Proc. Natl. Acad. Sci (PNAS) 2007
Tan K, Shlomi T, Feizi, H, Ideker T, and Sharan R.
Transcriptional regulation of protein complexes within and across species.
[Abstract] [Full Text] [PDF]

Nature Nov. 2005
Suthram S, Sittler T, Ideker T.
Plasmodium protein network diverges from those of other eukaryotes.
[Abstract] [Full Text] [PDF]

J Comput Biol. Jul-Aug 2005
Sharan R, Ideker T, Kelley B, Shamir R, Karp RM.
Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data.
[Abstract] [Full Text] [PDF]

Genome Biology. July 2005
Yeang CH, Mak HC, McCuine S, Workman C, Jaakkola T, Ideker T.
Validation and refinement of gene-regulatory pathways on a network of physical interactions.
[Abstract] [Full Text] [PDF]

Nature Biotechnology. May 2005
Kelley R, Ideker T.
Systematic interpretation of genetic interactions using protein networks.
[Abstract] [Full Text] [PDF]

Proteins, 2005
G Cavelier, D Anastassiou D.
Phenotype analysis using network motifs derived from changes in regulatory network dynamics.
[Abstract] [Full Text] [PDF]

BMC Bioinformatics 2005, 6:154
Tools enabling the elucidation of molecular pathways active in human disease: Application to Hepatitis C virus infection
David J Reiss , Iliana Avila-Campillo , Vesteinn Thorsson , Benno Schwikowski and Timothy Galitski
[Abstract] [Full Text] [PDF]

Genome Biology. March, 2005
Becky L Drees, Vesteinn Thorsson, Gregory W Carter, Alexander W Rives, Marisa Z Raymond, Iliana Avila-Campillo, Paul Shannon and Timothy Galitski.
Derivation of genetic networks from quantitative phenotype data. Genome Biology.
[Abstract] [Full Text] [PDF]

Proc Natl Acad Sci U S A. Feb 8, 2005
Sharan R, Suthram S, Kelley RM, Kuhn T, McCuine S, Uetz P, Sittler T, Karp RM, Ideker T.
Conserved patterns of protein interaction in multiple species.
Proc Natl Acad Sci U S A. 2005 Feb 8;102(6):1974-9. Epub 2005 Feb 01.
[Abstract] [Full Text] [PDF]

Genome Research, November 2004 (cover article)
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
Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea
Genome Res. 2004 Nov;14(11):2221-34
[Abstract] [PDF]

Bioinformatics August 2004
Reiss David, Schwikowski Benno
Predicting protein�peptide interactions via a network-based motif sampler
Bioinformatics. 2004 Aug 4;20 Suppl 1:I274-I282
[Abstract] [PDF]

Genome Biology, July 2004
Bonneau, Richard, Baliga Nitin S, Deutsch, Eric W, Shannon Paul and Hood, Leroy
Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1
Genome Biology 2004, 5:R52
[Abstract] [Full Text] [PDF]

Genome Research, June 2004 (cover article)
Baliga, NS, Bjork, SJ, Bonneau, R, Pan, M, Iloanusi, C, Kottemann, MCH, Hood, L, and DiRuggiero, J.
Systems level insights into the stress ersponds to UV radiation in the halophilic archaeon Halobacterium NRC-1.
Genome Res. 2004 14: 1025-35
[Abstract][PDF][Supplemental Research Data]

Genome Research, March 2004
Prinz S, Avila-Campillo I, Aldridge C, Srinivasan A, Dimitrov K, Siegel AF, and Galitski T.
Control of Yeast Filamentous-Form Growth by Modules in an Integrated Molecular Network.
Genome Res. 2004 14: 380-390.
[Abstract][PDF] [Supplemental Research Data]

Science, Feb 2004
Tong AH, et al., Global mapping of the yeast genetic interaction network.
Science. 2004 Feb 6;303(5659):808-13.
[Pub Med Entry] [Full Text]

Seminars in Immunology, January 2004
A systems approach to dissecting immunity and inflammation.
Aderem A, Smith KD.
Semin Immunol. 2004 Feb;16(1):55-67.
[Pub Med Entry] [Full Text]
 
PNAS, Septemer 2003
Kelley BP, Sharan R, Karp RM, Sittler T, Root DE, Stockwell BR, Ideker T.
Conserved pathways within bacteria and yeast as revealed by global protein network alignment.
Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11394-9.
[Pub Med Entry] [Full Text]

RECOMB 2003
Yeang C-H, Jaakkola T. Physical network models and multi-source data integration. The Seventh Annual International Conference on Research in Computational Molecular Biology, 2003
[PDF]

Molecular Cancer Research, 2002
Begley TJ, Rosenbach AS, Ideker T, Samson LD. Damage Recovery Pathways in Saccharomyces cerevisiae Revealed by Genomic Phenotyping and Interactome Mapping. Mol Cancer Res. 2002 Dec;1(2):103-12.
[PubMed entry]

ISMB 2002
Ideker T, Ozier O, Schwikowski B, Siegel A. Discovering regulatory and signaling circuits in molecular interaction networks. Bioinformatics 18, S233 (2002). [Abstract] [PDF] [PubMed entry] [Supplementary Material]

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the National Institutes of Health (NIH) under award number GM070743-01 and the U.S. National Science Foundation (NSF) .