Primary Research

2018

2017

  • Marty R, Kaabinejadian S, Rossell D, Slifker MJ, van de Haar J, Engin HB, de Prisco N, Ideker T, Hildebrand WH, Font-Burgada J, Carter H. MHC-I Genotype Restricts the Oncogenic Mutational Landscape. Cell. 2017 October 26. DOI: http://dx.doi.org/10.1016/j.cell.2017.09.050. PMID: 29107334 [PDF] [PubMed]
  • Du D, Roguev A, Gordon DE, Chen M, Chen SH, Shales M, Shen JP, Ideker T, Mali P, Qi LS, Krogan NJ. Genetic interaction mapping in mammalian cells using CRISPR interference. Nat Methods. 2017 Jun;14(6):577-580. doi: 10.1038/nmeth.4286. Epub 2017 May 8. PMID: 28481362 [PDF] [PubMed]
  • Buckley AR, Standish KA, Bhutani K, Ideker T, Lasken RS, Carter H, Harismendy O, Schork NJ. Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls. BMC Genomics. 2017 Jun 12;18(1):458. doi: 10.1186/s12864-017-3770-y. PMID: 28606096 [PDF] [PubMed]
  • Wang T, Tsui B, Kreisberg JF, Robertson NA, Gross AM, Yu MK, Carter H, Brown-Borg HM, Adams PD, Ideker T. Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment. Genome Biology. 2017 Mar 28;18(1):57. doi: 10.1186/s13059-017-1186-2. PMID: 28351423 [PDF] [PubMed] [Dataset] [GitHub]
  • Cole JJ, Robertson NA, Rather MI, Thomson JP, McBryan T, Sproul D, Wang T, Brock C, Clark W, Ideker T, Meehan RR, Miller RA, Brown-Borg HM, Adams PD. Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions. Genome Biol. 2017 Mar 28;18(1):58. doi: 10.1186/s13059-017-1185-3. PMID: 28351383 [PDF] [PubMed]
  • Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguev A, Lewis NE, Chang AN, Kreisberg JF, Krogan N, Qi L, Ideker T, Mali P. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nature Methods. 2017 Mar 20. doi: 10.1038/nmeth.4225. PMID: 28319113 [PDF] [PubMed]
  • Carter H, Marty R, Hofree M, Gross AM, Jensen J, Fisch KM, Wu X, DeBoever C, Van Nostrand EL, Song Y, Wheeler E, Kreisberg JF, Lippman SM, Yeo GW, Gutkind JS, Ideker T. Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer. Cancer Discovery. 2017 Feb 10. doi: 10.1158/2159-8290.CD-16-1045. PMID: 28188128 [PDF] [PubMed]
  • Kramer MH, Farré JC, Mitra K, Yu MK, Ono K, Demchak B, Licon K, Flagg M, Balakrishnan R, Cherry JM, Subramani S, Ideker T. Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy. Molecular Cell. 2017 Feb 16;65(4):761-774.e5. doi: 10.1016/j.molcel.2016.12.024. PMID: 28132844 [PDF] [PubMed] [Datasets]
  • Pillich RT, Chen J, Rynkov V, Welker D, Pratt D. NDEx: A Community Resource for Sharing and Publishing of Biological Networks. Methods Mol Biol. 2017 02 Feb;1558:271-301. doi: 10.1007/978-1-4939-6783-4_13. PMID: 28150243. Book chapter. [PDF] [PubMed

