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, Dr. Ideker’s publications may also be viewed at –
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. Nat Genet. 2025 Apr 16. doi: 10.1038/s41588-025-02163-9. Online ahead of print. PMID: 40240879 [PubMed] [PDF]
Schaffer LV, Hu M, Qian G, Moon KM, Pal A, Soni N, Latham AP, Pontano Vaites L, Tsai D, Mattson NM, Licon K, Bachelder R, Cesnik A, Gaur I, Le T, Leineweber W, Palar A, Pulido E, Qin Y, Zhao X, Churas C, Lenkiewicz J, Chen J, Ono K, Pratt D, Zage P, Echeverria I, Sali A, Harper JW, Gygi SP, Foster LJ, Huttlin EL, Lundberg E, Ideker T. Multimodal cell maps as a foundation for structural and functional genomics. Nature. 2025 Apr 9. doi: 10.1038/s41586-025-08878-3. Online ahead of print. PMID: 40205054 [PubMed] [PDF]
Mei Y, Gosztyla ML, Tan X, Dozier LE, Wilkinson B, McKetney J, Lee J, Chen M, Tsai D, Kopalle H, Gritsenko MA, Hartel N, Graham NA, Flores I, Gilmore-Hall SK, Xu S, Marquez CA, Liu SN, Fong D, Chen J, Licon K, Hong D, Wright SN, Kreisberg JF, Nott A, Smith RD, Qian WJ, Swaney DL, Iakoucheva LM, Krogan NJ, Patrick GN, Zhou Y, Feng G, Coba MP, Yeo GW, Ideker T. Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders. Cell Syst. 2025 Mar 3:101204. doi: 10.1016/j.cels.2025.101204. Online ahead of print. PMID: 40054464 [PubMed] [PDF]
Koch Z, Li A, Evans DS, Cummings S, Ideker T. Somatic mutation as an explanation for epigenetic aging. Nat Aging. 2025 Jan 13. doi: 10.1038/s43587-024-00794-x. Online ahead of print. PMID: 39806003 [PubMed] [PDF]
Begzati A, Godinez-Macias KP, Long T, Watrous JD, Moranchel R, Kantz ED, Tuomilehto J, Havulinna AS, Niiranen TJ, Jousilahti P, Salomaa V, Yu B, Norby F, Rebholz CM, Selvin E, Winzeler EA, Cheng S, Alotaibi M, Goyal R, Ideker T, Jain M, Majithia AR. Plasma Lipid Metabolites, Clinical Glycemic Predictors, and Incident Type 2 Diabetes. Diabetes Care. 2025 Jan 6:dc242266. doi: 10.2337/dc24-2266. Online ahead of print. PMID: 39761415 [PubMed] [PDF]
Singhal A, Zhao X, Wall P, So E, Calderini G, Partin A, Koussa N, Vasanthakumari P, Narykov O, Zhu Y, Jones SE, Abbas-Aghababazadeh F, Kadambat Nair S, Bélisle-Pipon JC, Jayaram A, Parker BA, Yeung KT, Griffiths JI, Weil R, Nath A, Haibe-Kains B, Ideker T. The Hallmarks of Predictive Oncology. Cancer Discovery. 2025 Jan 6:OF1-OF15. doi: 10.1158/2159-8290.CD-24-0760. Online ahead of print. PMID: 39760657 [PubMed] [PDF] (Review)
Wright SN, Colton S, Schaffer LV, Pillich RT, Churas C, Pratt D, Ideker T. State of the interactomes: an evaluation of molecular networks for generating biological insights. Mol Syst Biol. 2025 Jan;21(1):1-29. doi: 10.1038/s44320-024-00077-y. Epub 2024 Dec 9. PMID: 39653848 [PubMed] [PDF]
Fong SH. A blueprint to discovering synthetic lethal gene interactions for precision oncology. Nature Genetics. 2024 Dec 3. https://doi.org/10.1038/s41588-024-02024-x [PDF] (Research Briefing to accompany Fong, et al. Nature Genetics. 2024 Nov)
Turnham RE, Pitea A, Jang GM, Xu Z, Lim HC, Choi AL, Von Dollen J, Levin RS, Webber JT, McCarthy E, Hu J, Li X, Che L, Singh A, Yoon A, Chan G, Kelley RK, Swaney DL, Zhang W, Bandyopadhyay S, Theis FJ, Eckhardt M, Chen X, Shokat KM, Ideker T, Krogan NJ, Gordan JD. HBV Remodels PP2A Complexes to Rewire Kinase Signaling in Hepatocellular Carcinoma. Cancer Res. 2024 Dec 9. doi: 10.1158/0008-5472.CAN-24-0456. Online ahead of print. PMID: 39652575 [PubMed] [PDF]
Hu M, Alkhairy S, Lee I, Pillich RT, Fong D, Smith K, Bachelder R, Ideker T, Pratt D. Evaluation of large language models for discovery of gene set function. Nat Methods. 2024 Nov 28. doi: 10.1038/s41592-024-02525-x. Online ahead of print. PMID: 39609565 [PubMed] [PDF]
Fong SH, Kuenzi BM, Mattson NM, Lee J, Sanchez K, Bojorquez-Gomez A, Ford K, Munson BP, Licon K, Bergendahl S, Shen JP, Kreisberg JF, Mali P, Hager JH, White MA, Ideker T. A multilineage screen identifies actionable synthetic lethal interactions in human cancers. Nature Genetics. 2024 Nov 18. doi: 10.1038/s41588-024-01971-9. Online ahead of print. PMID: 39558023 [PubMed] [PDF]
Hu M, Ideker T. Putting proteins in context. Cell Systems. 2024 Nov 28. doi: 10.1038/s41592-024-02525-x. Online ahead of print. PMID: 39609565 [PubMed] [PDF] (Review)
Kong J, Zhao X, Singhal A, Park S, Bachelder R, Shen J, Zhang H, Moon J, Ahn C, Ock CY, Carter H, Ideker T. Prediction of immunotherapy response using mutations to cancer protein assemblies. Science Advances. 2024 Sep 20;10(38):eado9746. doi: 10.1126/sciadv.ado9746. Epub 2024 Sep 20. PMID: 39303028 [PubMed] [PDF]
Nasser R, Schaffer LV, Ideker T, Sharan R. Multi-modal contrastive learning of subcellular organization using DICE. Bioinformatics. 2024 Sep 1;40(Suppl 2):ii105-ii110. doi: 10.1093/bioinformatics/btae387. PMID: 39230695 [PubMed] [PDF]
Megagiannis P*, Mei Y*, Yan RE, Yuan L, Wilde JJ, Eckersberg H, Suresh R, Tan X, Chen H, Farmer WT, Cha K, Le PU, Catoire H, Rochefort D, Kwan T, Yee BA, Dion P, Krishnaswamy A, Cloutier JF, Stifani S, Petrecca K, Yeo GW, Murai KK, Feng G, Rouleau GA, Ideker T, Sanjana NE, Zhou Y. Autism-associated CHD8 controls reactive gliosis and neuroinflammation via remodeling chromatin in astrocytes. Cell Reports. 2024 Aug 27;43(8):114637. doi: 10.1016/j.celrep.2024.114637. Epub 2024 Aug 17. PMID: 39154337 [PubMed] [PDF] *Equal Contribution
Cesnik A*, Schaffer LV*, Gaur I, Jain M, Ideker T, Lundberg E. Mapping the Multiscale Proteomic Organization of Cellular and Disease Phenotypes. Annu Rev Biomed Data Sci. 2024 Aug;7(1):369-389. doi: 10.1146/annurev-biodatasci-102423-113534. Epub 2024 Jul 24. PMID: 38748859 *Equal Contribution [PubMed] [PDF] (Review)
Ozturk K, Panwala R, Sheen J, Ford K, Jayne N, Portell A, Zhang DE, Hutter S, Haferlach T, Ideker T, Mali P, Carter H. Interface-guided phenotyping of coding variants in the transcription factor RUNX1. Cell Reports. 2024 Jul 4;43(7):114436. doi: 10.1016/j.celrep.2024.114436. Online ahead of print. PMID: 38968069 [PubMed] [PDF]
Yin X, Pu Y, Yuan S, Pache L, Churas C, Weston S, Riva L, Simons LM, Cisneros WJ, Clausen T, De Jesus PD, Kim HN, Fuentes D, Whitelock J, Esko J, Lord M, Mena I, García-Sastre A, Hultquist JF, Frieman MB, Ideker T, Pratt D, Martin-Sancho L, Chanda SK. Global siRNA Screen Reveals Critical Human Host Factors of SARS-CoV-2 Multicycle Replication. bioRxiv [Preprint]. 2024 Jul 10:2024.07.10.602835. doi: 10.1101/2024.07.10.602835. PMID: 39026801 [PubMed]
