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. Visit our Research pages to learn more about our current projects and go here to view select Publication Highlights.
Additionally, publications may also be viewed at –
2023
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Baron M, Tagore M, Wall P, Zheng F, Barkley D, Yanai I, Yang J, Kiuru M, White RM, Ideker T. Desmosome mutations impact the tumor microenvironment to promote melanoma proliferation. bioRxiv. 2023 Sep 22:2023.09.19.558457. doi: 10.1101/2023.09.19.558457. Preprint. PMID: 37786690 [Preprint PDF] [PubMed]
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Hu M, Alkhairy S, Lee I, Pillich RT, Bachelder R, Ideker T, Pratt D. Evaluation of large language models for discovery of gene set function. ArXiv. 2023 Sep 7:arXiv:2309.04019v1. Preprint. PMID: 37731657 [Preprint PDF] [PubMed]
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Ozturk K, Panwala R, Sheen J, Ford K, Payne N, Zhang DE, Hutter S, Haferlach T, Ideker T, Mali P, Carter H. Interface-guided phenotyping of coding variants in the transcription factor RUNX1 with SEUSS. bioRxiv. 2023 Aug 4:2023.08.03.551876. doi: 10.1101/2023.08.03.551876. Preprint. PMID: 37577681 [Preprint PDF] [PubMed]
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Tagore M, Hergenreder E, Perlee SC, Cruz NM, Menocal L, Suresh S, Chan E, Baron M, Melendez S, Dave A, Chatila WK, Nsengimana J, Koche RP, Hollmann TJ, Ideker T, Studer L, Schietinger A, White RM. GABA Regulates Electrical Activity and Tumor Initiation in Melanoma. Cancer Discov. 2023 Oct 5;13(10):2270-2291. doi: 10.1158/2159-8290.CD-23-0389. PMID: 37553760 [PDF] [PubMed]
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Wright SN, Leger BS, Rosenthal SB, Liu SN, Jia T, Chitre AS, Polesskaya O, Holl K, Gao J, Cheng R, Garcia Martinez A, George A, Gileta AF, Han W, Netzley AH, King CP, Lamparelli A, Martin C, St Pierre CL, Wang T, Bimschleger H, Richards J, Ishiwari K, Chen H, Flagel SB, Meyer P, Robinson TE, Solberg Woods LC, Kreisberg JF, Ideker T, Palmer AA. Genome-wide association studies of human and rat BMI converge on synapse, epigenome, and hormone signaling networks. Cell Reports. 2023 Aug 29;42(8):112873. doi: 10.1016/j.celrep.2023.112873. Epub 2023 Jul 31. PMID: 37527041 [PDF] [PubMed]
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Carlin DE, Larsen SJ, Sirupurapu V, Cho MH, Silverman EK, Baumbach J, Ideker T. Hierarchical association of COPD to principal genetic components of biological systems. PLoS One. 2023 May 25;18(5):e0286064. doi: 10.1371/journal.pone.0286064. eCollection 2023. PMID: 37228113 [PDF] [PubMed]
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Kratz A, Kim M, Kelly MR, Zheng F, Koczor CA, Li J, Ono K, Qin Y, Churas C, Chen J, Pillich RT, Park J, Modak M, Collier R, Licon K, Pratt D, Sobol RW, Krogan NJ, Ideker T. A multi-scale map of protein assemblies in the DNA damage response. Cell Syst. 2023 May 16:S2405-4712(23)00116-3. doi: 10.1016/j.cels.2023.04.007. 22 May 2023. PMID: 37220749 [PDF] [PubMed]
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Ford K, Munson BP, Fong SH, Panwala R, Chu WK, Rainaldi J, Plongthongkum N, Arunachalam V, Kostrowicki J, Meluzzi D, Kreisberg JF, Jensen-Pergakes K, VanArsdale T, Paul T, Tamayo P, Zhang K, Bienkowska J, Mali P, Ideker T. Multimodal perturbation analyses of cyclin-dependent kinases reveal a network of synthetic lethalities associated with cell-cycle regulation and transcriptional regulation. Sci Rep. 2023 May 11;13(1):7678. doi: 10.1038/s41598-023-33329-2. PMID: 37169829 [PDF] [PubMed]
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Pillich RT, Chen J, Churas C, Fong D, Gyori BM, Ideker T, Karis K, Liu SN, Ono K, Pico A, Pratt D. NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange. Bioinformatics. 2023 Mar 1;39(3):btad118. doi: 10.1093/bioinformatics/btad118. PMID: 36882166 [PDF] [PubMed]
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Rosenthal SB, Wright SN, Liu S, Churas C, Chilin-Fuentes D, Chen CH, Fisch KM, Pratt D, Kreisberg JF, Ideker T. Mapping the common gene networks that underlie related diseases. Nat Protoc. 2023 Jun;18(6):1745-1759. doi: 10.1038/s41596-022-00797-1. Epub 2023 Jan 18. PMID: 36653526 [PDF] [PubMed]
2022
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Schantell M, Taylor BK, Spooner RK, May PE, O’Neill J, Morsey BM, Wang T, Ideker T, Bares SH, Fox HS, Wilson TW. Epigenetic aging is associated with aberrant neural oscillatory dynamics serving visuospatial processing in people with HIV. Aging (Albany NY). 2022 Dec 15;14(24):9818-9831. doi: 10.18632/aging.204437. Epub 2022 Dec 15. PMID: 36534452 [PDF] [PubMed]
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Van Oss SB, Parikh SB, Castilho Coelho N, Wacholder A, Belashov I, Zdancewicz S, Michaca M, Xu J, Kang YP, Ward NP, Yoon SJ, McCourt KM, McKee J, Ideker T, VanDemark AP, DeNicola GM, Carvunis AR. On the illusion of auxotrophy: met15Δ yeast cells can grow on inorganic sulfur, thanks to the previously uncharacterized homocysteine synthase Yll058w. J Biol Chem. 2022 Dec;298(12):102697. doi: 10.1016/j.jbc.2022.102697. Epub 2022 Nov 13. PMID: 36379252 [PDF] [PubMed]
