGICAL GENOMICS 23 (1): 103-118 SEP 21 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]] 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]] 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]] 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]] 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]] 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]] Drees BL, Thorsson V, Carter GW, et al.[[BR]] Derivation of genetic interaction networks from quantitative phenotype data [[BR]] GENOME BIOLOGY 6 (4): Art. No. R38 2005[[BR]] 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, et al.[[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]] 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, et al.[[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]] 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, et al.[[BR]] Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea [[BR]] GENOME RESEARCH 14 (11): 2221-2234 NOV 2004[[BR]] 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 R, Baliga NS, Deutsch EW, et al.[[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]] Yan W, Lee H, Yi EC, et al.[[BR]] System-based proteomic analysis of the interferon response in human liver cells [[BR]] GENOME BIOLOGY 5 (8): Art. No. R54 2004[[BR]] 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, et al.[[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]] 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]] |
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.
Krogan NJ, Cagney G, Yu HY, et al.BR Global landscape of protein complexes in the yeast Saccharomyces cerevisiaeBR NATURE 440 (7084): 637-643 MAR 30 2006BR
Junker BH, Klukas C, Schreiber FBR VANTED: A system for advanced data analysis and visualization in the context of biological networksBR BMC BIOINFORMATICS 7: Art. No. 109 MAR 6 2006BR
Titz B, Thomas S, Rajagopala SV, et al.BR Transcriptional activators in yeast BR NUCLEIC ACIDS RESEARCH 34 (3): 955-967 2006BR
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 2006BR
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 JHBR 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 2006BR
Joyce AR, Palsson BOBR The model organism as a system: integrating 'omics' data sets BR NATURE REVIEWS MOLECULAR CELL BIOLOGY 7 (3): 198-210 MAR 2006BR
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 2006BR
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 2006BR
Sarai N, Matsuoka S, Noma ABR
simBio: A Java package for the development of detailed cell models BR PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY 90 (1-3): 360-377 JAN-APR 2006BR
Scott MS, Calafell SJ, Thomas DY, et al.BR
Refining protein subcellular localization BR PLOS COMPUTATIONAL BIOLOGY 1 (6): 518-528 NOV 2005BR
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 2005BR
Suresh S, Mohan SS, Mishra G, et al.BR Proteomic resources: Integrating biomedical information in humans BR GENE 364: 13-18 DEC 30 2005BR
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 2005BR
Ashburner M, Bergman CMBR Drosophila melanogaster: A case study of a model genomic sequence and its consequences BR GENOME RESEARCH 15 (12): 1661-1667 DEC 2005BR
Hooper SD, Bork PBR Medusa: a simple tool for interaction graph analysis BR BIOINFORMATICS 21 (24): 4432-4433 DEC 15 2005BR
Prill RJ, Iglesias PA, Levchenko ABR Dynamic properties of network motifs contribute to biological network organization BR PLOS BIOLOGY 3 (11): 1881-1892 NOV 2005BR
Lacroix V, Fernandes CG, Sagot MFBR Reaction motifs in metabolic networks BR LECTURE NOTES IN COMPUTER SCIENCE 3692: 178-191 2005BR
Polpitiya AD, Cobb JP, Ghosh BKBR Genetic regulatory networks and co-regulation of genes: A dynamic model based approach BR LECTURE NOTES IN CONTROL AND INFORMATION SCIENCES 321: 291-304 2005BR
Lee DBR 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 2005BR
Albrecht M, Huthmacher C, Tosatto SCE, et al.BR Decomposing protein networks into domain-domain interactions BR BIOINFORMATICS 21: 220-221 Suppl. 2 SEP 2005BR
King JY, Ferrara R, Tabibiazar R, et al.BR Pathway analysis of coronary atherosclerosis BR PHYSIOLOGICAL GENOMICS 23 (1): 103-118 SEP 21 2005BR
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 2005BR
Khatri P, Draghici SBR Ontological analysis of gene expression data: current tools, limitations, and open problems BR BIOINFORMATICS 21 (18): 3587-3595 SEP 15 2005BR
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 2005BR
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 2005BR
Maere S, Heymans K, Kuiper MBR BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks BR BIOINFORMATICS 21 (16): 3448-3449 AUG 15 2005BR
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 2005BR
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 2005BR
Longabaugh WJR, Davidson EH, Bolouri HBR Computational representation of developmental genetic regulatory networks BR DEVELOPMENTAL BIOLOGY 283 (1): 1-16 JUL 1 2005BR
Cavelier G, Anastassiou DBR Phenotype analysis using network motifs derived from changes in regulatory network dynamics BR PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 60 (3): 525-546 AUG 15 2005BR
Khalil IG, Hill CBR Systems biology for cancer BR CURRENT OPINION IN ONCOLOGY 17 (1): 44-48 JAN 2005BR
