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Publications

Journal Articles

2011

  • Dutkowski J., Ideker T. Protein networks as logic functions in development and cancer. PLoS Comput Biol. 7(9) (2011) [Get PDF]
  • Mercer EM, Lin YC, Benner C, Jhunjhunwala S, Dutkowski J, Flores M, Sigvardsson M, Ideker T, Glass CK, Murre C. Multilineage priming of enhancer repertoires precedes commitment to the B and myeloid cell lineages in hematopoietic progenitors. Immunity. 35(3):413-25 (2011) [Get PDF]
  • Srivas R, Hannum G, Ruscheinski J, Ono K, Wang PL, Smoot M, Ideker T. Assembling global maps of cellular function through integrative analysis of physical and genetic networks. Nat. Protoc. 6(9) (2011) [Get PDF]
  • Smoot ME, Ono K, Ideker T. Maere, S. PiNGO: a Cytoscape plugin to find candidate genes in biological networks. Bioinformatics doi: 10.1093/bioinformatics/btr045 (2011) [Get PDF]
  • Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. Feb 1;27(3):431-2. (2011) [Get PDF]

2010

  • 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) [Get PDF] [Suppl Docs] [PubMed link]
  • Kuo D, Licon K, Bandyopadhyay S, Chuang R, Luo C, Catalana J, Ravasi T, Tan K, Ideker T. Coevolution within a transcriptional network by compensatory trans and cis mutations. Genome Research (2010) [Get PDF] [PubMed link]
  • Cannistraci CV, Ravasi T, Montevecchi FM, Ideker T, Alessio M. Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes. Bioinformatics 2 (18):i531-i539 (2010) [Get PDF] [PubMed link]
  • Bandyopadhyay S, Chiang C, Srivastava J, Gersten M, White S, Bell R, Kurschner C, Martin CH, Sahasrabudhe S, Barber DL, Chanda SK, Ideker T. A human MAP kinase interactome. Nature Methods doi:10.1038/nmeth.1506 (2010) [Get PDF]
  • Pentchev K, Ono K, Herwig R, Ideker T, Kamburov A. Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape. Bioinformatics (2010) [Get PDF] [PubMed link]
  • Kuo D, Tan K, Zinman G, Ravasi T, Bar-Joseph Z, Ideker T. Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. Genome Biology 11(7):R77 (2010) [Get PDF] [PubMed link]
  • Lin YC, Jhunjhunwala S, Benner C, Heinz S, Welinder E, Mansson R, Sigvardsson M, Hagman J, Espinoza CA, Dutkowski J, Ideker T, Glass CK, Murre C. A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate. Nature Immunology 11(7):635-643 (2010) [Get PDF] [PubMed link]
  • Kim, J., Lee, J.E., Heynen-Genel, S., Suyama, E., Ono, K., Lee, K., Ideker, T., Aza-Blanc, P., Gleeson, J.G. Functional genomic screen for modulators of ciliogenesis and cilium length. Nature 464(7291):1048-51 (2010) [Get PDF] [PubMed link]
  • Lee, K., Thorneycoft, D., Achuthan, P., Hermjakob, H., Ideker, T. Mapping Plant Interactomes Using Literature Curated and Predicted Protein-Protein Interaction Datasets. The Plant Cell (2010). [Get PDF]
  • Ravasi, T., Cannistraci, C.V., Katayama, S., Bajic, V.B., Tan, K., Akalin, A., Schmeier, S., Kanamori-Katayama, M., Bertin, N., Carninci, P., Daub, C.O., Forrest, A.R.R., Gough, J., Grimmond, S., Han, J., Hashimoto, T., Hide, W., Hofmann, O., Kaur, M., Kawaji, H., Kubosaki, A., Lassmann, T., van Nimwegen, E., MacPherson, C.R., Ogawa, C., Radovanovic, A., Schwartz, A., Teasdale, R.D., Tegnér, J., Lenhard, B., Teichmann, S.A., Hume, D.A., Ideker, T. An atlas of combinatorial transcriptional regulation in mouse and man. Cell 140(5):744-752 (2010)[Get PDF] [Pubmed link]
  • Konig, R., Stertz, S., Zhou, Y., Inoue, A., Hoffmann, H.H., Bhattacharyay, S., Alamares, J., Tscherne, D.M., Ortigoza, M.B., Liang, Y., Gao, Q., Andrews, S.E., Bandyopadhyay, S., De Jesus, P., Tu, B., Pache, L., Shih, C., Orth, A., Bonamy, G., Miraglia, L., Ideker, T., Garcia-Sastre, A., Young, J.A.T., Palese, P., Shaw, M.L., Chanda, S.K. Human Host Factors Required for Influenza Virus Replication. Nature, 463:813-817 (2010) [Get PDF] [Pubmed link]
  • van Steensel, B., Braunschweig, U., Filion, G.J., Chen, M., van Bemmel, J.G., Ideker, T. Bayesian network analysis of targeting interactions in chromatin. Genome Research, 20(2):190-200 (2010) [Get PDF] [Pubmed link]