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Li A, Koch Z, Ideker T. Epigenetic aging: Biological age prediction and informing a mechanistic theory of aging. J Intern Med. 2022 Nov;292(5):733-744. doi: 10.1111/joim.13533. Epub 2022 Jun 20. PMID: 35726002 [PDF] [PubMed] (Review)
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Kustatscher G, Collins T, Gingras AC, Guo T, Hermjakob H, Ideker T, Lilley KS, Lundberg E, Marcotte EM, Ralser M, Rappsilber J. Understudied proteins: opportunities and challenges for functional proteomics. Nat Methods. 2022 Jul;19(7):774-779. doi: 10.1038/s41592-022-01454-x. PMID: 35534633 [PDF] [PubMed]
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Kustatscher G, Collins T, Gingras AC, Guo T, Hermjakob H, Ideker T, Lilley KS, Lundberg E, Marcotte EM, Ralser M, Rappsilber J. An open invitation to the Understudied Proteins Initiative. Nat Biotechnol. 2022 Jun;40(6):815-817. doi: 10.1038/s41587-022-01316-z. PMID: 35534555 [PDF] [PubMed]
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Ottilie S, Luth MR, Hellemann E, Goldgof GM, Vigil E, Kumar P, Cheung AL, Song M, Godinez-Macias KP, Carolino K, Yang J, Lopez G, Abraham M, Tarsio M, LeBlanc E, Whitesell L, Schenken J, Gunawan F, Patel R, Smith J, Love MS, Williams RM, McNamara CW, Gerwick WH, Ideker T, Suzuki Y, Wirth DF, Lukens AK, Kane PM, Cowen LE, Durrant JD, Winzeler EA. Adaptive laboratory evolution in S. cerevisiae highlights role of transcription factors in fungal xenobiotic resistance. Commun Biol. 2022 Feb 11;5(1):128. doi: 10.1038/s42003-022-03076-7. PMID: 35149760 [PubMed] [PDF]
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Konno N, Kijima Y, Watano K, Ishiguro S, Ono K, Tanaka M, Mori H, Masuyama N, Pratt D, Ideker T, Iwasaki W, Yachie N. Deep distributed computing to reconstruct extremely large lineage trees. Nat Biotechnol. 2022 Apr;40(4):566-575. doi: 10.1038/s41587-021-01111-2. Epub 2022 Jan 6. PMID: 34992246 [PubMed] [PDF]
2021
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Fong SH, Munson BP, Ideker T. Uncovering Tumorigenesis Circuitry with Combinatorial CRISPR. Cancer Res. 2021 Dec 15;81(24):6078-6079. doi: 10.1158/0008-5472.CAN-21-3672. PMID: 34911780 [PubMed] [PDF]
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Qin Y, Huttlin EL, Winsnes CF, Gosztyla ML, Wacheul L, Kelly MR, Blue SM, Zheng F, Chen M, Schaffer LV, Licon K, Bäckström A, Vaites LP, Lee JJ, Ouyang W, Liu SN, Zhang T, Silva E, Park J, Pitea A, Kreisberg JF, Gygi SP, Ma J, Harper JW, Yeo GW, Lafontaine DLJ, Lundberg E, Ideker T. A multi-scale map of cell structure fusing protein images and interactions. Nature. 2021 Nov 24. doi: 10.1038/s41586-021-04115-9. Online ahead of print. PMID: 34819669 [PubMed] [PDF]
- Related press: “We Might Not Know Half of What’s in Our Cells, New AI Technique Reveals,” features Trey Ideker, PhD, and Yue Qin, grad student. See also GEN, SciTech Daily, ScienceDaily, The Medical News, Neuroscience News, Science Blog, Laboratory Equipment, La Jolla Light, Times of San Diego and Patch
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Zheng F*, Kelly MR*, Ramms DJ, Heintschel ML, Tao K, Tutuncuoglu B, Lee JJ, Ono K, Foussard H, Chen M, Herrington KA, Silva E, Liu SN, Chen J, Churas C, Wilson N, Kratz A, Pillich RT, Patel DN, Park J, Kuenzi B, Yu MK, Licon K, Pratt D, Kreisberg JF, Kim M, Swaney DL, Nan X, Fraley SI, Gutkind JS, Krogan NJ†, Ideker T†. Interpretation of cancer mutations using a multiscale map of protein systems. Science. 2021 Oct;374(6563):eabf3067. doi: 10.1126/science.abf3067. Epub 2021 Oct 1. PMID: 34591613 *Equal Contribution, †Co-Corresponding Authors [PubMed] [PDF]
- Related press: “Looking Beyond DNA to See Cancer with New Clarity,” features Trey Ideker, PhD. See also FierceBiotech, MSN, San Francisco Chronicle and Times of San Diego.
- Swaney DL, Ramms DJ, Wang Z, Park J, Goto Y, Soucheray M, Bhola N, Kim K, Zheng F, Zeng Y, McGregor M, Herrington KA, O’Keefe R, Jin N, VanLandingham NK, Foussard H, Von Dollen J, Bouhaddou M, Jimenez-Morales D, Obernier K, Kreisberg JF, Kim M, Johnson DE, Jura N, Grandis JR, Gutkind JS, Ideker T†, Krogan NJ†. A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity. Science. 2021 Oct;374(6563):eabf2911. doi: 10.1126/science.abf2911. Epub 2021 Oct 1. PMID: 34591642 †Co-Corresponding Authors [PubMed] [PDF]
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Kim M, Park J, Bouhaddou M, Kim K, Rojc A, Modak M, Soucheray M, McGregor MJ, O’Leary P, Wolf D, Stevenson E, Foo TK, Mitchell D, Herrington KA, Muñoz DP, Tutuncuoglu B, Chen KH, Zheng F, Kreisberg JF, Diolaiti ME, Gordan JD, Coppé JP, Swaney DL, Xia B, van ‘t Veer L, Ashworth A, Ideker T†, Krogan NJ†. A protein interaction landscape of breast cancer. Science. 2021 Oct;374(6563):eabf3066. doi: 10.1126/science.abf3066. Epub 2021 Oct 1. PMID: 34591612 †Co-Corresponding Authors [PubMed] [PDF]
