cached image

Trey Ideker - Publications

Affiliations: 
Departments of Medicine and Bioengineering University of California, San Diego, La Jolla, CA 
Area:
computational biology
Website:
http://chianti.ucsd.edu/idekerlab/

154 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Ideker T, Hood L. A Blueprint for Systems Biology. Clinical Chemistry. PMID 30593465 DOI: 10.1373/clinchem.2018.291062  1
2018 Ma J, Yu MK, Fong S, Ono K, Sage E, Demchak B, Sharan R, Ideker T. Using deep learning to model the hierarchical structure and function of a cell. Nature Methods. PMID 29505029 DOI: 10.1038/nmeth.4627  0.48
2018 Neal S, Jaeger PA, Duttke SH, Benner C, Glass CK, Ideker T, Hampton RY. The Dfm1 Derlin Is Required for ERAD Retrotranslocation of Integral Membrane Proteins. Molecular Cell. 69: 915. PMID 29499140 DOI: 10.1016/j.molcel.2018.02.014  0.48
2018 Jaeger PA, Ornelas L, McElfresh C, Wong LR, Hampton RY, Ideker T. Systematic Gene-to-Phenotype Arrays: A High-Throughput Technique for Molecular Phenotyping. Molecular Cell. 69: 321-333.e3. PMID 29351850 DOI: 10.1016/j.molcel.2017.12.016  0.48
2018 Neal S, Jaeger PA, Duttke SH, Benner CK, Glass C, Ideker T, Hampton R. The Dfm1 Derlin Is Required for ERAD Retrotranslocation of Integral Membrane Proteins. Molecular Cell. 69: 306-320.e4. PMID 29351849 DOI: 10.1016/j.molcel.2017.12.012  0.48
2017 Cowen L, Ideker T, Raphael BJ, Sharan R. Network propagation: a universal amplifier of genetic associations. Nature Reviews. Genetics. PMID 28607512 DOI: 10.1038/nrg.2017.38  0.48
2016 Hofree M, Carter H, Kreisberg JF, Bandyopadhyay S, Mischel PS, Friend S, Ideker T. Challenges in identifying cancer genes by analysis of exome sequencing data. Nature Communications. 7: 12096. PMID 27417679 DOI: 10.1038/ncomms12096  0.68
2016 Jaeger PA, Lucin KM, Britschgi M, Vardarajan B, Huang RP, Kirby ED, Abbey R, Boeve BF, Boxer AL, Farrer LA, Finch N, Graff-Radford NR, Head E, Hofree M, Huang R, ... ... Ideker T, et al. Erratum to: Network-driven plasma proteomics expose molecular changes in the Alzheimer's brain. Molecular Neurodegeneration. 11: 42. PMID 27216421 DOI: 10.1186/s13024-016-0105-4  0.48
2016 Jaeger PA, Lucin KM, Britschgi M, Vardarajan B, Huang RP, Kirby ED, Abbey R, Boeve BF, Boxer AL, Farrer LA, Finch N, Graff-Radford NR, Head E, Hoffree M, Huang R, ... ... Ideker T, et al. Network-driven plasma proteomics expose molecular changes in the Alzheimer's brain. Molecular Neurodegeneration. 11: 31. PMID 27112350 DOI: 10.1186/s13024-016-0095-2  0.68
2016 Gross AM, Jaeger PA, Kreisberg JF, Licon K, Jepsen KL, Khosroheidari M, Morsey BM, Swindells S, Shen H, Ng CT, Flagg K, Chen D, Zhang K, Fox HS, Ideker T. Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA. Molecular Cell. 62: 157-168. PMID 27105112 DOI: 10.1016/j.molcel.2016.03.019  0.68
2016 Yu MK, Kramer M, Dutkowski J, Srivas R, Licon K, Kreisberg J, Ng CT, Krogan N, Sharan R, Ideker T. Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems. Cell Systems. 2: 77-88. PMID 26949740 DOI: 10.1016/j.cels.2016.02.003  0.68
2015 Gross AM, Kreisberg JF, Ideker T. Analysis of Matched Tumor and Normal Profiles Reveals Common Transcriptional and Epigenetic Signals Shared across Cancer Types. Plos One. 10: e0142618. PMID 26555223 DOI: 10.1371/journal.pone.0142618  0.68
2015 Shen JP, Srivas R, Gross A, Li J, Jaehnig EJ, Sun SM, Bojorquez-Gomez A, Licon K, Sivaganesh V, Xu JL, Klepper K, Yeerna H, Pekin D, Qiu CP, van Attikum H, ... ... Ideker T, et al. Chemogenetic profiling identifies RAD17 as synthetically lethal with checkpoint kinase inhibition. Oncotarget. PMID 26437225 DOI: 10.18632/oncotarget.5928  0.68
2015 Gross AM, Ideker T. Molecular networks in context. Nature Biotechnology. 33: 720-1. PMID 26154012 DOI: 10.1038/nbt.3283  0.68
2015 Jaeger PA, McElfresh C, Wong LR, Ideker T. Beyond agar: gel substrates for microbial growth experiments with improved optical clarity and drug efficiency and reduced autofluorescence. Applied and Environmental Microbiology. PMID 26070672 DOI: 10.1128/AEM.01327-15  0.68
2015 Roosing S, Hofree M, Kim S, Scott E, Copeland B, Romani M, Silhavy JL, Rosti RO, Schroth J, Mazza T, Miccinilli E, Zaki MS, Swoboda KJ, Milisa-Drautz J, Dobyns WB, ... ... Ideker T, et al. Functional genome-wide siRNA screen identifies KIAA0586 as mutated in Joubert syndrome. Elife. 4. PMID 26026149 DOI: 10.7554/eLife.06602  0.68
2015 Krogan NJ, Lippman S, Agard DA, Ashworth A, Ideker T. The Cancer Cell Map Initiative: Defining the Hallmark Networks of Cancer. Molecular Cell. 58: 690-698. PMID 26000852 DOI: 10.1016/j.molcel.2015.05.008  0.68