Park S*, Silva E*, Singhal A*, Kelly MR, Licon K, Panagiotou I, Fogg C, Fong S, Lee JJY, Zhao X, Bachelder R, Parker BA, Yeung KT, Ideker T. A deep learning model of tumor cell architecture elucidates response and resistance to CDK4/6 inhibitors. Nat Cancer. 2024 Jul;5(7):996-1009. doi: 10.1038/s43018-024-00740-1. Epub 2024 Mar 5. PMID: 38443662; PMCID: PMC11286358. *Equal Contribution [PubMed] [PDF]
Wall P, Ideker T. Representing mutations for predicting cancer drug response. Bioinformatics. 2024 Jun 28;40(Supplement_1):i160-i168. doi: 10.1093/bioinformatics/btae209. PMID: 38940147 [PubMed] [PDF]
Leger BS, Meredith JJ, Ideker T, Sanchez-Roige S, Palmer AA. Rare and common variants associated with alcohol consumption identify a conserved molecular network. Alcohol, Clinical and Experimental Research. 21 June 2024 https://doi.org/10.1111/acer.15399 [PubMed] [PDF]
Jado JC*, Dow M*, Carolino K, Klie A, Fonseca GJ, Ideker T, Carter H, Winzeler EA. In vitro evolution and whole genome analysis to study chemotherapy drug resistance in haploid human cells. Sci Rep. 2024 Jun 18;14(1):13989. doi: 10.1038/s41598-024-63943-7. PMID: 38886371 *Equal Contribution [PubMed] [PDF]
Clark T†, Mohan J, Schaffer L, Obernier K, Al Manir S, Churas CP, Dailamy A, Doctor Y, Forget A, Hansen JN, Hu M, Lenkiewicz J, Levinson MA, Marquez C, Nourreddine S, Niestroy J, Pratt D, Qian G, Thaker S†, Bélisle-Pipon JC, Brandt C†, Chen J†, Ding Y†, Fodeh S†, Krogan N†, Lundberg E†, Mali P†, Payne-Foster P†, Ratcliffe S†, Ravitsky V†, Sali A†, Schulz W†, Ideker T. Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines. bioRxiv [Preprint]. 2024 May 24:2024.05.21.589311. doi: 10.1101/2024.05.21.589311. PMID: 38826258 †Co-Corresponding Authors [bioRxiv] [PDF] (Preprint)
Munson BP, Chen M, Bogosian A, Kreisberg JF, Licon K, Abagyan R, Kuenzi BM, Ideker T. De novo generation of multi-target compounds using deep generative chemistry. Nat Commun. 2024 May 6;15(1):3636. doi: 10.1038/s41467-024-47120-y. PMID: 38710699 [PubMed] [PDF]
Wright SN, Colton S, Schaffer LV, Pillich RT, Churas C, Pratt D, Ideker T. State of the Interactomes: an evaluation of molecular networks for generating biological insights. bioRxiv [Preprint]. 2024 Apr 29:2024.04.26.587073. doi: 10.1101/2024.04.26.587073. PMID: 38746239. [PubMed] [PDF] (Preprint)
Hu M, Alkhairy S, Lee I, Pillich RT, Fong D, Smith K, Bachelder R, Ideker T, Pratt D. Evaluation of large language models for discovery of gene set function. ArXiv [Preprint]. 2024 Apr 1:arXiv:2309.04019v2. PMID: 37731657 [PubMed] [PDF](Preprint)
Zhao X*, Singhal A*, Park S, Kong J, Bachelder R, Ideker T. Cancer mutations converge on a collection of protein assemblies to predict resistance to replication stress. Cancer Discovery. 2024 Mar 1;14(3):508-523. doi: 10.1158/2159-8290.CD-23-0641. PMID: 38236062 *Equal Contribution [PubMed] [PDF]
Wang B, Vartak R, Zaltsman Y, Naing ZZC, Hennick KM, Polacco BJ, Bashir A, Eckhardt M, Bouhaddou M, Xu J, Sun N, Lasser MC, Zhou Y, McKetney J, Guiley KZ, Chan U, Kaye JA, Chadha N, Cakir M, Gordon M, Khare P, Drake S, Drury V, Burke DF, Gonzalez S, Alkhairy S, Thomas R, Lam S, Morris M, Bader E, Seyler M, Baum T, Krasnoff R, Wang S, Pham P, Arbalaez J, Pratt D, Chag S, Mahmood N, Rolland T, Bourgeron T, Finkbeiner S, Swaney DL, Bandyopadhay S, Ideker T, Beltrao P, Willsey HR, Obernier K, Nowakowski TJ, Hüttenhain R, State MW, Willsey AJ, Krogan NJ. A foundational atlas of autism protein interactions reveals molecular convergence. bioRxiv [Preprint]. 2024 Feb 8:2023.12.03.569805. doi: 10.1101/2023.12.03.569805. PMID: 38076945 [PubMed] [PDF] (Preprint)
Sen SK, Green ED, Hutter CM, Craven M, Ideker T, Di Francesco V. Opportunities for basic, clinical, and bioethics research at the intersection of machine learning and genomics. Cell Genomics. 2024 Jan 10;4(1):100466. doi: 10.1016/j.xgen.2023.100466. Epub 2023 Dec 15. PMID: 38190108 [PubMed] [PDF] (Review)
Hu M, Zhang X, Latham A, Šali A, Ideker T, Lundberg E. Tools for assembling the cell: Towards the era of cell structural bioinformatics. Pac Symp Biocomput. 2024;29:661-665. PMID: 38160316. [PubMed] [PDF]
Koch Z, Li A, Evans DS, Cummings S, Ideker T. Somatic mutation as an explanation for epigenetic aging. bioRxiv. 2023 Dec 9:2023.12.08.569638. doi: 10.1101/2023.12.08.569638. PMID: 38106096; PMCID: PMC10723383. (Preprint) [PubMed]
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. PMID: 37786690; PMCID: PMC10541613. (Preprint) [PubMed]
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 [PubMed] [PDF]
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 [PubMed] [PDF]
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 [PubMed] [PDF]
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 [PubMed] [PDF]
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 *Equal Contribution [PubMed] [PDF]
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 [PubMed][PDF]
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 [PubMed] [PDF] (Review)
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 [PubMed] [PDF]
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 [PubMed] [PDF]
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 [PubMed] [PDF] (Review)
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 [PubMed] [PDF]
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 [PubMed ][PDF]
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 *Equal Contribution [PubMed] [PDF]
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 *Equal Contribution [PubMed] [PDF]
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]
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]
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]
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]
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]
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]
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] [Original PDF | Correction PDF] **Author Correction: Nat Neurosci. . 2025 Jan;28(1):213. doi: 10.1038/s41593-024-01853-7.
