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Trey Ideker: Defining and Advancing Systems Biology PDF Print E-mail
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Wednesday, 15 June 2011 16:37
As a graduate student, Trey Ideker published a paper that helped define the discipline of systems biology. His research goals today reflect those of the entire field: to integrate the myriad data that researchers can collect about a cell into coherent computer models. As an assistant professor of bioengineering, Ideker is not only improving these models but employing them in biological discovery. For instance, he is looking for protein networks uniquely present in pathogenic organisms; these could make good drug targets. He hopes that, ultimately, systems-derived models will let researchers simulate how potential drugs will affect the body -- long before the compounds are tested in humans.

Research Overview:

Our laboratory conducts bioinformatic and experimental research in the field of Network and Systems Biology. Click on the below links for more detailed information about each project.

BIOINFORMATICS. Our bioinformatics research is directed towards what we believe will be critical approaches for using biological network models in medicine and genetics.

Methods for assembling genome-scale data (molecular interactions and profiles) into models of signaling and regulatory pathways.
Methods for using network models of cells to diagnose disease and interpret personalized genetic information (network-based biomarkers).
Methods for comparison of networks across different species, network types, biological conditions, or points in time.
In addition, we are strong supporters of several community software projects, including the Cytoscape platform. We also are interested in Error Analysis and Modeling of DNA MIcroarrays.

GENOME-SCALE BIOLOGY. Experimentally, the lab is applying the above network modeling technologies to understand a variety of basic cell processes and diseases.

Genome-scale approaches to understand how cells respond to DNA damage.
Mapping protein networks in pathogenesis of disease (HIV, NeuroAIDS, Malaria, Herpes, others)
Galactose Utilization as a Model System

Publications:

2009

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.  Bioinformatics23(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]

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]
[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

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., 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]

 
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