Publications

Research in the Ideker Lab focuses on using genome-scale measurements (genomic, proteomic, and metabolomic) to construct computer-aided models of cellular processes and disease. These models have the potential to revolutionize biology and medicine by providing a comprehensive blueprint of normal and diseased cell functions and by allowing researchers to simulate the effects of drugs on cells long before they are tested in humans.  

Below is a complete list of research published by the Ideker Lab, in chronological order. Cover articles, Reviews, and book chapters are noted accordingly. Where applicable, associated datasets and press are linked. 

Additionally, publications may also be viewed at –

2020

  • Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O’Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Huettenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O’Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d’Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020 Apr 30. doi: 10.1038/s41586-020-2286-9. [Epub ahead of print] PMID: 32353859 [PDF] [PubMed]

  • Sun SM, Batté A, Tittel-Elmer M, van der Horst S, van Welsem T, Bean G, Ideker T, van Leeuwen F, van Attikum H. A genetic interaction map centered on cohesin reveals auxiliary factors in sister chromatid cohesion. J Cell Sci. 2020 Apr 16. pii: jcs.237628. doi: 10.1242/jcs.237628. [Epub ahead of print] PMID: 32299836 [PDF] [PubMed]

  • Jia T, Munson B, Lango Allen H, Ideker T, Majithia AR. Thousands of missing variants in the UK Biobank are recoverable by genome realignment. Ann Hum Genet. 2020 May;84(3):214-220. doi: 10.1111/ahg.12383. Epub 2020 Mar 31. PMID: 32232836 [PDF] [PubMed]

  • Kreisberg, J.F., Ideker, T., Meric-Bernstam, F. et al. Prospecting whole cancer genomes. Nature Cancer 1, 273–275. 20 Mar 2020. doi: https://doi.org/10.1038/s43018-020-0045-3. [PDF] [PubMed]

  • Kuenzi BM, Ideker T. A census of pathway maps in cancer systems biology. Nat Rev Cancer. 2020 Feb 17. doi: 10.1038/s41568-020-0240-7. [Epub ahead of print] PMID: 32066900 [PDF] [PubMed]

  • Vakirlis N, Acar O, Hsu B, Castilho Coelho N, Van Oss SB, Wacholder A, Medetgul-Ernar K, Bowman RW 2nd, Hines CP, Iannotta J, Parikh SB, McLysaght A, Camacho CJ, O’Donnell AF, Ideker T, Carvunis AR. De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences. Nat Commun. 2020 Feb 7;11(1):781. doi: 10.1038/s41467-020-14500-z. PMID: 32034123. PMCID: PMC7005711 [PDF] [PubMed]

  • Budzik JM, Swaney DL, Jimenez-Morales D, Johnson JR, Garelis NE, Repasy T, Roberts AW, Popov LM, Parry TJ, Pratt D, Ideker T, Krogan NJ, Cox JS. Dynamic post-translational modification profiling of Mycobacterium tuberculosis-infected primary macrophages. Elife. 2020 Jan 17;9. pii: e51461. doi: 10.7554/eLife.51461. PMID: 31951200. PMCID: PMC7030789. [PDF] [PubMed]

2019

2018

2017

2016

  • Ideker T. The Real Value of an Atlas. NIH Biomedical Informatics Blog. 31 Oct 2016. [PDF] (Review Article)

  • 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]

  • 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. Mol Cell. 2016 Apr 21;62(2):157-68. doi: 10.1016/j.molcel.2016.03.019. PMID: 27105112. [PDF][PubMed]

  • Ono, Kei. Technical aspects of “Panama Papers” analysis. Newsweek Japan, 12 April 2016. [PDF] (Review Article)

  • Yu M, Kramer M, Dutkowski J, Srivas R, Licon K, Kreisberg J, Ng C, Krogan N, Sharan R, Ideker T. Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems.* Cell Systems. 2016 Feb 24;2(2):77-88. doi: 10.1016/j.cels.2016.02.003. [PDF][PubMed] *Cover article

  • Liss MA, DeConde R, Caovan D, Hofler J, Gabe M, Palazzi KL, Patel ND, Lee HJ, Ideker T, Van Poppel H, Karow D, Aertsen M, Casola G, Derweesh IH. Parenchymal Volumetric Assessment as a Predictive Tool to Determine Renal Function Benefit of Nephron-Sparing Surgery Compared with Radical Nephrectomy. Journal of Endourology. 2016 Jan;30(1):114-21. doi: 10.1089/end.2015.0411. Epub 2015 Sep 25. [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]