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]
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]
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)
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]
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)
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]
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]
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]
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. [PubMed] [PDF]
Gordon DE*, Hiatt J*, Bouhaddou M*, Rezelj VV*, Ulferts S*, Braberg H*, Jureka AS*, Obernier K*, Guo JZ*, Batra J*, Kaake RM*, Weckstein AR*, Owens TW*, Gupta M*, Pourmal S*, Titus EW*, Cakir M*,… García-Sastre A†, Rassen JA†, Grosse R†, Rosenberg OS†, Verba KA†, Basler CF†, Vignuzzi M†, Peden AA†, Beltrao P†, 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 *Equal Contribution, †Co-Corresponding Authors [PDF] [PubMed]
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. PMID: 33024967 [PDF] [PubMed] (Preprint)
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]
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]
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]
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]
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
Related Press: Scientific American, BBC, NPR, Washington Post, Discover Magazine, Smithsonian, New York Post, (and more!)
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]
Gordon DE*, Jang GM*, Bouhaddou M*, Xu J*, Obernier K*,
White KM*, O’Meara MJ*, Rezelj VV*,… 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 *Equal Contribution [PDF] [PubMed]
Sun SM*, Batté A*, Tittel-Elmer M, van der Horst S, van Welsem T, Bean G, Ideker T, van Leeuwen F, van Attikum H. A genetic interaction map centered on cohesin reveals auxiliary factors in sister chromatid cohesion in S. cerevisiae. J Cell Sci. 2020 May 22;133(10):jcs237628. doi: 10.1242/jcs.237628. PMID: 32299836 *Equal Contribution [PDF] [PubMed]
Jia T, Munson B, Lango Allen H, Ideker T, Majithia AR. Thousands of missing variants in the UK Biobank are recoverable by genome realignment. Ann Hum Genet. 2020 May;84(3):214-220. doi: 10.1111/ahg.12383. Epub 2020 Mar 31. PMID: 32232836 [PDF] [PubMed]
Kreisberg, J.F., Ideker, T., Meric-Bernstam, F. et al. Prospecting whole cancer genomes. Nature Cancer. 1, 273–275. 20 Mar 2020. doi: https://doi.org/10.1038/s43018-020-0045-3. [PDF]
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]
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] (Review)
Vakirlis N, Acar O, Hsu B, Castilho Coelho N, Van Oss SB, Wacholder A, Medetgul-Ernar K, Bowman RW 2nd, Hines CP, Iannotta J, Parikh SB, McLysaght A, Camacho CJ, O’Donnell AF, Ideker T, Carvunis AR. De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences. Nat Commun. 2020 Feb 7;11(1):781. doi: 10.1038/s41467-020-14500-z. PMID: 32034123. PMCID: PMC7005711 [PDF] [PubMed]
Budzik JM, Swaney DL, Jimenez-Morales D, Johnson JR, Garelis NE, Repasy T, Roberts AW, Popov LM, Parry TJ, Pratt D, Ideker T, Krogan NJ, Cox JS. Dynamic post-translational modification profiling of Mycobacterium tuberculosis-infected primary macrophages. Elife. 2020 Jan 17;9. pii: e51461. doi: 10.7554/eLife.51461. PMID: 31951200. PMCID: PMC7030789. [PDF] [PubMed]
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)
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)
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)
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]
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]
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)
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]
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)
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]
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)
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]
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)
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]
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]
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]
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)
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]
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)
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)
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)
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]
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 *Equal Contribution, †Co-Corresponding Authors [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)
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]
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)
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)
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 *Equal Contribution [PDF] [PubMed]
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 *Equal Contribution, †Co-Corresponding Authors [PDF] [PubMed]
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]
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]
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
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]
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]
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]
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]
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]
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)
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]
Carlin DE, Demchak B, Pratt D, Sage E, Ideker T. Network propagation in the cytoscape cyberinfrastructure. PLoS Comput Biol. 2017 Oct 12;13(10):e1005598. doi: 10.1371/journal.pcbi.1005598. PMID: 29023449; PMCID: PMC5638226. [PDF] [PubMed]
Ideker T, Nussinov R. Network approaches and applications in biology. PLoS Comput Biol. 2017 Oct 12;13(10):e1005771. doi: 10.1371/journal.pcbi.1005771. PMID: 29023447; PMCID: PMC5638228 [PDF] [PubMed] (Editorial)