2015 Raju SC, Hauff SJ, Lemieux AJ, Orosco RK, Gross AM, Nguyen LT, Savariar E, Moss W, Whitney M, Cohen EE, Lippman SM, Tsien RY, Ideker T, Advani SJ, Nguyen QT. Combined TP53 mutation/3p loss correlates with decreased radiosensitivity and increased matrix-metalloproteinase activity in head and neck carcinoma. Oral Oncology. 51: 470-5. PMID 25735654 DOI: 10.1016/j.oraloncology.2015.01.014  0.68
2015 Lau E, Sedy J, Sander C, Shaw MA, Feng Y, Scortegagna M, Claps G, Robinson S, Cheng P, Srivas R, Soonthornvacharin S, Ideker T, Bosenberg M, Gonzalez R, Robinson W, et al. Transcriptional repression of IFNβ1 by ATF2 confers melanoma resistance to therapy. Oncogene. PMID 25728676 DOI: 10.1038/onc.2015.22  0.68
2015 Wilkinson DS, Jariwala JS, Anderson E, Mitra K, Meisenhelder J, Chang JT, Ideker T, Hunter T, Nizet V, Dillin A, Hansen M. Phosphorylation of LC3 by the Hippo kinases STK3/STK4 is essential for autophagy. Molecular Cell. 57: 55-68. PMID 25544559 DOI: 10.1016/j.molcel.2014.11.019  0.68
2015 Hustedt N, Seeber A, Sack R, Tsai-Pflugfelder M, Bhullar B, Vlaming H, van Leeuwen F, Guénolé A, van Attikum H, Srivas R, Ideker T, Shimada K, Gasser SM. Yeast PP4 interacts with ATR homolog Ddc2-Mec1 and regulates checkpoint signaling. Molecular Cell. 57: 273-89. PMID 25533186 DOI: 10.1016/j.molcel.2014.11.016  0.68
2014 Pico AR, Bader GD, Demchak B, Guitart Pla O, Hull T, Longabaugh W, Lopes C, Lotia S, Molenaar P, Montojo J, Morris JH, Ono K, Schwikowski B, Welker D, Ideker T. The Cytoscape app article collection. F1000research. 3: 138. PMID 25580224 DOI: 10.12688/f1000research.4642.1  0.68
2014 Ono K, Demchak B, Ideker T. Cytoscape tools for the web age: D3.js and Cytoscape.js exporters. F1000research. 3: 143. PMID 25520778 DOI: 10.12688/f1000research.4510.2  0.68
2014 . Integrated genomic characterization of papillary thyroid carcinoma. Cell. 159: 676-90. PMID 25417114 DOI: 10.1016/j.cell.2014.09.050  0.68
2014 Demchak B, Hull T, Reich M, Liefeld T, Smoot M, Ideker T, Mesirov JP. Cytoscape: the network visualization tool for GenomeSpace workflows. F1000research. 3: 151. PMID 25165537 DOI: 10.12688/f1000research.4492.2  0.68
2014 Hauff SJ, Raju SC, Orosco RK, Gross AM, Diaz-Perez JA, Savariar E, Nashi N, Hasselman J, Whitney M, Myers JN, Lippman SM, Tsien RY, Ideker T, Nguyen QT. Matrix-metalloproteinases in head and neck carcinoma-cancer genome atlas analysis and fluorescence imaging in mice. Otolaryngology--Head and Neck Surgery : Official Journal of American Academy of Otolaryngology-Head and Neck Surgery. 151: 612-8. PMID 25091190 DOI: 10.1177/0194599814545083  0.68
2014 Gross AM, Orosco RK, Shen JP, Egloff AM, Carter H, Hofree M, Choueiri M, Coffey CS, Lippman SM, Hayes DN, Cohen EE, Grandis JR, Nguyen QT, Ideker T. Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss. Nature Genetics. 46: 939-43. PMID 25086664 DOI: 10.1038/ng.3051  0.68
2014 Lee K, Sung MK, Kim J, Kim K, Byun J, Paik H, Kim B, Huh WK, Ideker T. Proteome-wide remodeling of protein location and function by stress. Proceedings of the National Academy of Sciences of the United States of America. 111: E3157-66. PMID 25028499 DOI: 10.1073/pnas.1318881111  0.68
2014 Kramer M, Dutkowski J, Yu M, Bafna V, Ideker T. Inferring gene ontologies from pairwise similarity data. Bioinformatics (Oxford, England). 30: i34-42. PMID 24932003 DOI: 10.1093/bioinformatics/btu282  0.68
2014 Emig-Agius D, Olivieri K, Pache L, Shih HL, Pustovalova O, Bessarabova M, Young JA, Chanda SK, Ideker T. An integrated map of HIV-human protein complexes that facilitate viral infection. Plos One. 9: e96687. PMID 24817247 DOI: 10.1371/journal.pone.0096687  0.68
2014 Joshi S, Singh AR, Zulcic M, Bao L, Messer K, Ideker T, Dutkowski J, Durden DL. Rac2 controls tumor growth, metastasis and M1-M2 macrophage differentiation in vivo. Plos One. 9: e95893. PMID 24770346 DOI: 10.1371/journal.pone.0095893  0.68
2014 Carvunis AR, Ideker T. Siri of the cell: what biology could learn from the iPhone. Cell. 157: 534-8. PMID 24766803 DOI: 10.1016/j.cell.2014.03.009  0.68
2014 Novarino G, Fenstermaker AG, Zaki MS, Hofree M, Silhavy JL, Heiberg AD, Abdellateef M, Rosti B, Scott E, Mansour L, Masri A, Kayserili H, Al-Aama JY, Abdel-Salam GM, Karminejad A, ... ... Ideker T, et al. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science (New York, N.Y.). 343: 506-11. PMID 24482476 DOI: 10.1126/science.1247363  0.68
