IDEKER LAB
University of California,San Diego
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Our research 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. Our publications reflect this research focus. Publications Shortlist 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). [Get PDF] [Supp. Info.] [PubMed link] Bandyopadhyay S, Sharan R, Ideker T. Cover Article: Systematic identification of functional orthologs based on protein network comparison. Genome Res. 16(3):428-35. (2006). [Get PDF] [PubMed link] Suthram, S., Sittler, T., and Ideker, T. The Plasmodium protein network diverges from those of other eukaryotes. Nature 438(7064):108-12 (2005). [Get PDF] [Supp. Info.] [PubMed link] Kelley, R. and Ideker, T. Systematic interpretation of genetic interactions using protein networks. Nature Biotechnology 23(5):561-566 (2005). [Get PDF] [PubMed link] Sharan, R., Suthram, S., Kelley, R. M., Kuhn, T., McCuine, S., Uetz, P., Sittler, T., Karp, R. M., and Ideker, T. Cover Article: Conserved patterns of protein interaction in multiple species. Proc Natl
Acad Sci U S A. 8:102(6) 1974-79 (2005). [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., 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). [Get PDF] [Companion Website][Raw Data][PubMed link] Journal Articles 2008 Bandyopadhyay S, Kelley R, Krogan NJ, Ideker T. Functional maps of protein complexes from quantitative genetic interaction data. PLoS Compu Biol. 4(4):e1000065 (2008). [Get PDF] [Pubmed link] Suthram S, Beyer A, Karp RM, Eldar Y, Ideker T. eQED: an efficient method for interpreting eQTL associations using protein networks. Mol Syst Biol. 4:162 (2008). [Get PDF] [Pubmed link] Tan K, Feizi H, Luo C, Fan SH, Ravasi T, Ideker TG. A systems approach to delineate functions of paralogous transcription factors: role of the Yap family in the DNA damage response. Proc Natl Acad Sci. 105(8):2934-9 (2008). [Get PDF] [Pubmed link] Kalaev M, Smoot M, Ideker T, Sharan R. NetworkBLAST: comparative analysis of protein networks. Bioinformatics. 24(4):594-6 (2008). [Get PDF] [Pubmed link] 2007 Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maerel S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T*, and Bader GB. (Ideker is corresponding author). Integration of Biological Networks and Gene Expression Data using Cytoscape. Nature Protocols, 2(10):2366-82 Oct 1 (2007). [Get PDF] [Online link] Chuang, HY, Lee, E, Liu, YT, Lee, D, and Ideker, T. Network-based classification of breast cancer metastasis. Mol Syst Biol. 3:140 (2007). [Get PDF] [Online link] Ourfali O, Shlomi T, Ideker T, Ruppin E, Sharan R. SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. Bioinformatics. 23(13):i359-i366. Jul 1 (2007). [Get PDF] [PubMed link] Parrish JR, Yu J, Liu G, Hines JA, Chan JE, Mangiola BA, Zhang H, Pacifico S, Fotouhi F, Dirita VJ, Ideker T, Andrews P, Finley RL Jr. A proteome-wide protein interaction map for Campylobacter jejuni. Genome Biol. 8(7):R130. Epub ahead of print. Jul 5 (2007). [Get PDF] [PubMed link] Kelley R, Feizi H, Ideker T. Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood. Bioinformatics. Epub ahead of print Jul 10 (2007). [Get PDF] [PubMed link] Ideker T, Bafna V, Lemberger T. Integrating scientific cultures. Mol Syst Biol.; 3:105. Epub Apr 17 (2007). [Get PDF] [PubMed link] Brockmann R, Beyer A, Heinisch JJ, Wilhelm T. Posttranscriptional Expression Regulation: What Determines Translation Rates? PLoS Computational Biology Vol. 3, No. 3, e57 doi:10.1371/journal.pcbi.0030057 (2007). [Get PDF] Tan K, Shlomi T, Feizi H, Ideker T, Sharan R. Transcriptional regulation of protein complexes within and across species. Proc Natl Acad Sci USA. Jan 16 (2007). [Get PDF] [PubMed link] Mak HC, Daly M, Gruebel B, Ideker T. CellCircuits: a database of protein network models. Nucleic Acids Res. Jan (2007) ;35(Database issue):D538-45. Epub. Nov 29 (2006). [Get PDF][PubMed link] 2006 Suthram S, Shlomi T, Ruppin E, Sharan R, Ideker T. A direct comparison of protein interaction confidence assignment schemes. BMC Bioinformatics. 