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)
Du D, Roguev A, Gordon DE, Chen M, Chen SH, Shales M, Shen JP, Ideker T, Mali P, Qi LS, Krogan NJ. Genetic interaction mapping in mammalian cells using CRISPR interference. Nat Methods. 2017 Jun;14(6):577-580. doi: 10.1038/nmeth.4286. Epub 2017 May 8. PMID: 28481362 [PDF] [PubMed]
Buckley AR, Standish KA, Bhutani K, Ideker T, Lasken RS, Carter H, Harismendy O, Schork NJ. Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls. BMC Genomics. 2017 Jun 12;18(1):458. doi: 10.1186/s12864-017-3770-y. PMID: 28606096 [PDF] [PubMed]
Cowen L, Ideker T, Raphael BJ, Sharan R. Network propagation: a universal amplifier of genetic associations. Nat Rev Genet. 2017 Sep;18(9):551-562. doi: 10.1038/nrg.2017.38. Epub 2017 Jun 12. PMID: 28607512. [PDF] [PubMed] (Review)
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. F1000Res. 2017 Jun 6;6:784. doi: 10.12688/f1000research.11616.2. PMID: 29487738; PMCID: PMC5806050. [PDF] [PubMed]
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)
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; PMCID: PMC5371228. [PDF] [PubMed]
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; PMCID: PMC5370462. [PDF] [PubMed]
Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguev A, Lewis NE, Chang AN, Kreisberg JF, Krogan N, Qi L, Ideker T, Mali P. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nat Methods. 2017 Jun;14(6):573-576. doi: 10.1038/nmeth.4225. Epub 2017 Mar 20. PMID: 28319113; PMCID: PMC5449203. [PDF] [PubMed]
Networks and visualizations: 293T_SyntheticLethal; A549_SyntheticLethal; HeLa_SyntheticLethal
Source code: http://idekerlab.ucsd.edu/papers/rsasik2017/dual_crispr_pipeline.zip
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)
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
Cover Art: About the Cover
Data generated by the TCGA Research Network: http://cancergenome.nih.gov/
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]
See [Datasets]
Pillich RT, Chen J, Rynkov V, Welker D, Pratt D. NDEx: A Community Resource for Sharing and Publishing of Biological Networks. Methods Mol Biol. 2017 02 Feb;1558:271-301. doi: 10.1007/978-1-4939-6783-4_13. PMID: 28150243. Book chapter. [PDF] [PubMed]
Ideker T. The Real Value of an Atlas. NIH Biomedical Informatics Blog. 31 Oct 2016. [PDF] (Review)
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. doi: 10.1172/jci.insight.87877. PMID: 27777973. [PDF] [PubMed]
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]
Srivas R, Shen JP, Yang CC, Sun SM, Li J, Gross AM, Jensen J, Licon K, Bojorquez-Gomez A, Klepper K, Huang J, Pekin D, Xu JL, Yeerna H, Sivaganesh V, Kollenstart L, van Attikum H, Aza-Blanc P, Sobol RW, Ideker T. A Network of Conserved Synthetic Lethal Interactions for Exploration of Precision Cancer Therapy. Molecular Cell. 2016 Jul 19. pii: S1097-2765(16)30280-5. doi: 10.1016/j.molcel.2016.06.022. PMID: 27453043. [PDF] [PubMed]
Hofree M, Carter H, Kreisberg JF, Bandyopadhyay S, Mischel PS, Friend S, Ideker T. Challenges in identifying cancer genes by analysis of exomesequencing data. Nat Commun. 2016 Jul 15;7:12096. doi: 10.1038/ncomms12096. PMID: 27417679; PMCID: PMC4947162. [PDF] [PubMed]
Get positive and negative datasets [Click to download ZIP file]
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; PMCID: PMC5579720. [PDF][PubMed]
Jaeger PA, Lucin KM, Britschgi M, Vardarajan B, Huang RP, Kirby ED, Abbey R, Boeve BF, Boxer AL, Farrer LA, Finch N, Graff-Radford NR, Head E, Hofree M, Huang R, Johns H, Karydas A, Knopman DS, Loboda A, Masliah E, Narasimhan R, Petersen RC, Podtelezhnikov A, Pradhan S, Rademakers R, Sun CH, Younkin SG, Miller BL, Ideker T, Wyss-Coray T. Network-driven plasma proteomics expose molecular changes in the Alzheimer’s brain. Mol Neurodegener. 2016 Apr 26;11:31. doi: 10.1186/s13024-016-0095-2. Erratum in: Mol Neurodegener. 2016 May 23;11(1):42. doi: 10.1186/s13024-016-0105-4. PMID: 27112350; PMCID: PMC4845325. [PDF] [PubMed]
Gross AM, Jaeger PA, Kreisberg JF, Licon K, Jepsen KL, Khosroheidari M, Morsey BM, Swindells S, Shen H, Ng CT, Flagg K, Chen D, Zhang K, Fox HS,Ideker T. Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA. Mol Cell. 2016 Apr 21;62(2):157-168. doi: 10.1016/j.molcel.2016.03.019. PMID: 27105112; PMCID: PMC4995115. [PDF] [PubMed]
Tutorial for implementing Hannum, et al., MOL CELL (2013): GitHub Source Code
Meet the Author: Interview with Andy Gross
Press: NPR Health: People Who Are HIV-Positive May Be Aging Faster Than Their Peers
Press: NIH Science News: Biomarker Tracks Accelerated HIV-Associated Aging
Press: UCSD Health: HIV Infection Prematurely Ages People by an Average of Five Years
Ono, Kei. Technical aspects of “Panama Papers” analysis. Newsweek Japan, 12 April 2016. [PDF] (Review)
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 Syst. 2016 Feb 24;2(2):77-88. doi: 10.1016/j.cels.2016.02.003. PMID: 26949740; PMCID: PMC4772745. [PDF][PubMed] *Cover article
Liss MA, DeConde R, Caovan D, Hofler J, Gabe M, Palazzi KL, Patel ND, Lee HJ, Ideker T, Van Poppel H, Karow D, Aertsen M, Casola G, Derweesh IH. Parenchymal Volumetric Assessment as a Predictive Tool to Determine Renal Function Benefit of Nephron-Sparing Surgery Compared with Radical Nephrectomy. J Endourol. 2016 Jan;30(1):114-21. doi: 10.1089/end.2015.0411. Epub 2015 Sep 25. PMID: 26192380; PMCID: PMC4841003. [PDF] [PubMed]
Qu K*, Garamszegi S*, Wu F*, Thorvaldsdottir H, Liefeld T, Ocana M, Borges-Rivera D, Pochet N, Robinson JT, Demchak B, Hull T, Ben-Artzi G, Blankenberg D, Barber GP, Lee BT, Kuhn RM, Nekrutenko A, Segal E, Ideker T, Reich M, Chang HY, Mesirov JP. Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. Nat Methods. 2016 Mar;13(3):245-247. doi: 10.1038/nmeth.3732. Epub 2016 Jan 18. PMID: 26780094; PMCID: PMC4767623. *Equal Contribution [PDF] [PubMed]