2014 Bean GJ, Jaeger PA, Bahr S, Ideker T. Development of ultra-high-density screening tools for microbial "omics". Plos One. 9: e85177. PMID 24465499 DOI: 10.1371/journal.pone.0085177  0.68
2014 Dutkowski J, Ono K, Kramer M, Yu M, Pratt D, Demchak B, Ideker T. NeXO Web: the NeXO ontology database and visualization platform. Nucleic Acids Research. 42: D1269-74. PMID 24271398 DOI: 10.1093/nar/gkt1192  0.68
2013 Srivas R, Costelloe T, Carvunis AR, Sarkar S, Malta E, Sun SM, Pool M, Licon K, van Welsem T, van Leeuwen F, McHugh PJ, van Attikum H, Ideker T. A UV-induced genetic network links the RSC complex to nucleotide excision repair and shows dose-dependent rewiring. Cell Reports. 5: 1714-24. PMID 24360959 DOI: 10.1016/j.celrep.2013.11.035  0.68
2013 Carter H, Hofree M, Ideker T. Genotype to phenotype via network analysis. Current Opinion in Genetics & Development. 23: 611-21. PMID 24238873 DOI: 10.1016/j.gde.2013.10.003  0.68
2013 Potts MB, Kim HS, Fisher KW, Hu Y, Carrasco YP, Bulut GB, Ou YH, Herrera-Herrera ML, Cubillos F, Mendiratta S, Xiao G, Hofree M, Ideker T, Xie Y, Huang LJ, et al. Using functional signature ontology (FUSION) to identify mechanisms of action for natural products. Science Signaling. 6: ra90. PMID 24129700 DOI: 10.1126/scisignal.2004657  0.68
2013 Mitra K, Carvunis AR, Ramesh SK, Ideker T. Integrative approaches for finding modular structure in biological networks. Nature Reviews. Genetics. 14: 719-32. PMID 24045689 DOI: 10.1038/nrg3552  0.68
2013 Hofree M, Shen JP, Carter H, Gross A, Ideker T. Network-based stratification of tumor mutations. Nature Methods. 10: 1108-15. PMID 24037242 DOI: 10.1038/nmeth.2651  0.68
2013 Sharma K, Karl B, Mathew AV, Gangoiti JA, Wassel CL, Saito R, Pu M, Sharma S, You YH, Wang L, Diamond-Stanic M, Lindenmeyer MT, Forsblom C, Wu W, Ix JH, ... Ideker T, et al. Metabolomics reveals signature of mitochondrial dysfunction in diabetic kidney disease. Journal of the American Society of Nephrology : Jasn. 24: 1901-12. PMID 23949796 DOI: 10.1681/ASN.2013020126  0.68
2013 Jaehnig EJ, Kuo D, Hombauer H, Ideker TG, Kolodner RD. Checkpoint kinases regulate a global network of transcription factors in response to DNA damage. Cell Reports. 4: 174-88. PMID 23810556 DOI: 10.1016/j.celrep.2013.05.041  0.68
2013 Chang KN, Zhong S, Weirauch MT, Hon G, Pelizzola M, Li H, Huang SS, Schmitz RJ, Urich MA, Kuo D, Nery JR, Qiao H, Yang A, Jamali A, Chen H, ... Ideker T, et al. Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. Elife. 2: e00675. PMID 23795294 DOI: 10.7554/eLife.00675  0.68
2013 Fukuyama H, Verdier Y, Guan Y, Makino-Okamura C, Shilova V, Liu X, Maksoud E, Matsubayashi J, Haddad I, Spirohn K, Ono K, Hetru C, Rossier J, Ideker T, Boutros M, et al. Landscape of protein-protein interactions in Drosophila immune deficiency signaling during bacterial challenge. Proceedings of the National Academy of Sciences of the United States of America. 110: 10717-22. PMID 23749869 DOI: 10.1073/pnas.1304380110  0.68
2013 Lee K, Byun K, Hong W, Chuang HY, Pack CG, Bayarsaikhan E, Paek SH, Kim H, Shin HY, Ideker T, Lee B. Proteome-wide discovery of mislocated proteins in cancer. Genome Research. 23: 1283-94. PMID 23674306 DOI: 10.1101/gr.155499.113  0.68
2013 Bilal E, Dutkowski J, Guinney J, Jang IS, Logsdon BA, Pandey G, Sauerwine BA, Shimoni Y, Moen Vollan HK, Mecham BH, Rueda OM, Tost J, Curtis C, Alvarez MJ, Kristensen VN, ... ... Ideker T, et al. Improving breast cancer survival analysis through competition-based multidimensional modeling. Plos Computational Biology. 9: e1003047. PMID 23671412 DOI: 10.1371/journal.pcbi.1003047  0.68
2013 Zhang EY, Cristofanilli M, Robertson F, Reuben JM, Mu Z, Beavis RC, Im H, Snyder M, Hofree M, Ideker T, Omenn GS, Fanayan S, Jeong SK, Paik YK, Zhang AF, et al. Genome wide proteomics of ERBB2 and EGFR and other oncogenic pathways in inflammatory breast cancer. Journal of Proteome Research. 12: 2805-17. PMID 23647160 DOI: 10.1021/pr4001527  0.68
2013 Chen M, Licon K, Otsuka R, Pillus L, Ideker T. Decoupling epigenetic and genetic effects through systematic analysis of gene position. Cell Reports. 3: 128-37. PMID 23291096 DOI: 10.1016/j.celrep.2012.12.003  0.68
2013 Guénolé A, Srivas R, Vreeken K, Wang ZZ, Wang S, Krogan NJ, Ideker T, van Attikum H. Dissection of DNA damage responses using multiconditional genetic interaction maps. Molecular Cell. 49: 346-58. PMID 23273983 DOI: 10.1016/j.molcel.2012.11.023  0.68
2013 Dutkowski J, Kramer M, Surma MA, Balakrishnan R, Cherry JM, Krogan NJ, Ideker T. A gene ontology inferred from molecular networks. Nature Biotechnology. 31: 38-45. PMID 23242164 DOI: 10.1038/nbt.2463  0.68
