Research in the Ideker Lab focuses on using genome-scale measurements (genomic, proteomic, and metabolomic) to construct computer-aided models of cellular processes and disease. These models have the potential to revolutionize biology and medicine by providing a comprehensive blueprint of normal and diseased cell functions and by allowing researchers to simulate the effects of drugs on cells long before they are tested in humans. The following list of Publication Highlights (in chronological order) reflect this focus.

Additionally, a complete listing of All Publications and their associated data sets are available here.

  • van de Haar J, Canisius S, Yu MK, Voest EE, Wessels LFA, Ideker T. Identifying Epistasis in Cancer Genomes: A Delicate Affair. Cell. 2019 May 30;177(6):1375-1383. doi: 10.1016/j.cell.2019.05.005. Review. PMID: 31150618 [PDF] [PubMed]  

  • Ma J, Yu MK, Fong S, Ono K, Sage E, Demchak B, Sharan R, Ideker T. Using deep learning to model the hierarchical structure and function of a cell.* Nat Methods. 2018 Mar 5. doi: 10.1038/nmeth.4627. PMID: 29505029 [PDF[PubMed] [Cover Art] *Cover article
  • Zhang W, Bojorquez-Gomez A, Velez DO, Xu G, Sanchez KS, Shen JP, Chen K, Licon K, Melton C, Olson KM, Yu MK, Huang JK, Carter H, Farley EK, Snyder M, Fraley SI, Kreisberg JF, Ideker T. A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. Nat Genet. 2018 Apr 2. doi: 10.1038/s41588-018-0091-2. PMID: 29610481 [PDF[PubMed]
  • Wang T, Tsui B, Kreisberg JF, Robertson NA, Gross AM, Yu MK, Carter H, Brown-Borg HM, Adams PD, Ideker T. Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment. Genome Biology. 2017 Mar 28;18(1):57. doi: 10.1186/s13059-017-1186-2. PMID: 28351423 [PDF] [PubMed]
  • Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguev A, Lewis NE, Chang AN, Kreisberg JF, Krogan N, Qi L, Ideker T, Mali P. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nature Methods. 2017 Mar 20. doi: 10.1038/nmeth.4225. PMID: 28319113 [PDF] [PubMed]
  • Hofree M, Shen JP, Carter H, Gross A, Ideker T. Network-based stratification of tumor mutations. Nat Methods 10(11):1108-15 (2013). [PDF[PubMed]
  • Dutkowski J, Kramer M, Surma MA, Balakrishnan R, Cherry JM, Krogan NJ, Ideker T. A gene ontology inferred from molecular networks.* Nat Biotechnol. 31, 38–45 (2013). doi: 10.1038/nbt.2463. [PDF] [Suppl Tables] [PubMed] [Cover] [News and Views by Dolinski/Botstein] *Cover article 
  • Hannum G, Guinney J, Zhao L, Zhang L, Hughes G, Sadda S, Klotzle B, Bibikova M, Fan JB, Gao Y, Deconde R, Chen M, Rajapakse I, Friend S, Ideker T*, Zhang K*., Genome-wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates. Mol Cell. 2013 Jan 24;49(2):359-367. doi: 10.1016/j.molcel.2012.10.016. Epub 2012 Nov 21. [PDF] [PubMed] *Corresponding authors
  • Bandyopadhyay S, Mehta M, Kuo D, Sung MK, Chuang R, Jaehnig EJ, Bodenmiller D, Licon K, Copeland W, Shales M, Fiedler D, Dutkowski J, Guenole A, van Attikum H, Shokat KM, Kolodner RD, Huh WK, Aebersold R, Keogh MC, Krogan NJ, Ideker T. Rewiring of genetic networks in response to DNA damage. Science 330:1385-1389 (2010). [PDF][Suppl Tables][PubMed]
    • Data: Differential epistasis mapping (dE-MAP) [Data]
  • Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest AR, Gough J, Grimmond S, Han JH, Hashimoto T, Hide W, Hofmann O, Kamburov A, Kaur M, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E, MacPherson CR, Ogawa C, Radovanovic A, Schwartz A, Teasdale RD, Tegnér J, Lenhard B, Teichmann SA, Arakawa T, Ninomiya N, Murakami K, Tagami M, Fukuda S, Imamura K, Kai C, Ishihara R, Kitazume Y, Kawai J, Hume DA, Ideker T, Hayashizaki Y. An atlas of combinatorial transcriptional regulation in mouse and man. Cell 140(5):744-752 (2010). [PDF[Pubmed]
  • Chuang HY, Lee E, Liu YT, Lee D, Ideker T. Network-based classification of breast cancer metastasis. Mol Syst Biol. 3:140 (2007). [PDF] [PubMed]
  • Workman CT, Mak HC, McCuine S, Tagne JB, Agarwal M, Ozier O, Begley TJ, Samson LD, Ideker T. A Systems Approach to Mapping DNA Damage Response Pathways. Science. 312 (5776):1054-1059 (2006). [PDF[PubMed]
  • Suthram, S., Sittler, T., and Ideker, T. The Plasmodium protein network diverges from those of other eukaryotes. Nature 438(7064):108-12 (2005). [PDF[PubMed] [Supp. Info.]
  • Sharan, R., Suthram, S., Kelley, R. M., Kuhn, T., McCuine, S., Uetz, P., Sittler, T., Karp, R. M., and Ideker, T.  Conserved patterns of protein interaction in multiple species.* Proc Natl Acad Sci U S A. 8:102(6) 1974-79 (2005).  [PDF[PubMed] [Suppl. Data] *Cover Article
  • Ideker, T., Thorsson, V., Ranish, J. A., Christmas, R., Buhler, J., Eng, J. K., Bumgarner, R., Goodlett, D. R., Aebersold, R., and Hood, L. Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network. Science, 292: 929-934 (2001). [PDF] [PubMed link] [Suppl Data]