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  Begley TJ, Rosenbach AS, Ideker T, Samson LD.
(2002)
Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping.
Molecular cancer research : MCR, 1(2):103-12

[PubMed]

  Bernard A, Hartemink AJ.
(2005)
Informative structure priors: joint learning of dynamic regulatory networks from multiple types of data.
Pacific Symposium on Biocomputing, :459-70

[PubMed]


  de Lichtenberg U, Jensen LJ, Brunak S, Bork P.
(2005)
Dynamic complex formation during the yeast cell cycle.
Science (New York, N, 307(5710):724-7

[PubMed]

  Gandhi TK, Zhong J, Mathivanan S, Karthick L, Chandrika KN, Mohan SSSharma S, Pinkert S, Nagaraju S, Periaswamy B, Mishra G, Nandakumar K, Shen B, Deshpande N, Nayak R, Sarker M, Boeke JD, Parmigiani G, Schultz J, Bader JS, Pandey A, .
(2006)
Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets.
Nature genetics, 38(3):285-93

[PubMed]


  Hartemink AJ, Gifford DK, Jaakkola TS, Young RA.
(2002)
Combining location and expression data for principled discovery of genetic regulatory network models.
Pacific Symposium on Biocomputing, :437-49

[PubMed]

  Haugen AC, Kelley R, Collins JB, Tucker CJ, Deng C, Afshari CA, Brown JM, Ideker T, Van Houten B.
(2004)
Integrating phenotypic and expression profiles to map arsenic-response networks.
Genome biology, 5(12):R95

[PubMed]


  Ideker T, Ozier O, Schwikowski B, Siegel AF.
(2002)
Discovering regulatory and signalling circuits in molecular interaction networks.
Bioinformatics (Oxford, England), 18 Suppl 1:S233-40

[PubMed]

  Kelley R, Ideker T.
(2005)
Systematic interpretation of genetic interactions using protein networks.
Nature biotechnology, 23(5):561-6

[PDF] [Supplemental Website] [PubMed]


  Sharan R, Suthram S, Kelley RM, Kuhn T, McCuine S, Uetz P, Sittler T, Karp RM, Ideker T.
(2005)
Conserved patterns of protein interaction in multiple species.
Proceedings of the National Academy of Sciences of the United States of America, 102(6):1974-9

[PDF] [Supplemental Website] [PubMed]

  Suthram S, Sittler T, Ideker T.
(2005)
The Plasmodium protein network diverges from those of other eukaryotes.
Nature, 438(7064):108-12

[PDF] [Supplementary Notes] [PubMed]


  Yeang CH, Mak HC, McCuine S, Workman C, Jaakkola T, Ideker T.
(2005)
Validation and refinement of gene-regulatory pathways on a network of physical interactions.
Genome biology, 6(7):R62

[PDF] [PubMed]

  Chuang HY, Lee E, Liu YT, Lee D, Ideker T.
(2007)
Network-based classification of breast cancer metastasis.
Molecular systems biology, 3:140

[PubMed]


  Tan K, Feizi H, Luo C, Fan SH, Ravasi T, Ideker TG.
(2008)
A systems approach to delineate functions of paralogous transcription factors: role of the Yap family in the DNA damage response.
Proceedings of the National Academy of Sciences of the United States of America, 105(8):2934-9

[PubMed]


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Funding provided by the National Science Foundation (NSF 0425926).