2013 Hannum G, Guinney J, Zhao L, Zhang L, Hughes G, Sadda S, Klotzle B, Bibikova M, Fan JB, Gao Y, Deconde R, Chen M, Rajapakse I, Friend S, Ideker T, et al. Genome-wide methylation profiles reveal quantitative views of human aging rates. Molecular Cell. 49: 359-67. PMID 23177740 DOI: 10.1016/j.molcel.2012.10.016  0.68
2012 Bean GJ, Ideker T. Differential analysis of high-throughput quantitative genetic interaction data. Genome Biology. 13: R123. PMID 23268787 DOI: 10.1186/gb-2012-13-12-r123  0.68
2012 Jaeger PA, Doherty C, Ideker T. Modeling transcriptome dynamics in a complex world. Cell. 151: 1161-2. PMID 23217702 DOI: 10.1016/j.cell.2012.11.031  0.68
2012 Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T. A travel guide to Cytoscape plugins. Nature Methods. 9: 1069-76. PMID 23132118 DOI: 10.1038/nmeth.2212  0.68
2012 Bark SJ, Wegrzyn J, Taupenot L, Ziegler M, O'Connor DT, Ma Q, Smoot M, Ideker T, Hook V. The protein architecture of human secretory vesicles reveals differential regulation of signaling molecule secretion by protein kinases. Plos One. 7: e41134. PMID 22916103 DOI: 10.1371/journal.pone.0041134  0.68
2012 Choi S, Srivas R, Fu KY, Hood BL, Dost B, Gibson GA, Watkins SC, Van Houten B, Bandeira N, Conrads TP, Ideker T, Bakkenist CJ. Quantitative proteomics reveal ATM kinase-dependent exchange in DNA damage response complexes. Journal of Proteome Research. 11: 4983-91. PMID 22909323 DOI: 10.1021/pr3005524  0.68
2012 Chuang HY, Rassenti L, Salcedo M, Licon K, Kohlmann A, Haferlach T, Foà R, Ideker T, Kipps TJ. Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with disease progression. Blood. 120: 2639-49. PMID 22837534 DOI: 10.1182/blood-2012-03-416461  0.68
2012 Califano A, Butte AJ, Friend S, Ideker T, Schadt E. Leveraging models of cell regulation and GWAS data in integrative network-based association studies. Nature Genetics. 44: 841-7. PMID 22836096 DOI: 10.1038/ng.2355  0.68
2012 Ryan CJ, Roguev A, Patrick K, Xu J, Jahari H, Tong Z, Beltrao P, Shales M, Qu H, Collins SR, Kliegman JI, Jiang L, Kuo D, Tosti E, Kim HS, ... ... Ideker T, et al. Hierarchical modularity and the evolution of genetic interactomes across species. Molecular Cell. 46: 691-704. PMID 22681890 DOI: 10.1016/j.molcel.2012.05.028  0.32
2012 Travesa A, Kuo D, de Bruin RA, Kalashnikova TI, Guaderrama M, Thai K, Aslanian A, Smolka MB, Yates JR, Ideker T, Wittenberg C. DNA replication stress differentially regulates G1/S genes via Rad53-dependent inactivation of Nrm1. The Embo Journal. 31: 1811-22. PMID 22333915 DOI: 10.1038/emboj.2012.28  0.68
2012 Lau E, Kluger H, Varsano T, Lee K, Scheffler I, Rimm DL, Ideker T, Ronai ZA. PKCε promotes oncogenic functions of ATF2 in the nucleus while blocking its apoptotic function at mitochondria. Cell. 148: 543-55. PMID 22304920 DOI: 10.1016/j.cell.2012.01.016  0.68
2012 Ideker T, Krogan NJ. Differential network biology. Molecular Systems Biology. 8: 565. PMID 22252388 DOI: 10.1038/msb.2011.99  0.68
2012 Zhang L, Lim SL, Du H, Zhang M, Kozak I, Hannum G, Wang X, Ouyang H, Hughes G, Zhao L, Zhu X, Lee C, Su Z, Zhou X, Shaw R, ... ... Ideker T, et al. High temperature requirement factor A1 (HTRA1) gene regulates angiogenesis through transforming growth factor-β family member growth differentiation factor 6. The Journal of Biological Chemistry. 287: 1520-6. PMID 22049084 DOI: 10.1074/jbc.M111.275990  0.68
2011 Atwood A, DeConde R, Wang SS, Mockler TC, Sabir JS, Ideker T, Kay SA. Cell-autonomous circadian clock of hepatocytes drives rhythms in transcription and polyamine synthesis. Proceedings of the National Academy of Sciences of the United States of America. 108: 18560-5. PMID 22042857 DOI: 10.1073/pnas.1115753108  0.68
2011 Dutkowski J, Ideker T. Protein networks as logic functions in development and cancer. Plos Computational Biology. 7: e1002180. PMID 21980275 DOI: 10.1371/journal.pcbi.1002180  0.68
2011 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: 413-25. PMID 21903424 DOI: 10.1016/j.immuni.2011.06.013  0.68
2011 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. Nature Protocols. 6: 1308-23. PMID 21886098 DOI: 10.1038/nprot.2011.368  0.68
2011 Ideker T, Dutkowski J, Hood L. Boosting signal-to-noise in complex biology: prior knowledge is power. Cell. 144: 860-3. PMID 21414478 DOI: 10.1016/j.cell.2011.03.007  0.68
2011 Friend SH, Ideker T. Point: Are we prepared for the future doctor visit? Nature Biotechnology. 29: 215-8. PMID 21390021 DOI: 10.1038/nbt.1794  0.68