  • Gross AM, Ideker T. Molecular networks in context. Nature Biotechnology 33, 720–721 (2015) doi:10.1038/nbt.3283. Published online 08 July 2015 [PDF][PubMed](Review Article)

  • 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]

  • Krogan NJ, Lippman S, Agard DA, Ashworth A, Ideker T. The cancer cell map initiative: defining the hallmark networks of cancer. Molecular Cell. 2015 May 21;58(4):690-8. doi: 10.1016/j.molcel.2015.05.008. Review. [PDF][PubMed](Review Article)

  • 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. eCollection 2014 [PDF][PubMed] (Review Article)

  • 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] (Review Article)

  • 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](Review Article)

  • 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. F1000 Research. 2014 Jul 1;3:138. doi: 10.12688/f1000research.4642.1. eCollection 2014. [PDF][PubMed Link](Review Article)

  • 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]

  • 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] [TI: Provided data analysis.] (Review Article)

  • 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. Siri of the cell: what biology could learn from the iPhone. Cell. 2014 Apr 24;157(3):534-8. doi: 10.1016/j.cell.2014.03.009. [PDF][PubMed](Review Article)

  • 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]

  • Altschul S, Demchak B, Durbin R, Gentleman R, Krzywinski M, Li H, Nekrutenko A, Robinson J, Rasband W, Taylor J, Trapnell C. The Anatomy of Successful Computational Biology Software. Nature Biotechnology 31(10):894-897 (2013) [PDF][PubMed] (Review Article)

  • Carter H, Hofree M, Ideker T. Genotype to phenotype via network analysis. Current Opinion in Genetics Development 23(6):611-21 (2013) [PDF] [PubMed] (Review Article)

  • Mitra K, Carvunis AR, Ramesh SK, Ideker T. Integrative approaches for finding modular structure in biology networks. Nature Review Genetics 14(10):719-732 (2013) [PDF] [PubMed] (Review Article)

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]

  • Jaeger P, Doherty C, Ideker T. Modeling Transcriptome Dynamics in a Complex World, Cell, Volume 151, Issue 6, 1161-1162, 7 December 2012. [Get PDF] [PubMed link] (Review Article)

  • 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. 2013 Jan 24;49(2):359-367. doi: 10.1016/j.molcel.2012.10.016. Epub 2012 Nov 21. [PDF] [PubMed] *Corresponding authors

  • 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. 2012 Nov;9(11):1069-76. doi: 10.1038/nmeth.2212. Epub 2012 Nov 6. [Get PDF] [PubMed link] (Review Article)

  • 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]

  • 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. 2012 Jul 27;44(8):841-7. doi: 10.1038/ng.2355. [Get PDF] [PubMed link] (Review Article)

  • 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]

  • Ideker T, Krogan NJ. Differential network biology. Molecular Systems Biology. 2012 Jan 17;8:565. doi: 10.1038/msb.2011.99. [Get PDF] [PubMed link] (Review Article)

  • 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]

  • Ideker T, Dutkowski J, Hood L. Boosting signal-to-noise in complex biology: prior knowledge is power. Cell. Mar 18;144(6):860-3 (2011). [PDF] [PubMed] (Review Article)

  • Friend SH, Ideker T. Point: Are we prepared for the future doctor visit? Nature Biotechnology Mar 29(3):215-8. (2011). [PDF] [PubMed] (Review Article)

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]

  • Bandyopadhyay, S. and Ideker T. Integrative systems biology. Nature Genetics 42(12) (2010). [Get Poster] (Review Article)

  • Chuang HY, Hofree M, Ideker T. A decade of systems biology. Annual Review of Cell and Developmental Biology(2010). [PDF] [PubMed] (Review Article)

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]

  • Ideker T. Book Review: “Wetware: A Computer in Every Living Cell” by Dennis Bray. Cell 138: 820-821 (2009) (Review Article)

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]

  • Ideker T. Forging new ties between E. coli genes. Cell. 133: 3-5 (2008). [Get PDF] [Pubmed link] (Review Article)