7(1):360 (2006). [Get PDF] [PubMed link] Reguly T., Breitkreutz A., Boucher L., Breitkreutz BJ., Hon GC., Myers CL., Parsons A., Friesen H., Oughtred R., Tong A., Stark C., Ho Y., Botstein D., Andrews B., Boone C., Troyanskya OG., Ideker T., Dolinski K., Batada NN., Tyers M. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J Biol. 5(4):11 (2006). [Get PDF] [PubMed link] Beyer, A., Workman, CT., Hollunder, J., Radke, D., Möller, U., Wilhelm, T., Ideker, T. Integrated Assessment and Prediction of Transcription Factor Binding. Proc Natl Acad Sci . 103(25):9464-9 (2006). [Get PDF] [PubMed link] 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) [Get PDF] [Supp. Info.] [PubMed link] Scott, J., Ideker, T., Karp, R., and Sharan, R.. Efficient algorithms for detecting protein signaling pathways in protein interaction networks. J Comput Biol. 13(2):133-44 (2006) [Get PDF] [PubMed link] Bandyopadhyay S, Sharan R, Ideker T. Cover Article: Systematic identification of functional orthologs based on protein network comparison. Genome Res. 16(3):428-35. (2006). [Get PDF] [PubMed link] Feist, A.M., Scholten, J.C.M., Palsson, B.Ø., Brockman, F.J., and Ideker T. Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Nature Molecular Systems Biology (MSB) 10.1038:msb4100046 (2006). [Get PDF] 2005 Suthram, S., Sittler, T., and Ideker, T. The Plasmodium protein network diverges from those of other eukaryotes. Nature 438(7064):108-12 (2005).[Get PDF] [Supp. Info.] [PubMed link] Sharan R., Ideker, T., Kelley, B., Shamir, R., Karp, RM. Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. J Comput Biol. 12(6):835-46. (2005). [Get PDF] [PubMed link] Yeang, C.H., Mak, H.C., McCuine, S., Workman, C., Jaakkola, T., and Ideker, T. Validation and refinement of gene regulatory pathways on a network of physical interactions. Genome Biology 6(7): R62 (2005).[Get PDF] [PubMed link] [Supp. Info.] Hsiao, A., Ideker, T. Olesfky, J. and Subramaniam, S. VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data Nucleic Acids Research. 33(Web Server issue):W627-32. (2005). [Get PDF] [PubMed link] Workman, CT., Yin, Y., Corcoran, DL., Ideker, T., Stormo, GD., and Benos, PV. enoLOGOS: a versatile web tool for energy normalized sequence logos Nucleic Acids Research. 33(Web Server issue):W389-92. (2005). [Get PDF] [PubMed link] Kelley, R. and Ideker, T. Systematic interpretation of genetic interactions using protein networks. Nature Biotechnology 23(5):561-566 (2005).[Get PDF] [PubMed link] Sharan, R., Suthram, S., Kelley, R. M., Kuhn, T., McCuine, S., Uetz, P., Sittler, T., Karp, R. M., and Ideker, T. Cover Article: Conserved patterns of protein interaction in multiple species. Proc Natl
Acad Sci U S A. 8:102(6) 1974-79 (2005). [Get PDF] [PubMed link] 2004 Haugen, A. C., Kelley, R. M., Collins, J. B., Tucker, C. J. Deng, C. D., Afshari, C. A., Brown, J. M., Ideker, T., Van Houten, B. Integrating phenotypic and expression profiles to map arsenic-response networks. Genome Biol. 5(12):R95. (2004). [Get PDF] [PubMed link] Yeang CH, Ideker T, Jaakkola T. Physical network models. J Comput Biol. 11(2-3):243-62. (2004).[Get PDF] [PubMed link] Kelley, B. P., Yuan, B., Lewitter, F., Sharan, R. Stockwell, B. R., Ideker, T. PathBLAST: a tool for alignment of protein interaction networks. Nucleic Acids Research 1;32: W83-8 (2004). [Get PDF][PubMed link] Begley, T. J., Rosenbach, A. S., Ideker, T., Samson, L. D. Damage-recovery hot spots identified by genomic phenotyping and location mapping. Molecular Cell 16(1): 117-25 (2004).[Get PDF] [PubMed link] 2003Kelley, B. P., Sharan, R., Karp, R., Sittler, E. T., Root, D. E., Stockwell, B. R., and Ideker, T. Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc Natl Acad Sci U S A 100, 11394-9 (2003). [Get PDF] [PathBLAST Website] [PubMed link] Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, D., Schwikowski, B., and Ideker, T. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research 13, 2498-504 (2003). [Get PDF] [Cytoscape Website][PubMed link] Ozier, O., Amin, N., and Ideker, T. Global architecture of genetic interactions on the protein interaction network. Nature Biotechnology 21: 490-491 (2003). [Get PDF] [PubMed link] Young ET, Dombek KM, Tachibana C, Ideker T. Multiple pathways are co-regulated by the protein kinase Snf1 and the transcription factors Adr1 and Cat8. J Biol. Chem., April 3 (2003).[Get PDF] [PubMed link] 2002Ideker, T., Ozier, O., Schwikowski, B., and Siegel, A. Discovering regulatory and signaling circuits in molecular interaction networks. Bioinformatics 18: S233 (2002). [Get PDF] [PubMed link] Begley, T., Rosenbach, A., Ideker, T., and Samson, L. Genomic Phenotyping and Interactome Mapping Pinpoints Damage Recovery Pathways in S. cerevisiae. Molecular Cancer Research 1: 103-112 (2002).[Get PDF] [PubMed link] Smith, J., Marelli, M., Christmas, R., Vizeacoumar, F., Dilworth, D., Ideker, T., Galitski, T., Dimitrov, K., Rachubinski, R., and Aitchison, J. Transcriptome profiling to identify genes involved in peroxisome assembly and function. J Cell Biol. 158(2):259-71 (2002).[Get PDF] [PubMed link] 2001Ideker, 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). [Get PDF] [Companion Website] [Raw Data][PubMed link] 2000Ideker, T., Thorsson, V., Siegel, A. and Hood, L. Testing for Differentially-Expressed Genes by Maximum-Likelihood Analysis of DNA Microarray Data. Journal of Computational Biology 7: 805-817 (2000).[Get PDF] [PubMed link] 1999 Vrolijk, L., Ideker, T., Pohl, M. Taylor, S. Addelston, M. Nickerson, D. and Boyce-Jacino, M. Mining Single Nucleotide Polymorphisms (SNPs) from Expressed Sequence Tag (EST) Databases. Genome Research 9(2):167-74 (1999). Nelson, P.,
Hawkins, V., Schummer, M., Bumgarner, R., Ng, V., Ideker, T.,
Picoult-Newberg L, Ideker TE, Pohl MG, Taylor SL, Donaldson MA, Nickerson DA, Boyce-Jacino M. Mining SNPs from EST databases. Genome Res. 9(2):167-74 (1999). [Get PDF] [PubMed link] Conference Proceedings 2006 Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics, San Diego, CA, USA; December 2-4, 2005, Revised Selected Papers. Lecture Notes in Computer Science, Springer Berlin / Heidelberg, Volume 4023/2006, 0302-9743 (Print) 1611-3349 (Online May 16 2007). [Get PDF] [Springer link] Bandyopadhyay, S., Kelley, R., and Ideker, T. Discovering Regulated Networks During HIV-1 Latency and Reactivation. Pacific Symposium on Biocomputing 11:354-366 (2006).[Get PDF] 2005Scott, J., Ideker, T., Karp, R., and 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). J Comput Biol. Mar;13(2):133-44 (2006) [Get PDF][PubMed link] 2004Sharan, R. Ideker, T., Kelley, B. P., Shamir, R., and 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). 2000Ideker, T., Thorsson, V. and Karp, R. Discovery of Regulatory Interactions Through Perturbation: Inference and Experimental Design. Pacific Symposium on Biocomputing 5:302-313 (2000). [Get PDF] [PubMed link] Review,Opinions and Book Chapters 2008 Ideker T. Forging new ties between E. coli genes. Cell. 133: 3-5 (2008). Ideker T, Sharan R. Protein networks in disease. Genome Res. 18(4): 644-52 (2008). [Get PDF] [Pubmed link] 2007 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] 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). 2001Ideker, 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] Other Published Work 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. Protein Networks and Analysis of Global Gene Expression. From DNA to Proteins: the multiple levels of regulation. One hour instructional video requisitioned by Henry Stewart Talks: www.hstalks.com. Epub:(in production). |