2011 Smoot M, Ono K, Ideker T, Maere S. PiNGO: a Cytoscape plugin to find candidate genes in biological networks. Bioinformatics (Oxford, England). 27: 1030-1. PMID 21278188 DOI: 10.1093/bioinformatics/btr045  0.68
2011 Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics (Oxford, England). 27: 431-2. PMID 21149340 DOI: 10.1093/bioinformatics/btq675  0.68
2010 Bandyopadhyay S, Mehta M, Kuo D, Sung MK, Chuang R, Jaehnig EJ, Bodenmiller B, Licon K, Copeland W, Shales M, Fiedler D, Dutkowski J, Guénolé A, van Attikum H, Shokat KM, ... ... Ideker T, et al. Rewiring of genetic networks in response to DNA damage. Science (New York, N.Y.). 330: 1385-9. PMID 21127252 DOI: 10.1126/science.1195618  0.6
2010 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. 20: 1672-8. PMID 20978140 DOI: 10.1101/gr.111765.110  0.68
2010 Bandyopadhyay S, Chiang CY, Srivastava J, Gersten M, White S, Bell R, Kurschner C, Martin C, Smoot M, Sahasrabudhe S, Barber DL, Chanda SK, Ideker T. A human MAP kinase interactome. Nature Methods. 7: 801-5. PMID 20936779 DOI: 10.1038/nmeth.1506  0.68
2010 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 (Oxford, England). 26: 2796-7. PMID 20847220 DOI: 10.1093/bioinformatics/btq522  0.68
2010 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 (Oxford, England). 26: i531-9. PMID 20823318 DOI: 10.1093/bioinformatics/btq376  0.44
2010 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: R77. PMID 20653936 DOI: 10.1186/gb-2010-11-7-r77  0.68
2010 Chuang HY, Hofree M, Ideker T. A decade of systems biology. Annual Review of Cell and Developmental Biology. 26: 721-44. PMID 20604711 DOI: 10.1146/annurev-cellbio-100109-104122  0.68
2010 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: 635-43. PMID 20543837 DOI: 10.1038/ni.1891  0.68
2010 Kim J, Lee JE, Heynen-Genel S, Suyama E, Ono K, Lee K, Ideker T, Aza-Blanc P, Gleeson JG. Functional genomic screen for modulators of ciliogenesis and cilium length. Nature. 464: 1048-51. PMID 20393563 DOI: 10.1038/nature08895  0.68
2010 Lee K, Thorneycroft D, Achuthan P, Hermjakob H, Ideker T. Mapping plant interactomes using literature curated and predicted protein-protein interaction data sets. The Plant Cell. 22: 997-1005. PMID 20371643 DOI: 10.1105/tpc.109.072736  0.68
2010 Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest AR, Gough J, Grimmond S, ... ... Ideker T, et al. An atlas of combinatorial transcriptional regulation in mouse and man. Cell. 140: 744-52. PMID 20211142 DOI: 10.1016/j.cell.2010.01.044  0.68
2010 König R, Stertz S, Zhou Y, Inoue A, Hoffmann HH, Bhattacharyya S, Alamares JG, Tscherne DM, Ortigoza MB, Liang Y, Gao Q, Andrews SE, Bandyopadhyay S, De Jesus P, Tu BP, ... ... Ideker T, et al. Human host factors required for influenza virus replication. Nature. 463: 813-7. PMID 20027183 DOI: 10.1038/nature08699  0.68
2010 van Steensel B, Braunschweig U, Filion GJ, Chen M, van Bemmel JG, Ideker T. Bayesian network analysis of targeting interactions in chromatin. Genome Research. 20: 190-200. PMID 20007327 DOI: 10.1101/gr.098822.109  0.68
2009 Hannum G, Srivas R, Guénolé A, van Attikum H, Krogan NJ, Karp RM, Ideker T. Genome-wide association data reveal a global map of genetic interactions among protein complexes. Plos Genetics. 5: e1000782. PMID 20041197 DOI: 10.1371/journal.pgen.1000782  0.68
2009 Gersten M, Alirezaei M, Marcondes MC, Flynn C, Ravasi T, Ideker T, Fox HS. An integrated systems analysis implicates EGR1 downregulation in simian immunodeficiency virus encephalitis-induced neural dysfunction. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 29: 12467-76. PMID 19812322 DOI: 10.1523/JNEUROSCI.3180-09.2009  0.68
2009 Fossum E, Friedel CC, Rajagopala SV, Titz B, Baiker A, Schmidt T, Kraus T, Stellberger T, Rutenberg C, Suthram S, Bandyopadhyay S, Rose D, von Brunn A, Uhlmann M, Zeretzke C, ... ... Ideker T, et al. Evolutionarily conserved herpesviral protein interaction networks. Plos Pathogens. 5: e1000570. PMID 19730696 DOI: 10.1371/journal.ppat.1000570  0.68
2009 Kelley R, Ideker T. Genome-wide fitness and expression profiling implicate Mga2 in adaptation to hydrogen peroxide. Plos Genetics. 5: e1000488. PMID 19503593 DOI: 10.1371/journal.pgen.1000488  0.68
2009 Bushman FD, Malani N, Fernandes J, D'Orso I, Cagney G, Diamond TL, Zhou H, Hazuda DJ, Espeseth AS, König R, Bandyopadhyay S, Ideker T, Goff SP, Krogan NJ, Frankel AD, et al. Host cell factors in HIV replication: meta-analysis of genome-wide studies. Plos Pathogens. 5: e1000437. PMID 19478882 DOI: 10.1371/journal.ppat.1000437  0.68
