Other Work

Professional Videos

  • Ideker, T. Protein Networks and Analysis of Global Gene Expression. One hour instructional video requisitioned by Henry Stewart Talks: www.hstalks.com
  • Introduction to the Network Data Exchange: https://youtu.be/ymn1HGPEwSA
  • Introduction to the National Resource for Network Biology: https://youtu.be/_nbqSe4Zaps
  • “Decoding patient genomes through the hierarchical pathway architecture of the cancer cell”. Trey Ideker. AACR Webcasts. Recorded at the AACR Annual Meeting 2018 on April 16, 2018. (Chicago, IL) WebCast



Books, Book Chapters

  • Uetz, P., Schwikowski, B., and Ideker, T. "Conceptualizing and display of protein-interaction networks," in Protein-Protein Interactions: A Laboratory Manual, E. Golemis ed. CSHL Press, Cold Spring Harbor, N.Y. (2002) [Book chapter]
  • 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) [Book chapter]
  • 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) [Book chapter]
  • 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) [Book]
  • Ideker, T., Tan, K. "Protein interaction networks and signal transduction" in Biological Networks. Kepes, F, Ed. World Scientific, Hackensack, N.J. (2007) [Book chapter]


 Refereed Conference Proceedings

  • Ideker, T., Thorsson, V. and Karp, R.  Discovery of Regulatory Interactions Through Perturbation: Inference and Experimental Design.  Pacific Symposium on Biocomputing 5:302-313 (2000)
  • Sharan, R. Ideker, T., Kelley, B. P., Shamir, R., Karp, R. Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. Proceedings of the Eighth Annual International Conference on Research in Computational Biology (RECOMB) p. 282-289 (2004)
  • Scott, J., Ideker, T., Karp, R., Sharan, R. Efficient algorithms for detecting protein signaling pathways in protein interaction networks. Proceedings of the Ninth Annual International Conference on Research in Computational Biology (RECOMB) (2005)
  • Bandyopadhyay, S., Kelley, R., Ideker, T. Discovering Regulated Networks During HIV-1 Latency and Reactivation.  Pacific Symposium on Biocomputing 11:354-366 (2006)
  • Suthram, S., Shlomi, T., Ruppin, E., Sharan, R., Ideker, T. "Comparison of protein-protein interaction confidence assignment schemes" in Lecture Notes in Computer Science: Systems Biology and Regulatory Genomics. Springer Berlin / Heidelberg.  Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics, San Diego, CA, USA. December 2-4, 2005.  Volume 4023 (2006)
  • Chuang, H., Ideker, T., Lee, E., Lee, D. "Network-based diagnosis and modeling of cancer development and progression" in Cell Biology 2008.  The American Society for Cell Biology 48th Annual Meeting, San Francisco, CA, USA. December 13-17 (2008)
  • Chuang, H., Rassenti, L., Ideker, T., Kipps, T.J. Interactome-based molecular prognosis of Chronic Lymphocytic Leukemia. 50th Meeting of the American Society of Hematology (ASH), San Francisco, CA, USA. December 6-9 (2008)
  • Wang S, Ma J, Yu MK, Zheng F, Huang EW, Han J, Peng J, Ideker T. Annotating gene sets by mining large literature collections with protein networks. Proceedings of the Pacific Symposium on Biocomputing.  2018; 23:602-613. Available in PMC 2018 Feb 9. https://doi.org/10.1142/9789813235533_0055. PMID: 29218918.