2009

  • Hannum, G., Srivas, R., Guenole, A., van Attikum, H., Krogan, N.J., Karp, R.M., Ideker, T. Genome-wide association data reveal a global map of genetic interactions among protein complexes. PLoS Genetics 5(12):e1000782 (2009) [Get PDF] [Pubmed link]
  • Gersten, M., Alirezaei, M., Marcondes, M.C., Flynn, C., Ravasi, T., Ideker, T., Fox, H.S. An integrated systems analysis implicates EGR1 downregulation in SIVE-induced neural dysfunction. Journal of Neuroscience 29(40):12467-76 (2009) [Get PDF] [Pubmed link]
  • Fossum, E., Friedel, C.C., Rajagopala, S.V., Titz, R., Baiker, A., Schmidt, T., Kraus, T., Stellberger, T., Rutenberg, C., Suthram, S., Bandyopadhyay, S., Rose, D., von Brunn, A., Uhlmann, M., Zeretzke, C., Dong, Y.A., Boulet, H., Koegl, M., Bailer, S.M., Koszinowski, U., Ideker, T., Uetz, P., Zimmer, R., Haas, J. Evolutionarily conserved herpesviral protein interaction networks. PLoS Pathogens 5(9):e1000570 (2009) [Get PDF] [Pubmed link]
  • Kelley, R., Ideker, T. Genome-wide fitness and expression profiling implicate Mga2 in adaptation to hydrogen peroxide. PLoS Genetics 5(5):e1000488 (2009) [Get PDF] [Pubmed link]
  • Bushman, F.D., Malani, N., Fernandes, J., D'Orso, I., Cagney, G., Diamond, T.L., Zhou, H., Hazuda, D.J., Espeseth, A.S., Konig, R., Bandyopadhyay, S., Ideker, T., Goff, S.P., Krogan, N.J., Frankel, A.D., Young, J.A., Chanda, S.K. Host cell factors in HIV replication: meta-analysis of genome-wide studies. PLoS Pathog 5(5):e1000437 (2009). [Get PDF] [Pubmed link]
  • Moxley, J.F., Jewett, M.C., Antoniewicz, M.R., Villas-Boas, S.G., Alper, H., Wheeler, R.T., Tong, L., Hinnebusch, A.G., Ideker, T., Nielsen, J., Stephanopoulos, G. Special Feature: Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p. Proc Natl Acad Sci U.S.A. 106(16): 6477-6482 (2009). [Get PDF] [Pubmed link]
  • Mak, H.C., Pillus, L., Ideker, T. Dynamic reprogramming of transcription factors to and from the subtelomere. Genome Research 19(6):1014-25 (2009). [Get PDF] [Pubmed link]
  • Schwartz, A.S., Yu, J., Gardenour, K.R., Finley, R.L. Jr., Ideker, T. Cost-effective strategies for completing the interactome. Nature Methods 6(1):55-61 (2009). [Get PDF] [Pubmed link]

2008

  • Wilmes, G.M., Bergkessel, M., Bandyopadhyay, S., Shales, M., Braberg, H., Cagney, G., Collins, S.R., Whitworth, G.B., Kress, T.L., Weissman, J.S., Ideker, T., Guthrie, C., Krogan, N.J. A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. Mol Cell 32(5):735-746 (2008). [Get PDF] [Pubmed link]
  • Konig, R., Zhou, Y., Elleder, D., Diamond, T.L., Bonamy, G.M., Irelan, J.T., Chiang, C.Y., Tu, B.P., De Jesus, P.D., Lilley, C.E., Seidel, S., Opaluch, A.M., Caldwell, J.S., Weitzman, M.D., Kuhen, K.L., Bandyopadhyay, S., Ideker, T., Orth, A.P., Miraglia, L.J., Bushman, F.D., Young, J.A., Chanda, S.K. Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell 135(1):49-60 (2008). [Get PDF] [Pubmed link]
  • Lee, E., Chuang, H.Y., Kim, J.W., Ideker, T., Lee, D. Inferring pathway activity toward precise disease classification. PLoS Compu Biol. 4(11): e1000217. doi: 10.1371/journal.pcbi.1000217 (2008). [Get PDF]
  • Lee, K.Y., Chuang, H.Y., Beyer, A., Sung, M.K., Huh, W.K., Lee, B., Ideker, T. Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species. Nucleic Acids Research. doi: 10.1093/nar/gkn619 (2008). [Get PDF] [Pubmed link]
  • Roguev, A., Bandyopadhyay, S., Zofall, M., Zhang, K., Fischer, T., Collins, S.R., Qu, H., Shales, M., Park, H.O., Hayles, J., Hoe, K.L., Kim, D.U., Ideker, T.*, Grewal, S.I.*, Weissman, J.S.*, Krogan, N.J.* Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science. 322:405-410 (2008). [Get PDF] [Pubmed link]
    *Corresponding Authors
  • 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. 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]
  • 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]
    [Suppl. Website and Database of Conserved Pathways]

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. Hot spots for modulating toxicity identified by genomic phenotyping and localization mapping. Molecular Cell 16(1): 117-25 (2004). [Get PDF] [PubMed link]

2003

  • Kelley, 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]

2002

  • Ideker, 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. Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping. Molecular Cancer Research 1: 103-112 (2002). [Get PDF] [PubMed link]
  • Griffin, T., Gygi, S., Ideker, T., Rist, B., Eng, J., Hood, L., and Aebersold, R. Complementary Profiling of Gene Expression at the Transcriptome and Proteome Levels in S. cerevisiae. Molecular and Cellular Proteomics 1: 323-333 (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]

2001

  • 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]

2000

  • Ideker, 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

  • Nelson, P., Hawkins, V., Schummer, M., Bumgarner, R., Ng, V., Ideker, T., Ferguson, C. and Hood, L. Negative Selection: A Method for Obtaining Low Abundance cDNAs Using High Density cDNA Clone Arrays. Genetic Analysis 15:209-215 (1999).[PubMed link]
  • 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]

2005

  • Scott, 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]

2004

  • Sharan, 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).

2000

  • 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). [Get PDF] [PubMed link]