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 2005BR
Bing N, Hoeschele IBR Genetical genomics analysis of a yeast segregant population for transcription network inference BR GENETICS 170 (2): 533-542 JUN 2005BR
Grijoriev ABR Understanding the yeast proteome: a bioinformatics perspective BR EXPERT REVIEW OF PROTEOMICS 1 (2): 193-205 AUG 2004BR
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 2005BR
Gutierrez RA, Shasha DE, Coruzzi GMBR Systems biology for the virtual plant BR PLANT PHYSIOLOGY 138 (2): 550-554 JUN 2005BR
Kelley R, Ideker TBR Systematic interpretation of genetic interactions using protein networks BR NATURE BIOTECHNOLOGY 23 (5): 561-566 MAY 2005BR
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 2005BR
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 2005BR
Cavalieri D, De Filippo CBR Bioinformatic methods for integrating whole-genome expression results into cellular networks BR DRUG DISCOVERY TODAY 10 (10): 727-734 MAY 15 2005BR
Li WJ, Kurata HBR A grid layout algorithm for automatic drawing of biochemical networks BR BIOINFORMATICS 21 (9): 2036-2042 MAY 1 2005BR
Drees BL, Thorsson V, Carter GW, et al.BR Derivation of genetic interaction networks from quantitative phenotype data BR GENOME BIOLOGY 6 (4): Art. No. R38 2005BR
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 2005BR
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 RLBR From protein networks to biological systems BR FEBS LETTERS 579 (8): 1821-1827 Sp. Iss. SI MAR 21 2005BR
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 2005BR
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 2005BR
Sharan R, Suthram S, Kelley RM, et al.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
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 2005BR
Smink LJ, Helton EM, Healy BC, et al.BR T1DBase, a community web-based resource for type 1 diabetes research BR NUCLEIC ACIDS RESEARCH 33: D544-D549 Sp. Iss. SI JAN 1 2005BR
Symeonidis A, Tollis IGBR Visualization of biological information with circular drawings BR LECTURE NOTES IN COMPUTER SCIENCE 3337: 468-478 2004BR
Iragne F, Nikolski M, Mathieu B, et al.BR ProViz: protein interaction visualization and exploration BR BIOINFORMATICS 21 (2): 272-274 JAN 15 2005BR
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 2004BR
Hurban PBR Toward an integrative systems toxicology BR PHARMACOGENOMICS 5 (8): 1163-1166 DEC 2004BR
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 2004BR
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 2004BR
Grotkjaer T, Nielsen JBR Enhancing yeast transcription analysis through integration of heterogeneous data BR CURRENT GENOMICS 5 (8): 673-686 DEC 2004BR
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 2004BR
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 2004BR
Smith KD, Thorsson VBR Exploring toll-like receptor regulation of innate immunity with the tools of systems biology BR CURRENT GENOMICS 5 (7): 545-557 NOV 2004BR
Ludemann A, Weicht D, Selbig J, et al.BR PaVESy: Pathway visualization and editing system BR BIOINFORMATICS 20 (16): 2841-2844 NOV 1 2004BR
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 2004BR
Paek E, Park J, Lee KJBR Multi-layered representation for cell signaling pathways BR MOLECULAR & CELLULAR PROTEOMICS 3 (10): 1009-1022 OCT 2004BR
Baliga NS, Bonneau R, Facciotti MT, et al.BR Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea BR GENOME RESEARCH 14 (11): 2221-2234 NOV 2004BR
Galitski TBR Molecular networks in model systems BR ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS 5: 177-187 2004BR
de Hoog CL, Mann MBR Proteomics BR ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS 5: 267-293 2004BR
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 2004BR
Blanchard JLBR Bioinformatics and Systems Biology, rapidly evolving tools for interpreting plant response to global change BR FIELD CROPS RESEARCH 90 (1): 117-131 NOV 8 2004BR
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Stephanopoulos G, Alper H, Moxley JBR Exploiting biological complexity for strain improvement through systems biology BR NATURE BIOTECHNOLOGY 22 (10): 1261-1267 OCT 2004BR
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Wei GH, Liu DP, Liang CCBR Charting gene regulatory networks: strategies, challenges and perspectives BR BIOCHEMICAL JOURNAL 381: 1-12 Part 1 JUL 1 2004BR
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Han KS, Ju BH, Jung HMBR WebInterViewer: visualizing and analyzing molecular interaction networks BR NUCLEIC ACIDS RESEARCH 32: W89-W95 Suppl. 2 JUL 1 2004BR
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 2004BR
Baliga NS, Bjork SJ, Bonneau R, et al.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 2004BR
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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]
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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]
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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&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]
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]