2016

  • Saito R, Rocanin-Arjo A, You YH, Darshi M, Van Espen B, Miyamoto S, Pham J, Pu M, Romoli S, Natarajan L, Ju W, Kretzler M, Nelson R, Ono K, Thomasova D, Mulay SR, Ideker T, D'Agati V, Beyret E, Belmonte JC, Anders HJ, Sharma K. Systems biology analysis reveals role of MDM2 in diabetic nephropathy. JCI Insight. 2016 Oct 20;1(17):e87877. [PDF] [PubMed]
  • Srivas R, Shen JP, Yang CC, Sun SM, Li J, Gross AM, Jensen J, Licon K, Bojorquez-Gomez A, Klepper K, Huang J, Pekin D, Xu JL, Yeerna H, Sivaganesh V, Kollenstart L, van Attikum H, Aza-Blanc P, Sobol RW, Ideker T. A Network of Conserved Synthetic Lethal Interactions for Exploration of Precision Cancer Therapy. Molecular Cell. 2016 Jul 19. pii: S1097-2765(16)30280-5. doi: 10.1016/j.molcel.2016.06.022. PMID: 27453043. [PDF] [PubMed]
  • Hofree M, Carter H, Kreisberg JF, Bandyopadhyay S, Mischel PS, Friend S, Ideker T. Challenges in identifying cancer genes by analysis of exomesequencing data. Nature Communications. 2016 Jul 15;7:12096. doi: 10.1038/ncomms12096. PMID: 27417679 [PDF] [PubMed]
  • Guo T, Gaykalova DA, Considine M, Wheelan S, Pallavajjala A, Bishop JA, Westra WH, Ideker T, Koch WM, Khan Z, Fertig EJ, Califano JA. Characterization of functionally active gene fusions in human papillomavirus related oropharyngeal squamous cell carcinoma. Int J Cancer. 2016 Jul 15;139(2):373-82. doi: 10.1002/ijc.30081. Epub 2016 Mar 30. PMID: 26949921. [PDF] [PubMed]
  • 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, Johns H, Karydas A, Knopman DS, Loboda A, Masliah E, Narasimhan R, Petersen RC, Podtelezhnikov A, Pradhan S, Rademakers R, Sun CH, Younkin SG, Miller BL, Ideker T, Wyss-Coray T. Network-driven plasma proteomics expose molecular changes in the Alzheimer's brain. Mol Neurodegener. 2016 Apr 26;11:31. doi: 10.1186/s13024-016-0095-2. PMID: 27112350 [PDF] [PubMed]
  • Qu K, Garamszegi S, Wu F, Thorvaldsdottir H, Liefeld T, Ocana M, Borges-Rivera D, Pochet N, Robinson JT, Demchak B, Hull T, Ben-Artzi G, Blankenberg D, Barber GP, Lee BT, Kuhn RM, Nekrutenko A, Segal E, Ideker T, Reich M, Chang HY, Mesirov JP. Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. Nature Methods. 2016 Jan 18. doi: 10.1038/nmeth.3732. [PDF] [PubMed]

