Review, Opinion and Book Chapters

2011

• 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]
• Friend SH, Ideker T. Point: Are we prepared for the future doctor visit? Nature Biotechnology Mar 29(3):215-8. (2011) [Get PDF]

2010

• 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]

2009

• 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]

2008

• Ideker T. Forging new ties between E. coli genes. Cell. 133: 3-5 (2008). [Get PDF] [Pubmed link]
• Ideker T, Sharan R. Protein networks in disease. Genome Res. 18(4): 644-52 (2008). [Get PDF] [Pubmed link]

2007

• Ideker T, Bafna V, Lemberger T. Integrating scientific cultures. Mol Syst Biol.; 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. Nat Rev Genet. (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]
• Chuang, H.Y., Lee, A., Sharma, V., Liu, Y.T., and Ideker, T. Deciphering breast cancer metastasis using protein networks. Systems to Synthesis Poster Awards, San Diego Consortium for Systems Biology. Jan 25 (2007). [Get Poster]
• 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 (online at http://www.hstalks.com/?t=BL0061117-Ideker)

2006

• 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. Ann Biomed Eng. Jul;34(7):1226-33. Review. (2006) [PubMed link]
• Ideker, R. Systems Biology: Applications and Perspectives, Springer Science and Business, Paris, France (in press).
• 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]
• Ideker, T and Tan, K. "Protein interaction networks and signal transduction" in Biological Networks, Kepes, F, Ed. World Scientific , Hackensack, N.J. (in press).
• 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]

2005

• Ideker, T., Winslow, R.., and Lauffenburger, D. Bioengineering and Systems Biology. Annals of Biomedical Engineering. 10.1007/s10439-005-9047-7. (2005). [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]

2004

• 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]

2003

• 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]

2002

• 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).

2001

• 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]