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Martin-Sancho L, Tripathi S, Rodriguez-Frandsen A, Pache L, Sanchez-Aparicio M, McGregor MJ, Haas KM, Swaney DL, Nguyen TT, Mamede JI, Churas C, Pratt D, Rosenthal SB, Riva L, Nguyen C, Beltran-Raygoza N, Soonthornvacharin S, Wang G, Jimenez-Morales D, De Jesus PD, Moulton HM, Stein DA, Chang MW, Benner C, Ideker T, Albrecht RA, Hultquist JF, Krogan NJ, García-Sastre A, Chanda SK. Restriction factor compendium for influenza A virus reveals a mechanism for evasion of autophagy. Nat Microbiol. 2021 Oct;6(10):1319-1333. doi: 10.1038/s41564-021-00964-2. Epub 2021 Sep 23. PMID: 34556855 [PubMed] [PDF]
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Tanaka H, Kreisberg JF†, Ideker T†. Genetic dissection of complex traits using hierarchical biological knowledge. PLoS Comput Biol. 2021 Sep 17;17(9):e1009373. doi: 10.1371/journal.pcbi.1009373. eCollection 2021 Sep. PMID: 34534210 †Co-Corresponding Authors [PubMed] [PDF]
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Karlsson Linnér R, Mallard TT, Barr PB, Sanchez-Roige S, Madole JW, Driver MN, Poore HE, de Vlaming R, Grotzinger AD, Tielbeek JJ, Johnson EC, Liu M, Rosenthal SB, Ideker T, Zhou H, Kember RL, Pasman JA, Verweij KJH, Liu DJ, Vrieze S; COGA Collaborators, Kranzler HR, Gelernter J, Harris KM, Tucker-Drob EM, Waldman ID, Palmer AA, Harden KP, Koellinger PD, Dick DM. Multivariate analysis of 1.5 million people identifies genetic associations with traits related to self-regulation and addiction. Nat Neurosci. 2021 Oct;24(10):1367-1376. doi: 10.1038/s41593-021-00908-3. Epub 2021 Aug 26. PMID: 34446935 [PubMed] [PDF]
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Rosenthal SB, Willsey HR, Xu Y, Mei Y, Dea J, Wang S, Curtis C, Sempou E, Khokha MK, Chi NC, Willsey AJ, Fisch KM, Ideker T. A convergent molecular network underlying autism and congenital heart disease. Cell Systems. 2021 Aug 13:S2405-4712(21)00287-8. doi: 10.1016/j.cels.2021.07.009. Online ahead of print. PMID: 34411509 [PubMed] [PDF]
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Spooner RK, Taylor BK, L’Heureux E, Schantell M, Arif Y, May PE, Morsey B, Wang T, Ideker T, Fox HS, Wilson TW. Stress-induced aberrations in sensory processing predict worse cognitive outcomes in healthy aging adults. Aging (Albany NY). 2021 Aug 18;13(16):19996-20015. doi: 10.18632/aging.203433. Epub 2021 Aug 18. PMID: 34410999 [PubMed] [PDF]
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Ma J, Fong SH, Luo Y., Bakkenist CJ, Shen JP, Mourragui S, Wessels LFA, Hafner M, Sharan R, Peng J, Ideker T. Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients. Nat Cancer. 2021 Feb;2(2):233-244. doi: 10.1038/s43018-020-00169-2. Epub 2021 Jan 25. PMID: 34223192 [PubMed] [PDF] (Analysis)
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Zhang Q, Carlin D, Zhu F, Cattaneo P, Ideker T, Evans SM, Bloomekatz J, Chi NC. Unveiling Complexity and Multipotentiality of Early Heart Fields. Circulation Research. 2021 Aug 6;129(4):474-487. doi: 10.1161/CIRCRESAHA.121.318943. Epub 2021 Jun 24. PMID: 34162224 [PubMed] [PDF]
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Schaffer LV, Ideker T. Mapping the multiscale structure of biological systems. Cell Systems. 2021 Jun 16;12(6):622-635. doi: 10.1016/j.cels.2021.05.012. PMID: 34139169 [PubMed] [PDF] (Review)
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Martin-Sancho L, Lewinski MK, Pache L, Stoneham CA, Yin X, Pratt D, Churas C, Rosenthal SB, Liu S, De Jesus PD, O’Neill AM, Gounder AP, Nguyen C, Pu Y, Oom AL, Miorin L, Rodriguez-Frandsen A, Urbanowski M, Shaw ML, Chang MW, Benner C, Frieman MB, García-Sastre A, Ideker T, Hultquist JF, Guatelli J, Chanda SK. Functional Landscape of SARS-CoV-2 Cellular Restriction. Molecular Cell. 2021 Jun 17;81(12):2656-2668.e8. doi: 10.1016/j.molcel.2021.04.008. Epub 2021 Apr 13. PMID: 33930332 [PubMed] [PDF]
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J Lew B, Schantell MD, O’Neill J, Morsey B, Wang T, Ideker T, Swindells S, S Fox H, Wilson TW. Reductions in Gray Matter Linked to Epigenetic HIV-Associated Accelerated Aging. Cereb Cortex. 2021 Jul 5;31(8):3752-3763. doi: 10.1093/cercor/bhab045. PMID: 33822880 [PubMed] [PDF]
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Zheng F, Zhang S, Churas C, Pratt D, Bahar I, Ideker T. HiDeF: identifying persistent structures in multiscale ‘omics data. Genome Biol. 2021 Jan 7;22(1):21. doi: 10.1186/s13059-020-02228-4. PMID: 33413539; PMCID: PMC7789082. [PubMed] [PDF]
2020
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Kuenzi BM, Park J, Fong SH, Sanchez KS, Lee J, Kreisberg JF, Ma J, Ideker T. Predicting Drug Response and Synergy Using a Deep Learning Model of Human Cancer Cells. Cancer Cell (2020), https://doi.org/10.1016/j.ccell.2020.09.014. PMID: 33096023. [PDF] [PubMed]
- Related Press: UCSD Health, AZoLifeSciences, Med India, Health IT Analytics and ScienceDaily.