2009 Mak HC, Pillus L, Ideker T. Dynamic reprogramming of transcription factors to and from the subtelomere. Genome Research. 19: 1014-25. PMID 19372386 DOI: 10.1101/gr.084178.108  0.68
2009 Moxley JF, Jewett MC, Antoniewicz MR, Villas-Boas SG, Alper H, Wheeler RT, Tong L, Hinnebusch AG, Ideker T, Nielsen J, Stephanopoulos G. Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p. Proceedings of the National Academy of Sciences of the United States of America. 106: 6477-82. PMID 19346491 DOI: 10.1073/pnas.0811091106  0.68
2009 Schwartz AS, Yu J, Gardenour KR, Finley RL, Ideker T. Cost-effective strategies for completing the interactome. Nature Methods. 6: 55-61. PMID 19079254 DOI: 10.1038/nmeth.1283  0.68
2009 Rocke DM, Ideker T, Troyanskaya O, Quackenbush J, Dopazo J. Papers on normalization, variable selection, classification or clustering of microarray data Bioinformatics. 25: 701-702. DOI: 10.1093/bioinformatics/btp038  0.68
2008 Wilmes GM, Bergkessel M, Bandyopadhyay S, Shales M, Braberg H, Cagney G, Collins SR, Whitworth GB, Kress TL, Weissman JS, Ideker T, Guthrie C, Krogan NJ. A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. Molecular Cell. 32: 735-46. PMID 19061648 DOI: 10.1016/j.molcel.2008.11.012  0.68
2008 Lee E, Chuang HY, Kim JW, Ideker T, Lee D. Inferring pathway activity toward precise disease classification. Plos Computational Biology. 4: e1000217. PMID 18989396 DOI: 10.1371/journal.pcbi.1000217  0.68
2008 König R, Zhou Y, Elleder D, Diamond TL, Bonamy GM, Irelan JT, Chiang CY, Tu BP, De Jesus PD, Lilley CE, Seidel S, Opaluch AM, Caldwell JS, Weitzman MD, Kuhen KL, ... ... Ideker T, et al. Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell. 135: 49-60. PMID 18854154 DOI: 10.1016/j.cell.2008.07.032  0.68
2008 Lee K, Chuang HY, Beyer A, Sung MK, Huh WK, Lee B, Ideker T. Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species. Nucleic Acids Research. 36: e136. PMID 18836191 DOI: 10.1093/nar/gkn619  0.68
2008 Roguev A, Bandyopadhyay S, Zofall M, Zhang K, Fischer T, Collins SR, Qu H, Shales M, Park HO, Hayles J, Hoe KL, Kim DU, Ideker T, Grewal SI, Weissman JS, et al. Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science (New York, N.Y.). 322: 405-10. PMID 18818364 DOI: 10.1126/science.1162609  0.68
2008 Ideker T. Forging new ties between E. coli genes. Cell. 133: 1135-7. PMID 18585345 DOI: 10.1016/j.cell.2008.06.003  0.68
2008 Bandyopadhyay S, Kelley R, Krogan NJ, Ideker T. Functional maps of protein complexes from quantitative genetic interaction data. Plos Computational Biology. 4: e1000065. PMID 18421374 DOI: 10.1371/journal.pcbi.1000065  0.68
2008 Ideker T, Sharan R. Protein networks in disease. Genome Research. 18: 644-52. PMID 18381899 DOI: 10.1101/gr.071852.107  0.68
2008 Suthram S, Beyer A, Karp RM, Eldar Y, Ideker T. eQED: an efficient method for interpreting eQTL associations using protein networks. Molecular Systems Biology. 4: 162. PMID 18319721 DOI: 10.1038/msb.2008.4  0.68
2008 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. Proceedings of the National Academy of Sciences of the United States of America. 105: 2934-9. PMID 18287073 DOI: 10.1073/pnas.0708670105  0.68
2008 Kalaev M, Smoot M, Ideker T, Sharan R. NetworkBLAST: comparative analysis of protein networks. Bioinformatics (Oxford, England). 24: 594-6. PMID 18174180 DOI: 10.1093/bioinformatics/btm630  0.68
2008 Kelley R, Feizi H, Ideker T. Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood. Bioinformatics (Oxford, England). 24: 71-7. PMID 17623705 DOI: 10.1093/bioinformatics/btm347  0.68
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, ... ... Ideker T, et al. Integration of biological networks and gene expression data using Cytoscape. Nature Protocols. 2: 2366-82. PMID 17947979 DOI: 10.1038/nprot.2007.324  0.68
2007 Chuang HY, Lee E, Liu YT, Lee D, Ideker T. Network-based classification of breast cancer metastasis. Molecular Systems Biology. 3: 140. PMID 17940530 DOI: 10.1038/msb4100180  0.68
2007 Beyer A, Bandyopadhyay S, Ideker T. Integrating physical and genetic maps: from genomes to interaction networks. Nature Reviews. Genetics. 8: 699-710. PMID 17703239 DOI: 10.1038/nrg2144  0.68
2007 Ourfali O, Shlomi T, Ideker T, Ruppin E, Sharan R. SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. Bioinformatics (Oxford, England). 23: i359-66. PMID 17646318 DOI: 10.1093/bioinformatics/btm170  0.68