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;4:e11615. doi: 10.7554/eLife.11615. PMID: 26682651; PMCID: PMC4764585. [PDF] [PubMed]
Yan JF, Kim H, Jeong SK, Lee HJ, Sethi MK, Lee LY, Beavis RC, Im H, Snyder MP, Hofree M, Ideker T, Wu SL, Paik YK, Fanayan S, Hancock WS. Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues. Journal of Proteome Research. 2015 Dec 4;14(12):4995-5006. doi: 10.1021/acs.jproteome.5b00827. Epub 2015 Oct 20. [PDF] [PubMed]
Gross AM, Kreisberg JF, Ideker T. Analysis of Matched Tumor and Normal Profiles Reveals Common Transcriptional and Epigenetic Signals Shared across Cancer Types. PLoS One. 2015 Nov 10;10(11):e0142618. doi: 10.1371/journal.pone.0142618. PMID: 26555223; PMCID: PMC4640835. [PDF] [PubMed]
Lau E, Sedy J, Sander C, Shaw MA, Feng Y, Scortegagna M, Claps G, Robinson S, Cheng P, Srivas R, Soonthornvacharin S, Ideker T, Bosenberg M, Gonzalez R, Robinson W, Chanda SK, Ware C, Dummer R, Hoon D, Kirkwood JM, Ronai ZA. Transcriptional repression of IFNβ1 by ATF2 confers melanoma resistance to therapy. Oncogene. 2015 Nov 12;34(46):5739-48. doi: 10.1038/onc.2015.22. Epub 2015 Mar 2. PMID: 25728676; PMCID: PMC4558399. [PDF] [PubMed]
Pratt D, Chen J, Welker D, Rivas R, Pillich R, Rynkov V, Ono K, Miello C, Hicks L, Szalma S, Stojmirovic A, Dobin R, Braxenthaler M, Kuentzer J, Demchak B, Ideker T. NDEx, the Network Data Exchange. Cell Syst. 2015 Oct 28;1(4):302-305. doi: 10.1016/j.cels.2015.10.001. PMID: 26594663; PMCID: PMC4649937. [PDF] [PubMed]
Shen JP, Srivas R, Gross A, Li J, Jaehnig EJ, Sun SM, Bojorquez-Gomez A, Licon K, Sivaganesh V, Xu JL, Klepper K, Yeerna H, Pekin D, Qiu CP, van Attikum H, Sobol RW, Ideker T. Chemogentic profiling identifies RAD17 as synthetically lethal with checkpoint kinase inhibition. Oncotarget. 2015 Nov 3;6(34):35755-69. doi: 10.18632/oncotarget.5928. PMID: 26437225; PMCID: PMC4742139. [PDF] [PubMed]
Summer G, Kelder T, Ono K, Radonjic M, Heymans S, Demchak B. cyNeo4j: connecting Neo4j and Cytoscape. Bioinformatics. 2015 Dec 1;31(23):3868-9. doi: 10.1093/bioinformatics/btv460. Epub 2015 Aug 12. PMID: 26272981; PMCID: PMC4653389. [PDF] [PubMed]
Till A, Saito R, Merkurjev D, Liu JJ, Syed GH, Kolnik M, Siddiqui A, Glas M, Scheffler B, Ideker T, Subramani S. Evolutionary trends and functional anatomy of the human expanded autophagy network. Autophagy. 2015;11(9):1652-67. doi: 10.1080/15548627.2015.1059558. PMID: 26103419; PMCID: PMC4590607. [PDF] [PubMed]
Jaeger PA, McElfresh C, Wong LR, Ideker T. Beyond Agar: Gel Substrates with Improved Optical Clarity and Drug Efficiency and Reduced Autofluorescence for Microbial Growth Experiments. Appl Environ Microbiol. 2015 Aug 15;81(16):5639-49. doi: 10.1128/AEM.01327-15. Epub 2015 Jun 12. PMID: 26070672; PMCID: PMC4510171. [PDF] [PubMed]
Ono K, Muetze T, Kolishovski, G, Shannon P, Demchak B. CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API. F1000Res. 2015 Aug 5;4:478. doi: 10.12688/f1000research.6767.1. PMID: 26672762; PMCID: PMC4670004. [PDF] [PubMed]
Gross AM, Ideker T. Molecular networks in context. Nat Biotechnol. 2015 Jul;33(7):720-1. doi: 10.1038/nbt.3283. PMID: 26154012. [PDF] [PubMed] (Review)
Choueiri MB, Shen JP, Gross AM, Huang JK, Ideker T, Fanta P. ERCC1 and TS Expression as Prognostic and Predictive Biomarkers in Metastatic Colon Cancer. PLoS One. 2015 Jun 17;10(6):e0126898. doi: 10.1371/journal.pone.0126898. PMID: 26083491; PMCID: PMC4470586. [PDF] [PubMed]
Roosing S, Hofree M, Kim S, Scott E, Copeland B, Romani M, Silhavy JL, Rosti RO, Schroth J, Mazza T, Miccinilli E, Zaki MS, Swoboda KJ, Milisa-Drautz J, Dobyns WB, Mikati MA, İncecik F, Azam M, Borgatti R, Romaniello R, Boustany RM, Clericuzio CL, D’Arrigo S, Strømme P, Boltshauser E, Stanzial F, Mirabelli-Badenier M, Moroni I, Bertini E, Emma F, Steinlin M, Hildebrandt F, Johnson CA, Freilinger M, Vaux KK, Gabriel SB, Aza-Blanc P, Heynen-Genel S, Ideker T, Dynlacht BD, Lee JE, Valente EM, Kim J, Gleeson JG. Functional genome-wide siRNA screen identifies KIAA0586 as mutated in Joubert syndrome. Elife. 2015 May 30;4:e06602. doi: 10.7554/eLife.06602. PMID: 26026149; PMCID: PMC4477441. [PDF] [PubMed]
Krogan NJ, Lippman S, Agard DA, Ashworth A, Ideker T. The cancer cell map initiative: defining the hallmark networks of cancer. Mol Cell. 2015 May 21;58(4):690-8. doi: 10.1016/j.molcel.2015.05.008. PMID: 26000852; PMCID: PMC5359018.[PDF] [PubMed] (Review)
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 Oncol. 2015 May;51(5):470-5. doi: 10.1016/j.oraloncology.2015.01.014. Epub 2015 Feb 27. PMID: 25735654; PMCID: PMC4427339. [PDF] [PubMed]
Hustedt N, Seeber A, Sack R, Tsai-Pflugfelder M, Bhullar B, Vlaming H, van Leeuwen F, Guénolé A, van Attikum H, Srivas R, Ideker T, Shimada K, Gasser SM. Yeast PP4 interacts with ATR homolog Ddc2-Mec1 and regulates checkpoint signaling. Mol Cell. 2015 Jan 22;57(2):273-89. doi: 10.1016/j.molcel.2014.11.016. Epub 2014 Dec 18. PMID: 25533186; PMCID: PMC5706562. [PDF] [PubMed]
Cancer Genome Atlas Research Network. Under a Creative Commons license. Integrated genomic characterization of papillary thyroid carcinoma. Cell. 2014 Oct 23;159(3):676-90. doi: 10.1016/j.cell.2014.09.050. PMID: 25417114; PMCID: PMC4243044. [PDF] [PubMed]
Wilkinson DS, Jariwala JS, Anderson E, Mitra K, Meisenhelder J, Chang JT, Ideker T, Hunter T, Nizet V, Dillin A, Hansen M. Phosphorylation of LC3 by the Hippo kinases STK3/STK4 is essential for autophagy. Mol Cell. 2015 Jan 8;57(1):55-68. doi: 10.1016/j.molcel.2014.11.019. Epub 2014 Dec 24. PMID: 25544559; PMCID: PMC4373083. [PDF] [PubMed]
Demchak B, Hull T, Reich M, Liefeld T, Smoot M, Ideker T, Mesirov JP. Cytoscape: the network visualization tool for GenomeSpace workflows. F1000Res. 2014 Jul 1;3:151. doi: 10.12688/f1000research.4492.2. PMID: 25165537; PMCID: PMC4133763. [PDF] [PubMed]