2015

  • Carvunis A, Wang T, Skola D, Yu A, Chen J, Kreisberg JF, Ideker T. Evidence for a common evolutionary rate in metazoan transcriptional networks. eLife 2015 Dec 18; 10.7554 /eLife.11615. [PDF] [PubMed]
  • Yan JF, Kim H, Jeong SK, Lee HJ, Sethi MK, Lee LY, Beavis RC, Im H, Snyder MP, Hofree M, Ideker T, Wu SL, Paik YK, Fanayan S, Hancock WS. Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues. Journal of Proteome Research. 2015 Dec 4;14(12):4995-5006. doi: 10.1021/acs.jproteome.5b00827. Epub 2015 Oct 20. [PDF] [PubMed]
  • 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. 2015 Nov 10;10(11):e0142618. doi: 10.1371/journal.pone.0142618. eCollection 2015. [PDF] [PubMed]
  • 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, Chanda SK, Ware C, Dummer R, Hoon D, Kirkwood JM, Ronai ZA. Transcriptional repression of IFNβ1 by ATF2 confers melanoma resistance to therapy. Oncogene. 2015 Nov 12;34(46):5739-48. doi: 10.1038/onc.2015.22. Epub 2015 Mar 2. [PDF] [PubMed]
  • Pratt D, Chen J, Welker D, Rivas R, Pillich R, Rynkov V, Ono K, Miello C, Hicks L, Szalma S, Stojmirovic A, Dobin R, Braxenthaler M, Kuentzer J, Demchak B, Ideker T. NDEx, the Network Data Exchange. Cell Systems. 2015 Oct 28;1(4):302-305. [PDF][PubMed]
  • 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, Sobol RW, Ideker T. Chemogentic profiling identifies RAD17 as synthetically lethal with checkpoint kinase inhibition. Oncotarget. Sept 2015; (in press). [PDF] [PubMed]
  • Summer G, Kelder T, Ono K, Radonjic M, Heymans S, Demchak B. cyNeo4j: connecting Neo4j and Cytoscape. Bioinformatics. 2015 Aug 12. pii btv460. [PDF] [PubMed]
  • Till A, Saito R, Merkurjev D, Liu JJ, Syed GH, Kolnik M, Siddiqui A, Glas M, Scheffler B, Ideker T, Subramani S. Evolutionary trends and functional anatomy of the human expanded autophagy network. Autophagy. 2015 Jun 23;11(9):1652-67. doi: 10.1080/15548627.2015.1059558. [PDF] [PubMed]
  • Jaeger PA, McElfresh C, Wong LR, Ideker T. Beyond Agar: Gel Substrates with Improved Optical Clarity and Drug Efficiency and Reduced Autofluorescence for Microbial Growth Experiments. Applied and Environmental Microbiology. 2015 Aug 15;81(16):5639-49. doi: 10.1128/AEM.01327-15. Epub 2015 Jun 12. [PDF] [PubMed]
  • Ono K, Muetze T, Kolishovski, G, Shannon P, Demchak B. CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API. F1000 Research. 2015 Aug 5;4:478. doi: 10.12688/f1000research.6767.1. eCollection 2015. [PDF] [PubMed]
  • Choueiri MB, Shen JP, Gross A, Huang JK, Ideker T, Fanta P. ERCC1 and TS Expression as Prognostic and Predictive Biomarkers in Metastatic Colon Cancer. PLOS ONE. June 2015; 10(6), e0126898. [PDF] [PubMed]
  • 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, Mikati MA, İncecik F, Azam M, Borgatti R, Romaniello R, Boustany RM, Clericuzio CL, D'Arrigo S, Strømme P, Boltshauser E, Stanzial F, Mirabelli-Badenier M, Moroni I, Bertini E, Emma F, Steinlin M, Hildebrandt F, Johnson CA, Freilinger M, Vaux KK, Gabriel SB, Aza-Blanc P, Heynen-Genel S, Ideker T, Dynlacht BD, Lee JE, Valente EM, Kim J, Gleeson JG. Functional genome-wide siRNA screen identifies KIAA0586 as mutated in Joubert syndrome. Elife. 2015 May 30;4:e06602. doi: 10.7554/eLife.06602. [PDF] [PubMed]
  • 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. 2015 May;51(5):470-5. doi: 10.1016/j.oraloncology.2015.01.014. Epub 2015 Feb 27. PMID: 25735654 [PDF] [PubMed]
  • 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. 2015 Jan 22;57(2):273-89. doi: 10.1016/j.molcel.2014.11.016. Epub 2014 Dec 18. [PDF] [PubMed]