2007 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. A proteome-wide protein interaction map for Campylobacter jejuni. Genome Biology. 8: R130. PMID 17615063 DOI: 10.1186/gb-2007-8-7-r130  0.68
2007 Ideker T, Bafna V, Lemberger T. Integrating scientific cultures. Molecular Systems Biology. 3: 105. PMID 17437030 DOI: 10.1038/msb4100145  0.68
2007 Tan K, Shlomi T, Feizi H, Ideker T, Sharan R. Transcriptional regulation of protein complexes within and across species. Proceedings of the National Academy of Sciences of the United States of America. 104: 1283-8. PMID 17227853 DOI: 10.1073/pnas.0606914104  0.68
2007 Mak HC, Daly M, Gruebel B, Ideker T. CellCircuits: a database of protein network models. Nucleic Acids Research. 35: D538-45. PMID 17135207 DOI: 10.1093/nar/gkl937  0.68
2007 Beyer A, Suthram S, Ideker T. Uncovering regulatory pathways with expression quantitative trait loci Gensips'07 - 5th Ieee International Workshop On Genomic Signal Processing and Statistics. DOI: 10.1109/GENSIPS.2007.4365837  0.68
2007 Suthram S, Shlomi T, Ruppin E, Sharan R, Ideker T. Comparison of protein-protein interaction confidence assignment schemes Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4023: 39-50.  0.68
2006 Ideker T, Valencia A. Bioinformatics in the human interactome project. Bioinformatics (Oxford, England). 22: 2973-4. PMID 17142816 DOI: 10.1093/bioinformatics/btl579  0.68
2006 Bandyopadhyay S, Kelley R, Ideker T. Discovering regulated networks during HIV-1 latency and reactivation. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 354-66. PMID 17094252  0.68
2006 Suthram S, Shlomi T, Ruppin E, Sharan R, Ideker T. A direct comparison of protein interaction confidence assignment schemes. Bmc Bioinformatics. 7: 360. PMID 16872496 DOI: 10.1186/1471-2105-7-360  0.68
2006 Beyer A, Workman C, Hollunder J, Radke D, Möller U, Wilhelm T, Ideker T. Integrated assessment and prediction of transcription factor binding. Plos Computational Biology. 2: e70. PMID 16789814 DOI: 10.1371/journal.pcbi.0020070  0.68
2006 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, ... ... Ideker T, et al. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. Journal of Biology. 5: 11. PMID 16762047 DOI: 10.1186/jbiol36  0.68
2006 Feist AM, Scholten JC, Palsson BØ, Brockman FJ, Ideker T. Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Molecular Systems Biology. 2: 2006.0004. PMID 16738551 DOI: 10.1038/msb4100046  0.68
2006 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 (New York, N.Y.). 312: 1054-9. PMID 16709784 DOI: 10.1126/science.1122088  0.68
2006 Sharan R, Ideker T. Modeling cellular machinery through biological network comparison. Nature Biotechnology. 24: 427-33. PMID 16601728 DOI: 10.1038/nbt1196  0.68
2006 Scott J, Ideker T, Karp RM, Sharan R. Efficient algorithms for detecting signaling pathways in protein interaction networks. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 133-44. PMID 16597231 DOI: 10.1089/cmb.2006.13.133  0.68
2006 Warner GJ, Adeleye YA, Ideker T. Interactome networks: the state of the science. Genome Biology. 7: 301. PMID 16515723 DOI: 10.1186/gb-2006-7-1-301  0.68
2006 Bandyopadhyay S, Sharan R, Ideker T. Systematic identification of functional orthologs based on protein network comparison. Genome Research. 16: 428-35. PMID 16510899 DOI: 10.1101/gr.4526006  0.68
2006 Ideker T, Winslow LR, Lauffenburger AD. Bioengineering and systems biology. Annals of Biomedical Engineering. 34: 257-64. PMID 16474915 DOI: 10.1007/s10439-005-9047-7  0.68
2005 Suthram S, Sittler T, Ideker T. The Plasmodium protein network diverges from those of other eukaryotes. Nature. 438: 108-12. PMID 16267557 DOI: 10.1038/nature04135  0.68
2005 Sharan R, Ideker T, Kelley B, Shamir R, Karp RM. Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 12: 835-46. PMID 16108720 DOI: 10.1089/cmb.2005.12.835  0.68
2005 Yeang CH, Mak HC, McCuine S, Workman C, Jaakkola T, Ideker T. Validation and refinement of gene-regulatory pathways on a network of physical interactions. Genome Biology. 6: R62. PMID 15998451 DOI: 10.1186/gb-2005-6-7-r62  0.68
2005 Hsiao A, Ideker T, Olefsky JM, Subramaniam S. VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data. Nucleic Acids Research. 33: W627-32. PMID 15980550 DOI: 10.1093/nar/gki443  0.68
2005 Workman CT, Yin Y, Corcoran DL, Ideker T, Stormo GD, Benos PV. enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Research. 33: W389-92. PMID 15980495 DOI: 10.1093/nar/gki439  0.68
2005 Kelley R, Ideker T. Systematic interpretation of genetic interactions using protein networks. Nature Biotechnology. 23: 561-6. PMID 15877074 DOI: 10.1038/nbt1096  0.68