- Singhal A, Cao S, Churas C, Pratt D, Fortunato S, Zheng F, Ideker T. Multiscale community detection in Cytoscape. PLoS Comput Biol. 2020 Oct 23;16(10):e1008239. doi: 10.1371/journal.pcbi.1008239. eCollection 2020 Oct. PMID: 33095781 [PDF] [PubMed]
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Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, … Krogan NJ. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science. 2020 Oct 15:eabe9403. doi: 10.1126/science.abe9403. Online ahead of print. PMID: 33060197 [PDF] [PubMed]
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Martin-Sancho L, Lewinski MK, Pache L, Stoneham CA, Yin X, Pratt D, Churas C, Rosenthal SB, Liu S, De Jesus PD, O’Neill AM, Gounder AP, Nguyen C, Pu Y, Oom AL, Miorin L, Rodriguez-Frandsen A, Urbanowski M, Shaw ML, Chang MW, Benner C, Frieman MB, García-Sastre A, Ideker T, Hultquist JF, Guatelli J, Chanda SK. Functional Landscape of SARS-CoV-2 Cellular Restriction. bioRxiv. 2020 Sep 30:2020.09.29.319566. doi: 10.1101/2020.09.29.319566. Preprint. PMID: 33024967 [PDF] [PubMed]
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Proskovec AL, Rezich MT, O’Neill J, Morsey B, Wang T, Ideker T, Swindells S, Fox HS, Wilson TW. Association of Epigenetic Metrics of Biological Age With Cortical Thickness. JAMA Netw Open. 2020 Sep 1;3(9):e2015428. doi: 10.1001/jamanetworkopen.2020.15428. PMID: 32926115 [PDF] [PubMed]
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Ren S, Gaykalova DA, Guo T, Favorov AV, Fertig EJ, Tamayo P, Callejas-Valera JL, Allevato M, Gilardi M, Santos J, Fukusumi T, Sakai A, Ando M, Sadat S, Liu C, Xu G, Fisch KM, Wang Z, Molinolo AA, Gutkind JS, Ideker T, Koch WM, Califano JA. HPV E2, E4, E5 drive alternative carcinogenic pathways in HPV positive cancers. Oncogene. 2020 Oct;39(40):6327-6339. doi: 10.1038/s41388-020-01431-8. Epub 2020 Aug 26. PMID: 32848210 [PDF] [PubMed]
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Ochsner, S.A., Pillich, R.T. & McKenna, N.J. Consensus transcriptional regulatory networks of coronavirus-infected human cells. Sci Data 7, 314 (2020). https://doi.org/10.1038/s41597-020-00628-6 [PDF] [PubMed]
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Silva E, Michaca M, Munson B, Bean GJ, Jaeger PA, Licon K, Winzeler EA, Ideker T. Genome-Wide Dynamic Evaluation of the UV-Induced DNA Damage Response. G3 (Bethesda). 2020 Sep 2;10(9):2981-2988. doi: 10.1534/g3.120.401417. PMID: 32732306 [PDF] [PubMed]
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Tina Wang, Jianzhu Ma, Andrew N. Hogan, Samson Fong, Katherine Licon, Brian Tsui, Jason F. Kreisberg, Peter D. Adams, Anne-Ruxandra Carvunis, Danika L. Bannasch, Elaine A. Ostrander, Trey Ideker. Quantitative Translation of Dog-to-Human Aging by Conserved Remodeling of the DNA Methylome. Cell Systems. 2020 Aug 26;11(2):176-185.e6. doi: 10.1016/j.cels.2020.06.006. Epub 2020 Jul 2. PMID: 32619550 [PDF] [PubMed] *Cover Article
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Related Press: Scientific American, BBC, NPR, Washington Post, Discover Magazine, Smithsonian, New York Post, (and more!)
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Zheng F, Zhang S, Churas C, Pratt D, Bahar I, Ideker T. Decoding of persistent multiscale structures in complex biological networks.Version 2. bioRxiv. 2020 Jun 18:2020.06.16.151555. doi: 10.1101/2020.06.16.151555. Preprint. PMID: 32587977 [PDF] [PubMed]
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Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, … Krogan NJ. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020 Jul;583(7816):459-468. doi: 10.1038/s41586-020-2286-9. Epub 2020 Apr 30. PMID: 32353859 [PDF] [PubMed]
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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 in S. cerevisiae. J Cell Sci. 2020 May 22;133(10):jcs237628. doi: 10.1242/jcs.237628. PMID: 32299836 [PDF] [PubMed]
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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]
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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]
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Wiesman AI, Rezich MT, O’Neill J, Morsey B, Wang T, Ideker T, Swindells S, Fox HS, Wilson TW. Epigenetic Markers of Aging Predict the Neural Oscillations Serving Selective Attention. Cereb Cortex. 2020 Mar 14;30(3):1234-1243. doi: 10.1093/cercor/bhz162. PMID: 31504270. [PDF] [PubMed]
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Kuenzi BM, Ideker T. A census of pathway maps in cancer systems biology. Nat Rev Cancer. 2020 Apr;20(4):233-246. doi: 10.1038/s41568-020-0240-7. Epub 2020 Feb 17. PMID: 32066900 [PDF] [PubMed]
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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]
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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
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Jonathan Flint, Trey Ideker. The great hairball gambit. PLOS Genetics 15(11): e1008519. 2019 Nov 25. https://doi.org/10.1371/journal.pgen.1008519. PMID: 31770365. [PDF] [PubMed] (Opinion Piece)
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Bell CG, Lowe R, Adams PD, Baccarelli AA, Beck S, Bell JT, Christensen BC, Gladyshev VN, Heijmans BT, Horvath S, Ideker T, Issa JJ, Kelsey KT, Marioni RE, Reik W, Relton CL, Schalkwyk LC, Teschendorff AE, Wagner W, Zhang K, Rakyan VK. DNA methylation aging clocks: challenges and recommendations. Genome Biol. 2019 Nov 25;20(1):249. doi: 10.1186/s13059-019-1824-y. PMID: 31767039. [PDF] [PubMed] (Review)
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Tina Wang, Jianzhu Ma, Andrew N. Hogan, Samson Fong, Katherine Licon, Brian Tsui, Jason F. Kreisberg, Peter D. Adams, Anne-Ruxandra Carvunis, Danika L. Bannasch, Elaine A. Ostrander, Trey Ideker. Quantitative translation of dog-to-human aging by conserved remodeling of epigenetic networks. BioRxiv. 2019 Nov 4. doi: https://doi.org/10.1101/829192. [PDF] [PubMed] (Preprint) (see also: Wang, et al. BioRxiv 2019)