  • Ideker T, Sharan R. Protein networks in disease. Genome Research. 18(4): 644-52 (2008). [Get PDF] [Pubmed link] (Review Article)

  • Ideker T. Forging new ties between E. coli genes. Cell. 133: 3-5 (2008). [Get PDF] [Pubmed link] (Review Article)

  • Ideker T, Sharan R. Protein networks in disease. Genome Research. 18(4): 644-52 (2008). [Get PDF] [Pubmed link] (Review Article)

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]

  • Ideker T, Bafna V, Lemberger T. Integrating scientific cultures. Molecular Systems Biology 3:105. Epub Apr 17 (2007). [Get PDF] [PubMed link] (Review Article)

  • Beyer A, Bandyopadhyay S, Ideker T. Integrating physical and genetic maps: from genomes to interaction networks. Nature Review Genetics. (9):699-710. Featured Review. Sep 8 (2007). [Get PDF] [PubMed link] (Review Article)

  • Ideker TE. Network genomics. Ernst Schering Res Found Workshop. (61):89-115. Review. (2007). [PubMed link] (Review Article)

  • Ideker, T. (2007), “Protein Networks and Analysis of Global Gene Expression”, in Tsonis, P. (ed.), From DNA to Proteins: The Multiple Levels of Regulation , The Biomedical & Life Sciences Collection, Henry Stewart Talks Ltd, London. (Review Article)

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]

  • Ideker, T., Valencia, A. Bioinformatics in the human interactome project. Bioinformatics. 22(24):2973-4. Dec 15 (2006). [Get PDF] [PubMed link] (Review Article)

  • Ideker T, Winslow LR, Lauffenburger DA. Bioengineering and systems biology. Annals of Biomedical Engineering. Jul;34(7):1226-33. Review. (2006). [Get PDF] [PubMed link] (Review Article)

  • Sharan, R., and Ideker, T. Modeling cellular machinery through biological network comparison. Nature Biotechnology.Review. 24(4):427-33. Apr (2006). [Get PDF] [PubMed link] (Review Article)

  • Warner, G.J., Adeleye, Y.A., Ideker, T. Interactome networks: the state of the science. Genome Biol. Review. 7(1):301. Jan 23 (2006). [Get PDF] [PubMed link] (Review Article)

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]

  • Ideker, T. “Data collection and analysis in systems biology.” Wiley Encyclopedia of Genetics, Genomics, Proteomics, and Bioinformatics, Dunn, M.J., Jorde, L.B., Little, P.F.R., Subramaniam, S. (Eds). 0-470-84974-6 (2005) [Book]

  • Ideker, T., Tan, K., Uetz, P. “Visualization and Integration of Protein Interaction Networks”,  in Protein-Protein Interactions Second Edition: A Molecular Cloning Manual, E. Golemis and P. Adams eds. CSHL Press, Cold Spring Harbor, N.Y. 7(42):839-856 (2005) [Book chapter]

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).

  • Ideker, T. A systems approach to discovering signaling and regulatory pathways–or, how to digest large interaction networks into relevant pieces. Adv. Exp. Med. Biol. 547: 21-30 (2004). [Get PDF] [PubMed link] (Review Article)

  • Ideker, T. Systems biology 101–what you need to know. Nature Biotechnology 22(4): 473-5 (2004). [Get PDF][PubMed link] (Review Article)

  • 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. and Lauffenburger, D. Building with a scaffold: Emerging strategies for high- to low-level cellular modeling. Trends in Biotechnology 21: 252-262 (2003). [Get PDF] [PubMed link] (Review Article)

  • 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., Grimmond, S., and Ibarra, S. “Hybridization and Post-Hybridization Washing,” in DNA Microarrays: A Molecular Cloning Manual, D. Bowtell and J. Sambrook eds. CSHL Press, Cold Spring Harbor, N.Y. (2002) [Book chapter]

  • Uetz, P., Schwikowski, B., and Ideker, T. “Visualization and Integration of Protein-Protein Interactions”, in Protein-Protein Interactions: A Molecular Cloning Manual, E. Golemis ed. CSHL Press, Cold Spring Harbor, N.Y. (2002). [Book chapter]

  • 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., Galitski, T., and Hood, L. A New Approach to Decoding Life: Systems Biology. Annual Review of Genomics and Human Genetics, 2:343 (2001). [Get PDF] [PubMed link] (Review Article)

  • 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]