2014

  • Cancer Genome Atlas Research Network. Under a Creative Commons license. Integrated genomic characterization of papillary thyroid carcinoma. Cell. 2014 October 23; 159(3): 676–690. doi: 10.1016/j.cell.2014.09.050 [PDF] [PubMed]
  • 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. 2015 Jan 8;57(1):55-68. doi: 10.1016/j.molcel.2014.11.019. Epub 2014 Dec 24. [PDF] [PubMed]
  • Demchak B, Hull T, Reich M, Liefeld T, Smoot M, Ideker T, Mesirov JP. Cytoscape: the network visualization tool for GenomeSpace workflows. F1000 Research. 3:151 (2014) [PDF] [PubMed]
  • Ono K, Demchak B, Ideker T. Cytoscape tools for the web age: D3.js and Cytoscape.js exporters. Version 2. F1000 Research. 2014 Jul 1 [revised 2014 Oct 28];3:143. doi: 10.12688/f1000research.4510.2. eCollection 2014. [PDF] [PubMed]
  • Su G, Morris JH, Demchak B, Bader GD. Biological network exploration with Cytoscape 3. Curr Protoc Bioinformatics. 2014 Sep 8;47:8.13.1-8.13.24. doi: 10.1002/0471250953.bi0813s47. [PDF] [PubMed]
  • Demchak B, Hull T, Reich M, Liefeld T, Smoot M, Ideker T, Mesirov JP. Cytoscape: the network visualization tool for GenomeSpace workflows. Version 2. F1000 Research. 2014 Jul 1 [revised 2014 Aug 26];3:151. doi: 10.12688/f1000research.4492.2. eCollection 2014. [PDF] [PubMed]
  • Porting and using PanGIA for Cytoscape 3: challenges and solutions.
  • Welker D, Demchak B. Porting and using PanGIA for Cytoscape 3: challenges and solutions. F1000 Research. 2014 Jul 1;3:150. doi: 10.12688/f1000research.4546.1. eCollection 2014. [PDF] [PubMed]
  • Shaughnessy DT, McAllister K, Worth L, Haugen AC, Meyer JN, Domann FE, Van Houten B, Mostoslavsky R, Bultman SJ, Baccarelli AA, Begley TJ, Sobol R, Hirschey MD, Ideker T, Santos JH, Copeland WC, Tice RR, Balshaw DM, Tyson FL. Mitochondria, Energetics, Epigenetics, and Cellular Responses to Stress. Environ Health Perspect (2014) [PDF] [PubMed]
  • 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. Otolaryngol Head Neck Surg. pii: 0194599814545083 (2014) [PDF] [PubMed]
  • 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. Nat Genet. 2014 Sep;46(9):939-43. doi: 10.1038/ng.3051. Epub 2014 Aug 3. PMID: 25086664 [PDF] [PubMed]
  • 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. Proc Natl Acad Sci U S A 111(30):E3157-66 (2014) [PDF] [PubMed]
  • Kramer M, Dutkowski J, Yu M, Bafna V, Ideker T. Inferring gene ontologies from pairwise similarity data. Bioinformatics 30(12):i34-42 (2014) [PDF] [PubMed]
  • 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(5):e96687. (2014) [PDF] [PubMed]
  • 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(4):e95893 (2014) [PDF] [PubMed]
  • Carvunis AR, Ideker T. Carvunis AR, Ideker T. Siri of the cell: what biology could learn from the iPhone. Cell 157(3):534-8. (2014) [PDF] [PubMed]
  • 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, Kara M, Kara B, Bozorgmehri B, Ben-Omran T, Mojahedi F, Mahmoud IG, Bouslam N, Bouhouche A, Benomar A, Hanein S, Raymond L, Forlani S, Mascaro M, Selim L, Shehata N, Al-Allawi N, Bindu PS, Azam M, Gunel M, Caglayan A, Bilguvar K, Tolun A, Issa MY, Schroth J, Spencer EG, Rosti RO, Akizu N, Vaux KK, Johansen A, Koh AA, Megahed H, Durr A, Brice A, Stevanin G, Gabriel SB, Ideker T, Gleeson JG. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science 343(6170):506-11 (2014) [PDF] [PubMed]
  • Bean GJ, Jaeger PA, Bahr S, Ideker T. Development of ultra-high-density screening tools for microbial "omics." PLoS One 9(1):e85177 (2014) [PDF] [PubMed]
  • 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 Res 42(1): D1269-74 (2014) [PDF] [PubMed]