Ono K, Demchak B, Ideker T. Cytoscape tools for the web age: D3.js and Cytoscape.js exporters. Version 2. F1000Res. 2014 Jul 1;3:143. doi: 10.12688/f1000research.4510.2. PMID: 25520778; PMCID: PMC4264639. [PDF] [PubMed]
Welker D, Demchak B. Porting and using PanGIA for Cytoscape 3: challenges and solutions. F1000Res. 2014 Jul 1;3:150. doi: 10.12688/f1000research.4546.1. PMID: 25075307; PMCID: PMC4103495. eCollection 2014. [PDF] [PubMed]
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. F1000Res. 2014 Jul 1;3:138. doi: 10.12688/f1000research.4642.1. PMID: 25580224; PMCID: PMC4288400. eCollection 2014. [PDF] [PubMed]
Su G, Morris JH, Demchak B, Bader GD. Biological network exploration with Cytoscape 3. Curr Protoc Bioinformatics. 2014 Sep 8;47:8.13.1-24. doi: 10.1002/0471250953.bi0813s47. PMID: 25199793; PMCID: PMC4174321. [PDF] [PubMed]
Shaughnessy DT, McAllister K, Worth L, Haugen AC, Meyer JN, Domann FE, Van Houten B, Mostoslavsky R, Bultman SJ, Baccarelli AA, Begley TJ, Sobol RW, 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 Dec;122(12):1271-8. doi: 10.1289/ehp.1408418. Epub 2014 Aug 15. PMID: 25127496; PMCID: PMC4256704. [PDF] [PubMed] [TI: Provided data analysis.] (Review)
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. 2014 Oct;151(4):612-8. doi: 10.1177/0194599814545083. Epub 2014 Aug 4. PMID: 25091190; PMCID: PMC4469264. [PDF] [PubMed]
Gross AM, Orosco RK, Shen JP, Egloff AM, Carter H, Hofree M, Choueiri M, Coffey CS, Lippman SM, Hayes DN, Cohen EE, Grandis JR, Nguyen QT, Ideker T. Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss. Nat Genet. 2014 Sep;46(9):939-43. doi: 10.1038/ng.3051. Epub 2014 Aug 3. PMID: 25086664; PMCID: PMC4146706. [PDF] [PubMed]
Lee K, Sung MK, Kim J, Kim K, Byun J, Paik H, Kim B, Huh WK, Ideker T. Proteome-wide remodeling of protein location and function by stress. Proc Natl Acad Sci U S A. 2014 Jul 29;111(30):E3157-66. doi: 10.1073/pnas.1318881111. Epub 2014 Jul 15. PMID: 25028499; PMCID: PMC4121818. [PDF] [PubMed]
Kramer M, Dutkowski J, Yu M, Bafna V, Ideker T. Inferring gene ontologies from pairwise similarity data. Bioinformatics. 2014 Jun 15;30(12):i34-42. doi: 10.1093/bioinformatics/btu282. PMID: 24932003; PMCID: PMC4058954.[PDF] [PubMed]
Emig-Agius D, Olivieri K, Pache L, Shih HL, Pustovalova O, Bessarabova M, Young JA, Chanda SK, Ideker T. An integrated map of HIV-human protein complexes that facilitate viral infection. PLoS One. 2014 May 9;9(5):e96687. doi: 10.1371/journal.pone.0096687. PMID: 24817247; PMCID: PMC4016004. [PDF] [PubMed]
Joshi S, Singh AR, Zulcic M, Bao L, Messer K, Ideker T, Dutkowski J, Durden DL. Rac2 controls tumor growth, metastasis and M1-M2 macrophage differentiation in vivo. PLoS One. 2014 Apr 25;9(4):e95893. doi: 10.1371/journal.pone.0095893. PMID: 24770346; PMCID: PMC4000195. [PDF] [PubMed]
Carvunis AR, Ideker T. Siri of the cell: what biology could learn from the iPhone. Cell. 2014 Apr 24;157(3):534-8. doi: 10.1016/j.cell.2014.03.009. PMID: 24766803; PMCID: PMC4154484. [PDF] [PubMed]
Novarino G*, Fenstermaker AG*, Zaki MS*, Hofree M, Silhavy JL, Heiberg AD, Abdellateef M, Rosti B, Scott E, Mansour L, Masri A, Kayserili H, Al-Aama JY, Abdel-Salam GM, Karminejad A, Kara M, Kara B, Bozorgmehri B, Ben-Omran T, Mojahedi F, Mahmoud IG, Bouslam N, Bouhouche A, Benomar A, Hanein S, Raymond L, Forlani S, Mascaro M, Selim L, Shehata N, Al-Allawi N, Bindu PS, Azam M, Gunel M, Caglayan A, Bilguvar K, Tolun A, Issa MY, Schroth J, Spencer EG, Rosti RO, Akizu N, Vaux KK, Johansen A, Koh AA, Megahed H, Durr A, Brice A, Stevanin G, Gabriel SB, Ideker T, Gleeson JG. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science. 2014 Jan 31;343(6170):506-511. doi: 10.1126/science.1247363. PMID: 24482476; PMCID: PMC4157572. *Equal Contribution [PDF][PubMed]
Bean GJ, Jaeger PA, Bahr S, Ideker T. Development of ultra-high-density screening tools for microbial “omics.”. PLoS One. 2014 Jan 21;9(1):e85177. doi: 10.1371/journal.pone.0085177. PMID: 24465499; PMCID: PMC3897414. [PDF] [PubMed]
Dutkowski J, Ono K, Kramer M, Yu M, Pratt D, Demchak B, Ideker T. NeXO Web: the NeXO ontology database and visualization platform. Nucleic Acids Res. 2014 Jan;42(Database issue):D1269-74. doi: 10.1093/nar/gkt1192. Epub 2013 Nov 23. PMID: 24271398; PMCID: PMC3965056. [PDF] [PubMed]
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. 2013 Oct 15;6(297):ra90. doi: 10.1126/scisignal.2004657. PMID: 24129700; PMCID: PMC4075427. [PDF] [PubMed]
Hofree M, Shen JP, Carter H, Gross A, Ideker T. Network-based stratification of tumor mutations. Nat Methods. 2013 Nov;10(11):1108-15. doi: 10.1038/nmeth.2651. Epub 2013 Sep 15. PMID: 24037242; PMCID: PMC3866081. [PDF] [PubMed]
Sharma K, Karl B, Mathew AV, Gangoiti JA, Wassel CL, Saito R, Pu M, Sharma S, You YH, Wang L, Diamond-Stanic M, Lindenmeyer MT, Forsblom C, Wu W, Ix JH, Ideker T, Kopp JB, Nigam SK, Cohen CD, Groop PH, Barshop BA, Natarajan L, Nyhan WL, Naviaux RK. Metabolomics reveals signature of mitochondrial dysfunction in diabetic kidney disease. J Am Soc Nephrol. 2013 Nov;24(11):1901-12. doi: 10.1681/ASN.2013020126. Epub 2013 Oct 10. PMID: 23949796; PMCID: PMC3810086. [PDF] [PubMed]
Jaehnig EJ, Kuo D, Hombauer H, Ideker TG, Kolodner RD. Checkpoint kinases regulate a global network of transcription factors in response to DNA damage. Cell Rep. 2013 Jul 11;4(1):174-88. doi: 10.1016/j.celrep.2013.05.041. Epub 2013 Jun 27. PMID: 23810556; PMCID: PMC3855057. [PDF] [PubMed]
Chang KN, Zhong S, Weirauch MT, Hon G, Pelizzola M, Li H, Huang SS, Schmitz RJ, Urich MA, Kuo D, Nery JR, Qiao H, Yang A, Jamali A, Chen H, Ideker T, Ren B, Bar-Joseph Z, Hughes TR, Ecker JR. Temporal transcription response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. Elife. 2013 Jun 11;2:e00675. doi: 10.7554/eLife.00675. PMID: 23795294; PMCID: PMC3679525. [PDF] [PubMed]