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Licon K, Shen JP, Munson BP, Michaca M, Fassino C, Fassino L, Kreisberg JF, Ideker T. Ultrahigh-Density Screens for Genome-Wide Yeast EMAPs in a Single Plate. 11 October 2019. In: Oliver S., Castrillo J. (eds) Yeast Systems Biology. Methods in Molecular Biology, vol 2049. Humana, New York, NY. 2019;2049:73-85. doi: 10.1007/978-1-4939-9736-7_4. PMID: 31602605. [PDF] [PubMed] (eBook PDF) (Book chapter)
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Otasek D, Morris JH, Bouças J, Pico AR, Demchak B. Cytoscape Automation: empowering workflow-based network analysis. Genome Biol. 2019 Sep 2;20(1):185. doi: 10.1186/s13059-019-1758-4. PMID: 31477170 [PDF] [PubMed]
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Chatterjee N, Pazarentzos E, Mayekar MK, Gui P, Allegakoen DV, Hrustanovic G, Olivas V, Lin L, Verschueren E, Johnson JR, Hofree M, Yan JJ, Newton BW, Dollen JV, Earnshaw CH, Flanagan J, Chan E, Asthana S, Ideker T, Wu W, Suzuki J, Barad BA, Kirichok Y, Fraser JS, Weiss WA, Krogan NJ, Tulpule A, Sabnis AJ, Bivona TG. Synthetic Essentiality of Metabolic Regulator PDHK1 in PTEN-Deficient Cells and Cancers. Cell Rep. 2019 Aug 27;28(9):2317-2330.e8. doi: 10.1016/j.celrep.2019.07.063. PMID: 31461649 [PDF] [PubMed]
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Bouhaddou M, Eckhardt M, Chi Naing ZZ, Kim M, Ideker T, Krogan NJ. Mapping the protein-protein and genetic interactions of cancer to guide precision medicine. Curr Opin Genet Dev. 2019 Jul 6;54:110-117. doi: 10.1016/j.gde.2019.04.005. [Epub ahead of print] . PMID: 31288129 [PDF] [PubMed] (Review)
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Carlin DE, Fong SH, Qin Y, Jia T, Huang JK, Bao B, Zhang C, Ideker T. A Fast and Flexible Framework for Network-Assisted Genomic Association. iScience. 2019 May 24;16:155-161. doi: 10.1016/j.isci.2019.05.025. [Epub ahead of print] PMID: 31174177 [PDF] [PubMed]
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van de Haar J, Canisius S, Yu MK, Voest EE, Wessels LFA, Ideker T. Identifying Epistasis in Cancer Genomes: A Delicate Affair. Cell. 2019 May 30;177(6):1375-1383. doi: 10.1016/j.cell.2019.05.005. PMID: 31150618 [PDF] [PubMed] (Review)
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Buckley AR, Ideker T, Carter H, Schork NJ. Rare variant phasing using paired tumor:normal sequence data. BMC Bioinformatics. 2019 May 27;20(1):265. doi: 10.1186/s12859-019-2753-1. PMID: 31132991 [PDF] [PubMed]
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Silva E, Ideker T. Transcriptional responses to DNA damage. DNA Repair (Amst). 2019 Jul;79:40-49. doi: 10.1016/j.dnarep.2019.05.002. Epub 2019 May 7. PMID: 31102970 [PDF] [PubMed] (Review)
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Ando M, Saito Y, Xu G, Bui NQ, Medetgul-Ernar K, Pu M, Fisch K, Ren S, Sakai A, Fukusumi T, Liu C, Haft S, Pang J, Mark A, Gaykalova DA, Guo T, Favorov AV, Yegnasubramanian S, Fertig EJ, Ha P, Tamayo P, Yamasoba T, Ideker T, Messer K, Califano JA. Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers. Nat Commun. 2019 May 16;10(1):2188. doi: 10.1038/s41467-019-09937-w. Erratum in: Nat Commun. 2019 May 29;10(1):2415. PMID: 31097695 [PDF] [PubMed]
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Fong SH, Carlin DE, Ozturk K; 2018 UCSD Network Biology Class, Ideker T. Strategies for Network GWAS Evaluated Using Classroom Crowd Science. Cell Syst. 2019 Apr 24;8(4):275-280. doi: 10.1016/j.cels.2019.03.013. PMID: 31022372 [PDF] [PubMed] (Corrected Author List, 23 Oct 2019)
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Lytle NK, Ferguson LP, Rajbhandari N, Gilroy K, Fox RG, Deshpande A, Schürch CM, Hamilton M, Robertson N, Lin W, Noel P, Wartenberg M, Zlobec I, Eichmann M, Galván JA, Karamitopoulou E, Gilderman T, Esparza LA, Shima Y, Spahn P, French R, Lewis NE, Fisch KM, Sasik R, Rosenthal SB, Kritzik M, Von Hoff D, Han H, Ideker T, Deshpande AJ, Lowy AM, Adams PD, Reya T. A Multiscale Map of the Stem Cell State in Pancreatic Adenocarcinoma. Cell. 2019 Mar 29. pii: S0092-8674(19)30272-7. doi:10.1016/j.cell.2019.03.010. [Epub ahead of print] PMID: 30955884 [PDF] [PubMed]
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Yu MK, Ma J, Ono K, Zheng F, Fong SH, Gary A, Chen J, Demchak B, Pratt D, Ideker T. DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies. Cell Syst. 2019 Mar 27;8(3):267-273.e3. doi: 10.1016/j.cels.2019.02.003. Epub 2019 Mar 13. PMID: 30878356 [PDF] [PubMed]
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Wallace ZS, Rosenthal SB, Fisch KM, Ideker T, Sasik R. On entropy and information in gene interaction networks. Bioinformatics. 2019 Mar 1;35(5):815-822. doi: 10.1093/bioinformatics/bty691. PMID: 30102349 [PDF] [PubMed]
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Ideker T, Hood L. A Blueprint for Systems Biology. Clin Chem. 2019 Feb;65(2):342-344. doi: 10.1373/clinchem.2018.291062. Epub 2018 Dec 28. Review. PMID: 30593465 [PDF] [PubMed] (Review)
2018
- van Welsem T, Korthout T, Ekkebus R, Morais D, Molenaar TM, van Harten K, Poramba-Liyanage DW, Sun SM, Lenstra TL, Srivas R, Ideker T, Holstege FCP, van Attikum H, El Oualid F, Ovaa H, Stulemeijer IJE, Vlaming H, van Leeuwen F. Dot1 promotes H2B ubiquitination by a methyltransferase-independent mechanism. Nucleic Acids Res. 2018 Nov 30;46(21):11251-11261. doi: 10.1093/nar/gky801. PMID: 30203048 [PDF][PubMed]
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Wang S, Ma J, Zhang W, Shen JP, Huang J, Peng J, Ideker T. Typing tumors using pathways selected by somatic evolution. Nat Commun. 2018 Oct 8;9(1):4159. doi: 10.1038/s41467-018-06464-y. PMID: 30297789 [PDF][PubMed]
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Field AE, Robertson NA, Wang T, Havas A, Ideker T, Adams PD. DNA Methylation Clocks in Aging: Categories, Causes, and Consequences. Mol Cell. 2018 Sep 20;71(6):882-895. doi: 10.1016/j.molcel.2018.08.008. Review. PMID: 30241605 [PDF][PubMed] (Review)
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Barry Demchak, Jason F. Kreisberg, Juan I. Fuxman Bass. Special Issue: Theory and Application of Network Biology Toward Precision Medicine.* Journal of Molecular Biology. Volume 430, Issue 18, Part A, Pages 2873-3028 (14 September 2018) [PDF][PubMed] [Flyer] (Review)
- *Special Issue, Edited by Barry Demchak, Jason F. Kreisberg, Juan I. Fuxman Bass.
- *Cover art by Kivilcim Ozturk, Michelle Dow and Hannah Carter.