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 Rep 5(6):1714-24 (2013) [PDF] [PubMed]
    • Yeast UV-induced genetic network (Differential Score) [Data]
    • Yeast UV-induced genetic network (Static Score) [Data]
  • 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, Lewis RE, Macmillan JB, White MA. Using Functional Signature Ontology (FUSION) to identify mechanisms of action for natural products. Sci Signal 6(297):ra90 (2013) [PDF] [PubMed]
  • Hofree M, Shen JP, Carter H, Gross A, Ideker T. Network-based stratification of tumor mutations. Nat Methods 10(11):1108-15 (2013) [PDF] [PubMed]
  • 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, Kopp JB, Nigam SK, Cohen CD, Groop PH, Barshop BA, Natarajan L, Nyhan WL, Naviaux RK. Metabolomics reveals signature of mitochondrial dysfunction in diabetic kidney disease. J Am Soc Nephrol 24(11):1901-12(2013) [PDF] [PubMed]
  • 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 Rep 4(1):174-88 (2013) [PDF] [PubMed]
  • 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, Ren B, Bar-Joseph Z, Hughes TR, Ecker JR. Temporal transcription response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. Elife 2:e00675 (2013) [PDF] [PubMed]
  • 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, Vinh J, Hoffmann JA. Landscape of protein-protein interactions in Drosophila immune deficiency signaling during bacterial challenge. Proc Natl Acad Sci USA 110(26):10717-22 (2013) [PDF] [PubMed]
  • 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 Res 23(8):1283-94 (2013) [PDF] [PubMed]
  • 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, Aparicio S, Børresen-Dale AL, Caldas C, Califano A, Friend SH, Ideker T, Schadt EE, Stolovitzky GA, Margolin AA. Improving breast cancer survival analysis through competition-based multidimensional modeling. PLoS Comput Biol 9(5):e1003047 (2013) [PDF] [PubMed]
  • 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, Wu SL, Hancock WS. Genome wide proteomics of ERBB2 and EGRF and other oncogenic pathways in inflammatory breast cancer. J Proteome Res 12(6):2805-17 (2013) [PDF] [PubMed]
  • Dutkowski J, Kramer M, Surma MA, Balakrishnan R, Cherry JM, Krogan NJ, Ideker T. A gene ontology inferred from molecular networks*. Nat Biotechnol. 31, 38–45 (2013). doi: 10.1038/nbt.2463. [PDF] [PubMed] [Cover] *Cover article
    • Data: Quantitative genetic interaction profiles [Data]
  • Chen M, Licon K, Otsuka R, Pillus L, Ideker T. Decoupling Epigenetic and Genetic Effects through Systematic Analysis of Gene Position. Cell Reports 2013 January 3 doi: 10.1016/j.celrep.2012.12.003. [PDF][PubMed]
    • Data included are RNA-Seq data for 4 heterozygous diploid yeast strains and diploid wild-type. There are three replicates for each heterozygous strain, and six replicates for wild-type. [GEO data set]
    • Primers used for quantitative PCR, related to experimental procedures [Table S1]

2012

  • 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. Mol Cell. 2012 Dec 22. doi:pii: S1097-2765(12)00980-X. 10.1016/j.molcel.2012.11.023. [PDF] [PubMed] *Corresponding authors
    • Yeast DNA damage response (Static Score) [Data]
    • Yeast DNA damage response (Differential Score) [Data]
  • Bean GJ, Ideker T. Differential analysis of high-throughput quantitative genetic interaction data. Genome Biol. 2012 Dec 26;13(12):R123. [PDF] [PubMed]
  • 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*, Zhang K*., Genome-wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates. Mol Cell. 2012 Nov 20. pii: S1097-2765(12)00893-3. [PDF] [PubMed] *Corresponding authors
  • 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, J Proteome Res. 2012 Oct 5;11(10):4983-91. doi: 10.1021/pr3005524. Epub 2012 Sep 18. [PDF] [PubMed]
  • 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. 2012 Sep 27;120(13):2639-49. Epub 2012 Jul 26. [PDF] [PubMed] *Corresponding authors
  • 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, Edelmann W, Keogh MC, Greene D, Tang C, Cunningham P, Shokat KM, Cagney G, Svensson JP, Guthrie C, Espenshade PJ, Ideker T, Krogan NJ Hierarchical modularity and the evolution of genetic interactomes across species. Mol Cell. 2012 Jun 8;46(5):691-704. [PDF] [PubMed]
  • 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. 2012;7(8):e41134. doi: 10.1371/journal.pone.0041134. Epub 2012 Aug 16. [PDF] [PubMed]
  • Travesa A, Kuo D, de Bruin RA, Kalashnikova TI, Guaderrama M, Thai K, Aslanian A, Smolka MB, Yates JR 3rd, Ideker T, Wittenberg C. DNA replication stress differentially regulates G1/S genes via Rad53-dependent inactivation of Nrm1. EMBO Journal. 2012 Feb 14;31(7):1811-22. doi: 10.1038/emboj.2012.28. [PDF] [PubMed]
  • Lau E, Kluger H, Varsano T, Lee K, Scheffler I, Rimm DL, Ideker T, Ronai ZA. PKCe promotes oncogenic functions of ATF2 in the nucleus while blocking its apoptotic function at mitochondria. Cell. 2012 Feb 3;148(3):543-55. [PDF] [PubMed]
  • 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, Geum D, Wei X, Zhu J, Ideker T, Oka C, Wang N, Yang Z, Shaw PX, Zhang K. High temperature requirement factor A1 (HTRA1) gene regulates angiogenesis through transforming growth factor-ß family member growth differentiation factor 6. J Biol Chem. 2012 Jan 6;287(2):1520-6. Epub 2011 Nov 2 .[PDF] [PubMed]