Fukuyama H, Verdier Y, Guan Y, Makino-Okamura C, Shilova V, Liu X, Maksoud E, Matsubayashi J, Haddad I, Spirohn K, Ono K, Hetru C, Rossier J, Ideker T, Boutros M, Vinh J, Hoffmann JA. Landscape of protein-protein interactions in Drosophila immune deficiency signaling during bacterial challenge. Proc Natl Acad Sci U S A. 2013 Jun 25;110(26):10717-22. doi: 10.1073/pnas.1304380110. Epub 2013 Jun 7. PMID: 23749869; PMCID: PMC3696746.[PDF] [PubMed]
Lee K, Byun K, Hong W, Chuang HY, Pack CG, Bayarsaikhan E, Paek SH, Kim H, Shin HY, Ideker T, Lee B. Proteome-wide discovery of mislocated proteins in cancer. Genome Res. 2013 Aug;23(8):1283-94. doi: 10.1101/gr.155499.113. Epub 2013 May 14. PMID: 23674306; PMCID: PMC3730102. [PDF] [PubMed]
Bilal E, Dutkowski J, Guinney J, Jang IS, Logsdon BA, Pandey G, Sauerwine BA, Shimoni Y, Moen Vollan HK, Mecham BH, Rueda OM, Tost J, Curtis C, Alvarez MJ, Kristensen VN, Aparicio S, Børresen-Dale AL, Caldas C, Califano A, Friend SH, Ideker T, Schadt EE, Stolovitzky GA, Margolin AA. Improving breast cancer survival analysis through competition-based multidimensional modeling. PLoS Comput Biol. 2013;9(5):e1003047. doi: 10.1371/journal.pcbi.1003047. Epub 2013 May 9. PMID: 23671412; PMCID: PMC3649990. [PDF] [PubMed]
Zhang EY, Cristofanilli M, Robertson F, Reuben JM, Mu Z, Beavis RC, Im H, Snyder M, Hofree M, Ideker T, Omenn GS, Fanayan S, Jeong SK, Paik YK, Zhang AF, Wu SL, Hancock WS. Genome wide proteomics of ERBB2 and EGRF and other oncogenic pathways in inflammatory breast cancer. J Proteome Res. 2013 Jun 7;12(6):2805-17. doi: 10.1021/pr4001527. Epub 2013 May 22. PMID: 23647160; PMCID: PMC4142215. [PDF] [PubMed]
Dutkowski J, Kramer M, Surma MA, Balakrishnan R, Cherry JM, Krogan NJ, Ideker T. A gene ontology inferred from molecular networks. Nat Biotechnol. 31, 38–45 (2013). doi: 10.1038/nbt.2463. [PDF] [PubMed] *Cover article
Cover Art: About the cover
Data: Quantitative genetic interaction profiles [Data]
Chen M, Licon K, Otsuka R, Pillus L, Ideker T. Decoupling Epigenetic and Genetic Effects through Systematic Analysis of Gene Position. Cell Rep. 2013 Jan 31;3(1):128-37. doi: 10.1016/j.celrep.2012.12.003. Epub 2013 Jan 3. PMID: 23291096; PMCID: PMC3563736. [PDF] [PubMed]
Data included are RNA-Seq data for 4 heterozygous diploid yeast strains and diploid wild-type. There are three replicates for each heterozygous strain, and six replicates for wild-type. [GEO data set]
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. Nat Biotechnol. 2013 Oct;31(10):894-7. doi: 10.1038/nbt.2721. PMID: 24104757; PMCID: PMC4166496. [PDF] [PubMed]
Carter H, Hofree M, Ideker T. Genotype to phenotype via network analysis. Curr Opin Genet Dev. 2013 Dec;23(6):611-21. doi: 10.1016/j.gde.2013.10.003. Epub 2013 Nov 14. PMID: 24238873; PMCID: PMC3866044. [PDF] [PubMed] (Review)
Mitra K, Carvunis AR, Ramesh SK, Ideker T. Integrative approaches for finding modular structure in biology networks. Nat Rev Genet. 2013 Oct;14(10):719-32. doi: 10.1038/nrg3552. PMID: 24045689; PMCID: PMC3940161. [PDF] [PubMed] (Review)
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. PMID: 23177740; PMCID: PMC3780611 *Equal Contribution, †Co-Corresponding Authors [PDF] [PubMed]
Tutorial for implementing Hannum, et al., MOL CELL (2013): https://github.com/theandygross/HIV_Methylation
Data sets: http://idekerlab.ucsd.edu/papers/ghannum2013/paper.pdf
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
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
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)
Bean GJ, Ideker T. Differential analysis of high-throughput quantitative genetic interaction data. Genome Biol. 2012 Dec 26;13(12):R123. [PDF] [PubMed]
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)
Choi S, Srivas R, Fu KY, Hood BL, Dost B, Gibson GA, Watkins SC, Van Houten B, Bandeira N, Conrads TP, Ideker T, Bakkenist CJ. Quantitative Proteomics Reveal ATM Kinase-dependent Exchange in DNA Damage Response Complexes. J Proteome Res. 2012 Oct 5;11(10):4983-91. doi: 10.1021/pr3005524. Epub 2012 Sep 18. [PDF] [PubMed]
Califano A, Butte AJ, Friend S, Ideker T, Schadt E. Leveraging models of cell regulation and GWAS data in integrative network-based association studies. Nature Genetics. 2012 Jul 27;44(8):841-7. doi: 10.1038/ng.2355. [PDF] [PubMed] (Review Article)
Chuang HY, Rassenti L, Salcedo M, Licon K, Kohlmann A, Haferlach T, Foà R, Ideker T*, Kipps TJ*. Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with disease progression. Blood. 2012 Sep 27;120(13):2639-49. Epub 2012 Jul 26. *Corresponding authors [PDF] [PubMed]
Supplemental Figures, Methods and Data [Suppl. Data]
Expression data from untreated CLL patients [GEO Data Set]
Ryan CJ, Roguev A, Patrick K, Xu J, Jahari H, Tong Z, Beltrao P, Shales M, Qu H, Collins SR, Kliegman JI, Jiang L, Kuo D, Tosti E, Kim HS, Edelmann W, Keogh MC, Greene D, Tang C, Cunningham P, Shokat KM, Cagney G, Svensson JP, Guthrie C, Espenshade PJ, Ideker T, Krogan NJ Hierarchical modularity and the evolution of genetic interactomes across species. Mol Cell. 2012 Jun 8;46(5):691-704. [PDF] [PubMed]
Bark SJ, Wegrzyn J, Taupenot L, Ziegler M, O’Connor DT, Ma Q, Smoot M, Ideker T, Hook V. The protein architecture of human secretory vesicles reveals differential regulation of signaling molecule secretion by protein kinases. PLoS One. 2012;7(8):e41134. doi: 10.1371/journal.pone.0041134. Epub 2012 Aug 16. [PDF] [PubMed]
Travesa A, Kuo D, de Bruin RA, Kalashnikova TI, Guaderrama M, Thai K, Aslanian A, Smolka MB, Yates JR 3rd, Ideker T, Wittenberg C. DNA replication stress differentially regulates G1/S genes via Rad53-dependent inactivation of Nrm1. EMBO Journal. 2012 Feb 14;31(7):1811-22. doi: 10.1038/emboj.2012.28. [PDF] [PubMed]
Lau E, Kluger H, Varsano T, Lee K, Scheffler I, Rimm DL, Ideker T, Ronai ZA. PKCe promotes oncogenic functions of ATF2 in the nucleus while blocking its apoptotic function at mitochondria. Cell. 2012 Feb 3;148(3):543-55. [PDF] [PubMed]