2005 Sharan R, Suthram S, Kelley RM, Kuhn T, McCuine S, Uetz P, Sittler T, Karp RM, Ideker T. Conserved patterns of protein interaction in multiple species. Proceedings of the National Academy of Sciences of the United States of America. 102: 1974-9. PMID 15687504 DOI: 10.1073/pnas.0409522102  0.68
2004 Haugen AC, Kelley R, Collins JB, Tucker CJ, Deng C, Afshari CA, Brown JM, Ideker T, Van Houten B. Integrating phenotypic and expression profiles to map arsenic-response networks. Genome Biology. 5: R95. PMID 15575969 DOI: 10.1186/gb-2004-5-12-r95  0.68
2004 Begley TJ, Rosenbach AS, Ideker T, Samson LD. Hot spots for modulating toxicity identified by genomic phenotyping and localization mapping. Molecular Cell. 16: 117-25. PMID 15469827 DOI: 10.1016/j.molcel.2004.09.005  0.68
2004 Yeang CH, Ideker T, Jaakkola T. Physical network models. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 11: 243-62. PMID 15285891 DOI: 10.1089/1066527041410382  0.68
2004 Ideker T. A systems approach to discovering signaling and regulatory pathways--or, how to digest large interaction networks into relevant pieces. Advances in Experimental Medicine and Biology. 547: 21-30. PMID 15230090  0.68
2004 Kelley BP, Yuan B, Lewitter F, Sharan R, Stockwell BR, Ideker T. PathBLAST: a tool for alignment of protein interaction networks. Nucleic Acids Research. 32: W83-8. PMID 15215356 DOI: 10.1093/nar/gkh411  0.68
2004 Ideker T. Systems biology 101--what you need to know. Nature Biotechnology. 22: 473-5. PMID 15085805 DOI: 10.1038/nbt0404-473  0.68
2003 Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research. 13: 2498-504. PMID 14597658 DOI: 10.1101/gr.1239303  0.68
2003 Kelley BP, Sharan R, Karp RM, Sittler T, Root DE, Stockwell BR, Ideker T. Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proceedings of the National Academy of Sciences of the United States of America. 100: 11394-9. PMID 14504397 DOI: 10.1073/pnas.1534710100  0.68
2003 Ideker T, Lauffenburger D. Building with a scaffold: emerging strategies for high- to low-level cellular modeling. Trends in Biotechnology. 21: 255-62. PMID 12788545 DOI: 10.1016/S0167-7799(03)00115-X  0.68
2003 Ozier O, Amin N, Ideker T. Global architecture of genetic interactions on the protein network. Nature Biotechnology. 21: 490-1. PMID 12721566 DOI: 10.1038/nbt0503-490  0.68
2003 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. The Journal of Biological Chemistry. 278: 26146-58. PMID 12676948 DOI: 10.1074/jbc.M301981200  0.68
2002 Begley TJ, Rosenbach AS, Ideker T, Samson LD. Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping Molecular Cancer Research. 1: 103-112. PMID 12496357  0.68
2002 Smith JJ, Marelli M, Christmas RH, Vizeacoumar FJ, Dilworth DJ, Ideker T, Galitski T, Dimitrov K, Rachubinski RA, Aitchison JD. Transcriptome profiling to identify genes involved in peroxisome assembly and function. The Journal of Cell Biology. 158: 259-71. PMID 12135984 DOI: 10.1083/jcb.200204059  0.68
2002 Griffin TJ, Gygi SP, Ideker T, Rist B, Eng J, Hood L, Aebersold R. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Molecular & Cellular Proteomics : McP. 1: 323-33. PMID 12096114  0.68
2002 Ideker T, Ozier O, Schwikowski B, Siegel AF. Discovering regulatory and signalling circuits in molecular interaction networks Bioinformatics. 18: S233-S240.  0.68
2001 Ideker T, Galitski T, Hood L. A new approach to decoding life: systems biology. Annual Review of Genomics and Human Genetics. 2: 343-72. PMID 11701654 DOI: 10.1146/annurev.genom.2.1.343  0.68
2001 Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science (New York, N.Y.). 292: 929-34. PMID 11340206 DOI: 10.1126/science.292.5518.929  0.68
2000 Ideker T, Thorsson V, Siegel AF, Hood LE. Testing for differentially-expressed genes by maximum-likelihood analysis of microarray data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 7: 805-17. PMID 11382363 DOI: 10.1089/10665270050514945  0.68
2000 Ideker TE, Thorsson V, Karp RM. Discovery of regulatory interactions through perturbation: inference and experimental design. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 305-16. PMID 10902179  0.52
1999 Nelson PS, Hawkins V, Schummer M, Bumgarner R, Ng WL, Ideker T, Ferguson C, Hood L. Negative selection: a method for obtaining low-abundance cDNAs using high-density cDNA clone arrays. Genetic Analysis : Biomolecular Engineering. 15: 209-15. PMID 10609756 DOI: 10.1016/S1050-3862(99)00006-6  1
Show low-probability matches.