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. Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18560-5. Epub 2011 Oct 31. [PDF] [PubMed]
  • Dutkowski J., Ideker T. Protein networks as logic functions in development and cancer. PLoS Comput Biol. 7(9) (2011). [PDF][PubMed]
  • 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). [PDF] [PubMed]
  • 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). [PDF][PubMed]
  • 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). [PDF][PubMed]
  • 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). [PDF][PubMed]

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). [PDF] [PubMed] [Suppl Docs]
  • Differential epistasis mapping (dE-MAP) [Data]
  • 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). [PDF] [PubMed]
  • 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). [PDF] [PubMed]
  • 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). [PDF] [PubMed] [Supplemental Docs]
    • Core MAPK Y2H [Data]
    • Full MAPK Y2H [Data]
  • 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). [PDF] [PubMed]
  • 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). [PDF] [PubMed]
  • Expression profiles of three yeast species after exposure to fluconazole. [Data]
  • 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). [PDF] [PubMed]
  • 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). [PDF] [PubMed]
  • 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). [PDF][PubMed]
    • Protein sub-cellular localization in A. taliana [Data]
  • 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, Han JH, Hashimoto T, Hide W, Hofmann O, Kamburov A, Kaur M, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E, MacPherson CR, Ogawa C, Radovanovic A, Schwartz A, Teasdale RD, Tegnér J, Lenhard B, Teichmann SA, Arakawa T, Ninomiya N, Murakami K, Tagami M, Fukuda S, Imamura K, Kai C, Ishihara R, Kitazume Y, Kawai J, Hume DA, Ideker T, Hayashizaki Y. An atlas of combinatorial transcriptional regulation in mouse and man. Cell 140(5):744-752 (2010). [PDF] [Pubmed]
    • Human TF interactions [Data]
    • Mouse TF interactions [Data]
  • 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). [PDF] [PubMed]
  • 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). [PDF] [PubMed]
    • Targeting Interactions in Chromatin. [Data]

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). [PDF] [PubMed]
  • 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). [PDF] [PubMed]
    • RNA from duplicate hippocampal samples taken from nine control monkeys and nine monkeys with evidence of SIV encephalitis were hybridized to Affymetrix arrays.[Data Set]
  • 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). [PDF] [PubMed]
  • Kelley, R., Ideker, T. Genome-wide fitness and expression profiling implicate Mga2 in adaptation to hydrogen peroxide. PLoS Genetics 5(5):e1000488 (2009). [PDF] [PubMed]
    • Enrichment Summary: Differentially expressed or sensitive members of each significantly over-represented condition or transcription factor target set mentioned in the study. [Data Set]
    • Expression Table: Log ratios and p-values for all micro-array expression profiling experiments conducted in this study. [Data Set]
    • Fitness Table: P-values for acute and adaptive screens conducted in this study. [Data Set]
    • TFs Table: Table containing all of the transcription factor target sets used in this study. [Data Set]
  • 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). [PDF] [PubMed]
  • 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). [PDF] [PubMed]
  • Mak, H.C., Pillus, L., Ideker, T. Dynamic reprogramming of transcription factors to and from the subtelomere. Genome Research 19(6):1014-25 (2009). [PDF] [PubMed]
  • 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). [PDF] [PubMed]

