Review Articles



  • Demchak B, Otasek D, Pico AR, Bader GD, Ono K, Settle B, Sage E, Morris JH, Longabaugh W, Lopes C, Kucera M, Treister A, Schwikowski B, Molenaar P, Ideker T. The Cytoscape Automation app article collectionF1000Res. 2018 Jun 20;7:800. doi: 10.12688/f1000research.15355.1. eCollection 2018. PMID: 29983926 [PDF] [PubMed]
  • Michael K. Yu, Jianzhu Ma, Jasmin Fisher, Jason F. Kreisberg, Benjamin J. Raphael, Trey Ideker. Visible Machine Learning for BiomedicineCELL. Volume 173, Issue 7, 14 June 2018, Pages 1562–1565. doi: [PDF] [PubMed]


  • Farré JC, Kramer M, Ideker T, Subramani S. Active Interaction Mapping as a tool to elucidate hierarchical functions of biological processes. Autophagy. 2017 Jul 3;13(7):1248-1249. doi: 10.1080/15548627.2017.1313946. Epub 2017 May 9. PMID: 28486053 [PDF] [PubMed]
  • Huan T, Forsberg EM, Rinehart D, Johnson CH, Ivanisevic J, Benton HP, Fang M, Aisporna A, Hilmers B, Poole FL, Thorgersen MP, Adams MWW, Krantz G, Fields MW, Robbins PD, Niedernhofer LJ, Ideker T, Majumder EL, Wall JD, Rattray NJW, Goodacre R, Lairson LL, Siuzdak G. Systems biology guided by XCMS Online metabolomics. Nat Methods. 2017 Apr 27;14(5):461-462. doi: 10.1038/nmeth.4260. PMID: 28448069 [PDF] [PubMed]
  • Carter H, Ideker T. Common genetic variation in the germline influences where and how tumors develop. Mol Cell Oncol. 2017 Mar 10;4(3):e1302905. doi: 10.1080/23723556.2017.1302905. eCollection 2017. PMID: 28616579 [PDF] [PubMed] 



  • Gross AM, Ideker T. Molecular networks in context. Nature Biotechnology 33, 720–721 (2015) doi:10.1038/nbt.3283. Published online 08 July 2015 [Get PDF] [PubMed Link]
  • Krogan NJ, Lippman S, Agard DA, Ashworth A, Ideker T. The cancer cell map initiative: defining the hallmark networks of cancer. Molecular Cell. 2015 May 21;58(4):690-8. doi: 10.1016/j.molcel.2015.05.008. Review. [Get PDF] [PubMed Link]


  • Carvunis AR, Ideker T. Carvunis AR, Ideker T. Siri of the cell: what biology could learn from the iPhone. Cell 157(3):534-8. (2014) [Get PDF] [PubMed] 
  • Pico AR, Bader GD, Demchak B, Guitart Pla O, Hull T, Longabaugh W, Lopes C, Lotia S, Molenaar P, Montojo J, Morris JH, Ono K, Schwikowski B, Welker D, Ideker T. The Cytoscape app article collection. F1000 Research. 2014 Jul 1;3:138. doi: 10.12688/f1000research.4642.1. eCollection 2014. [Get PDF] [PubMed Link]
  • Shaughnessy DT, McAllister K, Worth L, Haugen AC, Meyer JN, Domann FE, Van Houten B, Mostoslavsky R, Bultman SJ, Baccarelli AA, Begley TJ, Sobol R, Hirschey MD, Ideker T, Santos JH, Copeland WC, Tice RR, Balshaw DM, Tyson FL. Mitochondria, Energetics, Epigenetics, and Cellular Responses to Stress. Environ Health Perspect (2014). [TI: Provided data analysis.]


  • Altschul S, Demchak B, Durbin R, Gentleman R, Krzywinski M, Li H, Nekrutenko A, Robinson J, Rasband W, Taylor J, Trapnell C. The Anatomy of Successful Computational Biology Software. Nature Biotechnology 31(10):894-897 (2013) [Get PDF] [PubMed link]
  • Carter H, Hofree M, Ideker T. Genotype to phenotype via network analysis. Current Opinion in Genetics Development 23(6):611-21 (2013) [Get PDF] [PubMed link]
  • Mitra K, Carvunis AR, Ramesh SK, Ideker T. Integrative approaches for finding modular structure in biology networks. Nature Review Genetics 14(10):719-732 (2013) [Get PDF] [PubMed link]


  • Jaeger P, Doherty C, Ideker T. Modeling Transcriptome Dynamics in a Complex World, Cell, Volume 151, Issue 6, 1161-1162, 7 December 2012. [Get PDF] [PubMed link]
  • Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T. A travel guide to Cytoscape plugins, Nature Methods. 2012 Nov;9(11):1069-76. doi: 10.1038/nmeth.2212. Epub 2012 Nov 6. [Get PDF] [PubMed link]
  • Califano A, Butte AJ, Friend S, Ideker T, Schadt E. Leveraging models of cell regulation and GWAS data in integrative network-based association studies. Nature Genetics. 2012 Jul 27;44(8):841-7. doi: 10.1038/ng.2355. [Get PDF] [PubMed link]
  • Ideker T, Krogan NJ. Differential network biology. Molecular Systems Biology. 2012 Jan 17;8:565. doi: 10.1038/msb.2011.99. [Get PDF] [PubMed link]