- Kivilcim Ozturk, Michelle Dow, Daniel E. Carlin, Rafael Bejar and Hannah Carter. The Emerging Potential for Network Analysis to Inform Precision Cancer Medicine.* Journal of Molecular Biology. Volume 430, Issue 18, Part A, Pages 2875–2899 (14 September 2018) [PDF] [PubMed] [Flyer] (Review)
- *Special Issue, Edited by Barry Demchak, Jason F. Kreisberg, Juan I. Fuxman Bass.
- *Cover art by Kivilcim Ozturk, Michelle Dow and Hannah Carter.
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Shen JP, Ideker T. Synthetic Lethal Networks for Precision Oncology: Promises and Pitfalls.* Journal of Molecular Biology. Volume 430, Issue 18, Part A, Pages 2900–2912 (14 September 2018). [Epub ahead of print: 2018 Jun 19] doi: 10.1016/j.jmb.2018.06.026. PMID: 29932943 [PDF] [PubMed] (Review)
- *Special Issue, Edited by Barry Demchak, Jason F. Kreisberg, Juan I. Fuxman Bass.
- *Cover art by Kivilcim Ozturk, Michelle Dow and Hannah Carter.
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Buckley AR, Ideker T, Carter H, Harismendy O, Schork NJ. Exome-wide analysis of bi-allelic alterations identifies a Lynch phenotype in The Cancer Genome Atlas. Genome Med. 2018 Sep 14;10(1):69. doi: 10.1186/s13073-018-0579-5. PMID: 30217226 [PDF] [PubMed]
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Eckhardt M, Zhang W, Gross AM, Von Dollen J, Johnson JR, Franks-Skiba KE, Swaney DL, Johnson TL, Jang GM, Shah PS, Brand TM, Archambault J, Kreisberg JF, Grandis JR, Ideker T, Krogan NJ. Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus-Host Protein Network. Cancer Discov. 2018 Nov;8(11):1474-1489. doi: 10.1158/2159-8290.CD-17-1018. Epub 2018 Sep 12. PMID: 30209081 [PDF] [PubMed]
- Ang CS, Shen JP, Hardy-Abeloos CJ, Huang JK, Ross JS, Miller VA, Jacobs MT, Chen IL, Xu D, Ali SM, Baumgartner J, Lowy A, Fanta P, Ideker T, Millis SZ, Harismendy O. Genomic Landscape of Appendiceal Neoplasms. JCO Precis Oncol. 2018 Aug 8;2:PO.17.00302. doi: 10.1200/PO.17.00302. eCollection 2018.
PMID: 32913983 [PDF] [PubMed] -
Willsey AJ, Morris MT, Wang S, Willsey HR, Sun N, Teerikorpi N, Baum TB, Cagney G, Bender KJ, Desai TA, Srivastava D, Davis GW, Doudna J, Chang E, Sohal V, Lowenstein DH, Li H, Agard D, Keiser MJ, Shoichet B, von Zastrow M, Mucke L, Finkbeiner S, Gan L, Sestan N, Ward ME, Huttenhain R, Nowakowski TJ, Bellen HJ, Frank LM, Khokha MK, Lifton RP, Kampmann M, Ideker T, State MW, Krogan NJ. The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders. Cell. 2018 Jul 26;174(3):505-520. doi: 10.1016/j.cell.2018.06.016. Review. PMID: 30053424 [PDF] [PubMed] (Review)
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Zhang W, Ma J, Ideker T. Classifying tumors by supervised network propagation. Bioinformatics. 2018 Jul 1;34(13):i484-i493. doi: 10.1093/bioinformatics/bty247. Erratum in: Bioinformatics. 2019 Feb 4;35(14):2528. PMID: 29949979 [PDF] [PubMed]
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Demchak B, Otasek D, Pico AR, Bader GD, Ono K, Settle B, Sage E, Morris JH, Longabaugh W, Lopes C, Kucera M, Treister A, Schwikowski B, Molenaar P, Ideker T. The Cytoscape Automation app article collection. F1000Res. 2018 Jun 20;7:800. doi: 10.12688/f1000research.15355.1. eCollection 2018. PMID: 29983926 [PDF] [PubMed] (Review)
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Yu MK, Ma J, Fisher J, Kreisberg JF, Raphael BJ, Ideker T. Visible Machine Learning for Biomedicine. CELL. Volume 173, Issue 7, 14 June 2018, Pages 1562–1565. doi: https://doi.org/10.1016/j.cell.2018.05.056 [PDF] [PubMed](Review)
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Zhang W, Bojorquez-Gomez A, Velez DO, Xu G, Sanchez KS, Shen JP, Chen K, Licon K, Melton C, Olson KM, Yu MK, Huang JK, Carter H, Farley EK, Snyder M, Fraley SI, Kreisberg JF, Ideker T. A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. Nat Genet. 2018 Apr 2. doi: 10.1038/s41588-018-0091-2. PMID: 29610481. [PDF] [PubMed]
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Bui N, Huang JK, Bojorquez-Gomez A, Licon K, Sanchez KS, Tang SN, Beckett AN, Wang T, Zhang W, Shen JP, Kreisberg JF, Ideker T. Disruption of NSD1 in head and neck cancer promotes favorable chemotherapeutic responses linked to hypomethylation. Mol Cancer Ther. 2018 Jul;17(7):1585-1594. doi: 10.1158/1535-7163.MCT-17-0937. Epub 2018 Apr 10. PMID: 29636367 [PDF] [PubMed]
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Huang JK, Jia T, Carlin DE, Ideker T. pyNBS: A Python implementation for network-based stratification of tumor mutations. Bioinformatics. 2018 Mar 28. doi: 10.1093/bioinformatics/bty186. PMID: 29608663 [PDF] [PubMed]
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Huang JK, Carlin DE, Yu MK, Zhang W, Kreisberg JF, Tamayo P, Ideker T. Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. Cell Syst. 2018 Mar 26. pii: S2405-4712(18)30095-4. doi: 10.1016/j.cels.2018.03.001. PMID: 29605183 [PDF] [PubMed]
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Ma J, Yu MK, Fong S, Ono K, Sage E, Demchak B, Sharan R, Ideker T. Using deep learning to model the hierarchical structure and function of a cell. Nat Methods. 2018 Mar 5. doi: 10.1038/nmeth.4627. PMID: 29505029 [PDF] [PubMed] *Cover Article
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Zhao D, Badur MG, Luebeck J, Magaña JH, Birmingham A, Sasik R, Ahn CS, Ideker T, Metallo CM, Mali P. Combinatorial CRISPR-Cas9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP1-NRF2 Regulatory Axis. Mol Cell. 2018 Feb 15;69(4):699-708.e7. doi: 10.1016/j.molcel.2018.01.017. PMID: 29452643 [PDF] [PubMed]
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Auer F, Hammoud Z, Ishkin A, Pratt D, Ideker T, Kramer F. ndexr-an R package to interface with the network data exchange. Bioinformatics. 2018 Feb 15;34(4):716-717. doi: 10.1093/bioinformatics/btx683. PMID: 29087446 [PDF] [PubMed]
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Jaeger PA, Ornelas L, McElfresh C, Wong LR, Hampton RY, Ideker T. Systematic Gene-to-Phenotype Arrays: A High-Throughput Technique for Molecular Phenotyping. Mol Cell. 2018 Jan 18;69(2):321-333.e3. doi: 10.1016/j.molcel.2017.12.016. PMID: 29351850 [PDF] [PubMed]
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Neal S, Jaeger PA, Duttke SH, Benner C, Glass CK, Ideker T, Hampton RY. The Dfm1 Derlin Is Required for ERAD Retrotranslocation of Integral Membrane Proteins. Mol Cell. 2018 Jan 18;69(2):306-320.e4. doi: 10.1016/j.molcel.2017.12.012. PMID: 29351849 [PDF] [PubMed]
2017
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Moder M, Velimezi G, Owusu M, Mazouzi A, Wiedner M, Ferreira da Silva J, Robinson-Garcia L, Schischlik F, Slavkovsky R, Kralovics R, Schuster M, Bock C, Ideker T, Jackson SP, Menche J, Loizou JI. Parallel genome-wide screens identify synthetic viable interactions between the BLM helicase complex and Fanconi anemia. Nat Commun. 2017 Nov 1;8(1):1238. doi: 10.1038/s41467-017-01439-x. PMID: 29089570 [PDF] [PubMed]
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Pratt D, Chen J, Pillich R, Rynkov V, Gary A, Demchak B, Ideker T. NDEx 2.0: A Clearinghouse for Research on Cancer Pathways. Cancer Res. 2017 Nov 1;77(21):e58-e61. doi: 10.1158/0008-5472.CAN-17-0606. PMID: 29092941 [PDF] [PubMed] (Review)
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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]
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Carlin DE, Demchak B, Pratt D, Sage E, Ideker T. Network propagation in the cytoscape cyberinfrastructure. PLoS Comput Biol. 2017 Oct;13(10):e1005598. doi: 10.1371/journal.pcbi.1005598. eCollection 2017 Oct. PubMed PMID: 29023449; PubMed Central PMCID: PMC5638226. [PDF] [PubMed]
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Ideker T, Nussinov R. Network approaches and applications in biology. PLoS Comput Biol. 2017 Oct;13(10):e1005771. doi: 10.1371/journal.pcbi.1005771. eCollection 2017 Oct. PubMed PMID: 29023447; PubMed Central PMCID: PMC5638228. [PDF] [PubMed] (Editorial)
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Farré JC, Kramer M, Ideker T, Subramani S. Active Interaction Mapping as a tool to elucidate hierarchical functions of biological processes. Autophagy. 2017 Jul 3;13(7):1248-1249. doi: 10.1080/15548627.2017.1313946. Epub 2017 May 9. PMID: 28486053 [PDF] [PubMed] (Review)
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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]
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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]
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Cowen L, Ideker T, Raphael BJ, Sharan R. Network propagation: a universal amplifier of genetic associations. Nature Reviews Genetics. 2017 Jun 12. doi:10.1038/nrg.2017.38 [PDF] [PubMed] (Review)
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Carlin D, Kosnicki K, Garamszegi S et al. A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression. F1000Research. 06 Jun 2017, 6:784 (doi: 10.12688/f1000research.11616.1) [PDF] [PubMed]
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Huan T, Forsberg EM, Rinehart D, Johnson CH, Ivanisevic J, Benton HP, Fang M, Aisporna A, Hilmers B, Poole FL, Thorgersen MP, Adams MWW, Krantz G, Fields MW, Robbins PD, Niedernhofer LJ, Ideker T, Majumder EL, Wall JD, Rattray NJW, Goodacre R, Lairson LL, Siuzdak G. Systems biology guided by XCMS Online metabolomics. Nat Methods. 2017 Apr 27;14(5):461-462. doi: 10.1038/nmeth.4260. PMID: 28448069 [PDF] [PubMed] (Review)
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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]
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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]
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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]
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Networks and visualizations: 293T_SyntheticLethal; A549_SyntheticLethal; HeLa_SyntheticLethal
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Source code: http://ideker.ucsd.edu/papers/rsasik2017/
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Carter H, Ideker T. Common genetic variation in the germline influences where and how tumors develop. Mol Cell Oncol. 2017 Mar 10;4(3):e1302905. doi: 10.1080/23723556.2017.1302905. eCollection 2017. PMID: 28616579 [PDF] [PubMed] (Review)
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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] *Cover article
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Cover article: About the Cover
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Data generated by the TCGA Research Network: http://cancergenome.nih.gov/
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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]
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See [Datasets]
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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
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Ideker T. The Real Value of an Atlas. NIH Biomedical Informatics Blog. 31 Oct 2016. [PDF] (Review)