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). [PDF] [PubMed]
  • 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). [PDF] [PubMed]
  • 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). [PDF][PubMed]
  • 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). [PDF] [PubMed]
  • 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*, Krogan NJ*. Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science. 322:405-410 (2008). [PDF] [PubMed] *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). [PDF] [PubMed]
  • 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). [PDF] [PubMed]
  • 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). [PDF] [PubMed]
    • Data: Chip-chip of five YAPs in each drug-treated (MMS or CDDP) and untreated (SC media) conditions [Data Set]
  • Kalaev M, Smoot M, Ideker T, Sharan R. NetworkBLAST: comparative analysis of protein networks. Bioinformatics. 24(4):594-6 (2008). [PDF] [PubMed]
  • Kelley R, Feizi H, Ideker T. Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood. Bioinformatics 24:71-77 (2008). [PDF] [PubMed]

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). [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). [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). [PDF] [PubMed]
  • 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). [PDF] [PubMed]
  • 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). [PDF] [PubMed]
  • 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). [PDF] [PubMed]

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). [PDF] [SpringerLink]
  • Bandyopadhyay, S., Kelley, R., and Ideker, T. Discovering Regulated Networks During HIV-1 Latency and Reactivation. Pacific Symposium on Biocomputing 11:354-366 (2006). [PDF]
  • 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). [PDF] [PubMed]
  • 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). [PDF] [PubMed]
  • 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). [PDF] [PubMed]
  • 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). [PDF] [PubMed] [Supp. Info.]
  • 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). [PDF] [PubMed]
  • 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). [PDF] [PubMed]
  • 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). [PDF][PubMed]

2005

  • Suthram, S., Sittler, T., and Ideker, T. The Plasmodium protein network diverges from those of other eukaryotes. Nature 438(7064):108-12 (2005). [PDF] [PubMed] [Supp. Info.]
  • 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). [PDF] [PubMed]
  • 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). [PDF] [PubMed] [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). [PDF] [PubMed]
  • 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). [PDF] [PubMed]
  • Kelley, R. and Ideker, T. Systematic interpretation of genetic interactions using protein networks. Nature Biotechnology 23(5):561-566 (2005). [PDF] [PubMed]
  • Sharan, R., Suthram, S., Kelley, R. M., Kuhn, T., McCuine, S., Uetz, P., Sittler, T., Karp, R. M., and Ideker, T. Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci U S A. 8:102(6) 1974-79 (2005). *Cover Article [PDF] [PubMed] [Suppl. Data]
  • 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). [PDF] [PubMed]

2004 and prior

  • 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). [PDF] [PubMed]
  • Yeang CH, Ideker T, Jaakkola T. Physical network models. J Comput Biol. 11(2-3):243-62. (2004). [PDF] [PubMed]
  • 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). [PDF] [PubMed]
  • 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). [PDF] [PubMed]
  • 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).
  • 2003 and prior
  • 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). [PDF] [PubMed] [PathBLAST Website]
  • 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). [PDF] [PubMed] [Cytoscape Website]
  • Ozier, O., Amin, N., and Ideker, T. Global architecture of genetic interactions on the protein interaction network. Nature Biotechnology 21: 490-491 (2003). [PDF] [PubMed]
  • 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). [PDF] [PubMed]
  • Ideker, T., Ozier, O., Schwikowski, B., and Siegel, A. Discovering regulatory and signaling circuits in molecular interaction networks. Bioinformatics 18: S233 (2002). [PDF] [PubMed]
  • 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). [PDF] [PubMed]
  • 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). [PDF] [PubMed]
  • 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). [PDF] [PubMed]
  • 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). [PDF] [PubMed] [Suppl Data]
  • 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). [PDF] [PubMed]
  • 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). [PDF] [PubMed]
  • 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]
  • 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). [PDF] [PubMed]