  • Ideker T, Dutkowski J, Hood L. Boosting signal-to-noise in complex biology: prior knowledge is power. Cell. Mar 18;144(6):860-3 (2011). [Get PDF] [PubMed link]
  • Friend SH, Ideker T. Point: Are we prepared for the future doctor visit? Nature Biotechnology Mar 29(3):215-8. (2011). [Get PDF] [PubMed link]


  • Bandyopadhyay, S. and Ideker T. Integrative systems biology. Nature Genetics 42(12) (2010). [Get Poster]
  • Chuang HY, Hofree M, Ideker T. A decade of systems biology. Annual Review of Cell and Developmental Biology (2010). [Get PDF] [PubMed link]


  • Ideker, T. Book Review: “Wetware: A Computer in Every Living Cell” by Dennis Bray. Cell 138: 820-821 (2009)
  • Rocke, D.M., Ideker, T., Troyanskaya, Quackenbush, J., Dopazo, J. Papers on normalization, variable selection, classification or clustering of microarray data. Bioinformatics 25: 701-702 (Editorial; 2009). [Get PDF]



  • Ideker T, Bafna V, Lemberger T. Integrating scientific cultures. Molecular Systems Biology 3:105. Epub Apr 17 (2007). [Get PDF] [PubMed link]
  • Beyer A, Bandyopadhyay S, Ideker T. Integrating physical and genetic maps: from genomes to interaction networks. Nature Review Genetics. (9):699-710. Featured Review. Sep 8 (2007). [Get PDF] [PubMed link]
  • Ideker TE. Network genomics. Ernst Schering Res Found Workshop. (61):89-115. Review. (2007). [PubMed link]
  • Ideker, T. (2007), "Protein Networks and Analysis of Global Gene Expression", in Tsonis, P. (ed.), From DNA to Proteins: The Multiple Levels of Regulation , The Biomedical & Life Sciences Collection, Henry Stewart Talks Ltd, London.
  • Ideker, T and Tan, K. "Protein Interaction Networks" in Biological Networks, Kepes, F, Ed. World Scientific , Hackensack, N.J. [Get book chapter]


  • Ideker, T., Valencia, A. Bioinformatics in the human interactome project. Bioinformatics. 22(24):2973-4. Dec 15 (2006). [Get PDF] [PubMed link]
  • Ideker T, Winslow LR, Lauffenburger DA. Bioengineering and systems biology. Annals of Biomedical Engineering. Jul;34(7):1226-33. Review. (2006). [Get PDF] [PubMed link]
  • Sharan, R., and Ideker, T. Modeling cellular machinery through biological network comparison. Nature Biotechnology. Review. 24(4):427-33. Apr (2006). [Get PDF] [PubMed link]
  • Warner, G.J., Adeleye, Y.A., Ideker, T. Interactome networks: the state of the science. Genome Biol. Review. 7(1):301. Jan 23 (2006). [Get PDF] [PubMed link]


  • Ideker, T., Tan, K., Uetz, P. “Visualization and Integration of Protein Interaction Networks”, in Protein-Protein Interactions Second Edition: A Molecular Cloning Manual, E. Golemis and P. Adams eds. CSHL Press, Cold Spring Harbor, N.Y. 7(42): 839-856 (2005). [Get PDF]
  • Ideker, T. “Data collection and analysis in systems biology.” Wiley Encyclopedia of Genetics, Genomics, Proteomics, and Bioinformatics Dunn, M.J., Jorde, L.B., Little, P.F.R., Subramaniam, S. (Eds): 0-470-84974-6 (2005). [Get PDF]


  • Ideker, T. A systems approach to discovering signaling and regulatory pathways--or, how to digest large interaction networks into relevant pieces. Adv. Exp. Med. Biol. 547: 21-30 (2004). [Get PDF] [PubMed link]
  • Ideker, T. Systems biology 101--what you need to know. Nature Biotechnology 22(4): 473-5 (2004). [Get PDF] [PubMed link]


  • Ideker, T. and Lauffenburger, D. Building with a scaffold: Emerging strategies for high- to low-level cellular modeling. Trends in Biotechnology 21: 252-262 (2003). [Get PDF] [PubMed link]


  • Uetz, P., Schwikowski, B., and Ideker, T. "Visualization and Integration of Protein-Protein Interactions", in Protein-Protein Interactions: A Molecular Cloning Manual, E. Golemis ed. CSHL Press, Cold Spring Harbor, N.Y. (2002).
  • Ideker, T., Grimmond, S., and Ibarra, S. "Hybridization and Post-Hybridization Washing," in DNA Microarrays: A Molecular Cloning Manual, D. Bowtell and J. Sambrook eds. CSHL Press, Cold Spring Harbor, N.Y. (2002).


  • Ideker, T., Galitski, T., and Hood, L. A New Approach to Decoding Life: Systems Biology. Annual Review of Genomics and Human Genetics, 2:343 (2001). [Get PDF] [PubMed link]