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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]
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Spira A, Disis ML, Schiller JT, Vilar E, Rebbeck TR, Bejar R, Ideker T, Arts J, Yurgelun MB, Mesirov JP, Rao A, Garber J, Jaffee EM, Lippman SM. Leveraging premalignant biology for immune-based cancer prevention. Proc Natl Acad Sci U S A. 2016 Sep 27;113(39):10750-8. doi: 10.1073/pnas.1608077113. Epub 2016 Sep 16. PubMed PMID: 27638202; PubMed Central PMCID: PMC5047191. [PDF] [PubMed]
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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]
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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]
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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]
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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]
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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]
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Tutorial for implementing Hannum, et al., MOL CELL (2013): GitHub Source Code
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Meet the Author: Interview with Andy Gross
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Press: NPR Health: People Who Are HIV-Positive May Be Aging Faster Than Their Peers
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Press: NIH Science News: Biomarker Tracks Accelerated HIV-Associated Aging
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Press: UCSD Health: HIV Infection Prematurely Ages People by an Average of Five Years
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Ono, Kei. Technical aspects of “Panama Papers” analysis. Newsweek Japan, 12 April 2016. [PDF] (Review)
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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
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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]
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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
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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)
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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]
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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]
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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. [PDF] [PubMed] (Review)
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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]
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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
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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]
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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]
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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)
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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)
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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)
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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)
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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]
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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)
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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]
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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]
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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]
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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]
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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]
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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]
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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)
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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
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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]
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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
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Data: Quantitative genetic interaction profiles [Data]
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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]
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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]
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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)
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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)
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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)
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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
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Tutorial for implementing Hannum, et al., MOL CELL (2013): https://github.com/theandygross/HIV_Methylation
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Data sets: http://ideker.ucsd.edu/papers/ghannum2013/
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Bisulphite converted DNA from the 656 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. GEO Data Set: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40279
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2012
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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
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Jaeger P, Doherty C, Ideker T. Modeling Transcriptome Dynamics in a Complex World, Cell, Volume 151, Issue 6, 1161-1162, 7 December 2012. [PDF] [PubMed] (Review Article)
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Bean GJ, Ideker T. Differential analysis of high-throughput quantitative genetic interaction data. Genome Biol. 2012 Dec 26;13(12):R123. [PDF] [PubMed]
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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. [PDF] [PubMed] (Review Article)
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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]
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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. [PDF] [PubMed] (Review Article)
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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
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Supplemental Figures, Methods and Data [Suppl. Data]
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Expression data from untreated CLL patients [GEO Data Set]
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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]
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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]
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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]
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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]
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Ideker T, Krogan NJ. Differential network biology. Molecular Systems Biology. 2012 Jan 17;8:565. doi: 10.1038/msb.2011.99. [PDF] [PubMed] (Review Article)
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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
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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]
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Dutkowski J., Ideker T. Protein networks as logic functions in development and cancer. PLoS Comput Biol. 7(9) (2011). [PDF][PubMed]
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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]
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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]
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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]
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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]
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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)
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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
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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. Data]
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Differential epistasis mapping (dE-MAP) [Data]
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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]
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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]
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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] [Suppl. Docs]
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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]
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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]
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Expression profiles of three yeast species after exposure to fluconazole. [Data]
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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]
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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]
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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]
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Protein sub-cellular localization in A. taliana [Data]
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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]
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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]
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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]
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Targeting Interactions in Chromatin. [Data]
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Bandyopadhyay, S. and Ideker T. Integrative systems biology. Nature Genetics 42(12) (2010). [Poster] (Review Article)
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Chuang HY, Hofree M, Ideker T. A decade of systems biology. Annual Review of Cell and Developmental Biology(2010). [PDF] [PubMed] (Review Article)
2009
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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]
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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]
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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]
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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]
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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]
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Enrichment Summary: Differentially expressed or sensitive members of each significantly over-represented condition or transcription factor target set mentioned in the study. [Data Set]
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Expression Table: Log ratios and p-values for all micro-array expression profiling experiments conducted in this study. [Data Set]
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Fitness Table: P-values for acute and adaptive screens conducted in this study. [Data Set]
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TFs Table: Table containing all of the transcription factor target sets used in this study. [Data Set]
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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]
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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]
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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]
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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]
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Ideker T. Book Review: “Wetware: A Computer in Every Living Cell” by Dennis Bray. Cell 138: 820-821 (2009) (Review Article)
2008
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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]
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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]
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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]
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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]
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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
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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]
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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]
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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]
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Data: Chip-chip of five YAPs in each drug-treated (MMS or CDDP) and untreated (SC media) conditions [Data Set]
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Kalaev M, Smoot M, Ideker T, Sharan R. NetworkBLAST: comparative analysis of protein networks. Bioinformatics. 24(4):594-6 (2008). [PDF] [PubMed]
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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]
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Ideker T. Forging new ties between E. coli genes. Cell. 133: 3-5 (2008). [PDF] [PubMed] (Review Article)
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Ideker T, Sharan R. Protein networks in disease. Genome Research. 18(4): 644-52 (2008). [PDF] [PubMed] (Review Article)
2007
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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] [PubMed]
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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] [PubMed]
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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]
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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]
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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]
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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 (2007). [PDF] [PubMed]
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Ideker T, Bafna V, Lemberger T. Integrating scientific cultures. Molecular Systems Biology 3:105. Epub Apr 17 (2007). [PDF] [PubMed] (Review Article)
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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). [PDF] [PubMed](Review Article)
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Ideker TE. Network genomics. Ernst Schering Res Found Workshop. (61):89-115. Review. (2007). [PDF] [PubMed] (Review Article)
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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
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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]
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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] [PubMed]
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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]
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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]
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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]
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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] [Suppl. Info.]
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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]
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Bandyopadhyay S, Sharan R, Ideker T. Systematic identification of functional orthologs based on protein network comparison. Genome Res. 16(3):428-35. (2006). [PDF] [PubMed] (Cover Article)
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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]
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Ideker, T., Valencia, A. Bioinformatics in the human interactome project. Bioinformatics. 22(24):2973-4. Dec 15 (2006). [PDF] [PubMed] (Review Article)
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Ideker T, Winslow LR, Lauffenburger DA. Bioengineering and systems biology. Annals of Biomedical Engineering. Jul;34(7):1226-33. Review. (2006). [PDF] [PubMed] (Review Article)
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Sharan, R., and Ideker, T. Modeling cellular machinery through biological network comparison. Nature Biotechnology. Review. 24(4):427-33. Apr (2006). [PDF] [PubMed] (Review Article)
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Warner, G.J., Adeleye, Y.A., Ideker, T. Interactome networks: the state of the science. Genome Biol. Review. 7(1):301. Jan 23 (2006). [PDF] [PubMed] (Review Article)
2005
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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.]
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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]
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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] [Suppl. Info.]
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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]
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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]
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Kelley, R. and Ideker, T. Systematic interpretation of genetic interactions using protein networks. Nature Biotechnology 23(5):561-566 (2005). [PDF] [PubMed]
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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]
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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]
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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]
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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
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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]
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Yeang CH, Ideker T, Jaakkola T. Physical network models. J Comput Biol. 11(2-3):243-62. (2004). [PDF] [PubMed]
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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]
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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]
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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). [PDF] [PubMed]
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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). [PDF] [PubMed] (Review Article)
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Ideker, T. Systems biology 101–what you need to know. Nature Biotechnology 22(4): 473-5 (2004). [PDF] [PubMed] (Review Article)
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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]
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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]
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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]
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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]
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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). [PDF] [PubMed] (Review Article)
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Ideker, T., Ozier, O., Schwikowski, B., and Siegel, A. Discovering regulatory and signaling circuits in molecular interaction networks. Bioinformatics 18: S233 (2002). [PDF] [PubMed]
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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]
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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]
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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]
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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]
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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]
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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]
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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). [PDF] [PubMed] (Review Article)
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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]
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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]
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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]
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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]