Ideker T, Krogan NJ. Differential network biology. Molecular Systems Biology. 2012 Jan 17;8:565. doi: 10.1038/msb.2011.99. [PDF] [PubMed] (Review Article)
Zhang L, Lim SL, Du H, Zhang M, Kozak I, Hannum G, Wang X, Ouyang H, Hughes G, Zhao L, Zhu X, Lee C, Su Z, Zhou X, Shaw R, Geum D, Wei X, Zhu J, Ideker T, Oka C, Wang N, Yang Z, Shaw PX, Zhang K. High temperature requirement factor A1 (HTRA1) gene regulates angiogenesis through transforming growth factor-ß family member growth differentiation factor 6. J Biol Chem. 2012 Jan 6;287(2):1520-6. Epub 2011 Nov 2. [PDF] [PubMed]
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. doi: 10.1073/pnas.1115753108. Epub 2011 Oct 31. PMID: 22042857; PMCID: PMC3215069. *Equal Contribution [PDF] [PubMed]
Dutkowski J., Ideker T. Protein networks as logic functions in development and cancer. PLoS Comput Biol. 2011 Sep;7(9):e1002180. doi: 10.1371/journal.pcbi.1002180. Epub 2011 Sep 29. PMID: 21980275; PMCID: PMC3182870. [PDF][PubMed]
Mercer EM, Lin YC, Benner C, Jhunjhunwala S, Dutkowski J, Flores M, Sigvardsson M, Ideker T, Glass CK, Murre C. Multilineage priming of enhancer repertoires precedes commitment to the B and myeloid cell lineages in hematopoietic progenitors. Immunity. 2011 Sep 23;35(3):413-25. doi: 10.1016/j.immuni.2011.06.013. Epub 2011 Sep 8. PMID: 21903424; PMCID: PMC3183365. [PDF] [PubMed]
Srivas R, Hannum G, Ruscheinski J, Ono K, Wang PL, Smoot M, Ideker T. Assembling global maps of cellular function through integrative analysis of physical and genetic networks. Nat Protoc. 2011 Aug 11;6(9):1308-23. doi: 10.1038/nprot.2011.368. PMID: 21886098; PMCID: PMC3383003. [PDF] [PubMed]
Smoot ME, Ono K, Ideker T. Maere, S. PiNGO: a Cytoscape plugin to find candidate genes in biological networks. Bioinformatics. 2011 Apr 1;27(7):1030-1. doi: 10.1093/bioinformatics/btr045. Epub 2011 Jan 28. PMID: 21278188; PMCID: PMC3065683. [PDF] [PubMed]
Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2011 Feb 1;27(3):431-2. doi: 10.1093/bioinformatics/btq675. Epub 2010 Dec 12. PMID: 21149340; PMCID: PMC3031041. [PDF] [PubMed]
Ideker T, Dutkowski J, Hood L. Boosting signal-to-noise in complex biology: prior knowledge is power. Cell. 2011 Mar 18;144(6):860-3. doi: 10.1016/j.cell.2011.03.007. PMID: 21414478; PMCID: PMC3102020. [PDF] [PubMed] (Review)
Friend SH, Ideker T. Point: Are we prepared for the future doctor visit?. Nat Biotechnol. 2011 Mar;29(3):215-8. doi: 10.1038/nbt.1794. PMID: 21390021. [PDF] [PubMed] (Comment)
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. 2010 Dec 3;330(6009):1385-9. doi: 10.1126/science.1195618. Erratum in: Science. 2011 Jan 21;331(6015):284. PMID: 21127252; PMCID: PMC3006187. [PDF] [PubMed]
Supplemental Data: Supporting Online Material for Rewiring of Genetic Networks in Response to DNA Damage
Differential epistasis mapping (dE-MAP) [Data]
Kuo D, Licon K, Bandyopadhyay S, Chuang R, Luo C, Catalana J, Ravasi T, Tan K†, Ideker T†. Coevolution within a transcriptional network by compensatory trans and cis mutations. Genome Res. 2010 Dec;20(12):1672-8. doi: 10.1101/gr.111765.110. Epub 2010 Oct 26. PMID: 20978140; PMCID: PMC2989993. †Co-Corresponding Authors [PDF] [PubMed]
Cannistraci CV, Ravasi T, Montevecchi FM, Ideker T, Alessio M. Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes. Bioinformatics. 2010 Sep 15;26(18):i531-9. doi: 10.1093/bioinformatics/btq376. PMID: 20823318; PMCID: PMC2935424. [PDF] [PubMed]
Bandyopadhyay S, Chiang CY, Srivastava J, Gersten M, White S, Bell R, Kurschner C, Martin C, Smoot M, Sahasrabudhe S, Barber DL, Chanda SK, Ideker T. A human MAP kinase interactome. Nat Methods. 2010 Oct;7(10):801-5. doi: 10.1038/nmeth.1506. PMID: 20936779; PMCID: PMC2967489. [PDF] [PubMed]
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 Nov 1;26(21):2796-7. doi: 10.1093/bioinformatics/btq522. Epub 2010 Sep 16. PMID: 20847220; PMCID: PMC2958747. *Equal Contribution [PDF] [PubMed]
Kuo D, Tan K, Zinman G, Ravasi T, Bar-Joseph Z, Ideker T. Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. Genome Biol. 2010;11(7):R77. doi: 10.1186/gb-2010-11-7-r77. Epub 2010 Jul 23. PMID: 20653936; PMCID: PMC2926788. [PDF] [PubMed]
Expression profiles of three yeast species after exposure to fluconazole. [Data]
Lin YC, Jhunjhunwala S, Benner C, Heinz S, Welinder E, Mansson R, Sigvardsson M, Hagman J, Espinoza CA, Dutkowski J, Ideker T, Glass CK, Murre C. A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate. Nat Immunol. 2010 Jul;11(7):635-43. doi: 10.1038/ni.1891. Epub 2010 Jun 13. PMID: 20543837; PMCID: PMC2896911. [PDF] [PubMed]
Kim J, Lee JE, Heynen-Genel S, Suyama E, Ono K, Lee K, Ideker T, Aza-Blanc P, Gleeson JG. Functional genomic screen for modulators of ciliogenesis and cilium length. Nature. 2010 Apr 15;464(7291):1048-51. doi: 10.1038/nature08895. PMID: 20393563; PMCID: PMC2929961. [PDF] [PubMed]
Lee, K., Thorneycoft, D., Achuthan, P., Hermjakob, H., Ideker, T. Mapping Plant Interactomes Using Literature Curated and Predicted Protein-Protein Interaction Datasets. Plant Cell. 2010 Apr;22(4):997-1005. doi: 10.1105/tpc.109.072736. Epub 2010 Apr 6. PMID: 20371643; PMCID: PMC2879763. [PDF] [PubMed]
Protein sub-cellular localization in A. taliana [Data]
Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, et al. An atlas of combinatorial transcriptional regulation in mouse and man. Cell. 2010 Mar 5;140(5):744-52. doi: 10.1016/j.cell.2010.01.044. Erratum in: Cell. 2010 Apr 16;141(2):369. PMID: 20211142; PMCID: PMC2836267. [PDF] [Pubmed]
König R, Stertz S, Zhou Y, Inoue A, Hoffmann HH, Bhattacharyya S, Alamares JG, Tscherne DM, Ortigoza MB, Liang Y, Gao Q, Andrews SE, Bandyopadhyay S, De Jesus P, Tu BP, Pache L, Shih C, Orth A, Bonamy G, Miraglia L, Ideker T, García-Sastre A, Young JA, Palese P, Shaw ML, Chanda SK. Human Host Factors Required for Influenza Virus Replication. Nature. 2010 Feb 11;463(7282):813-7. doi: 10.1038/nature08699. PMID: 20027183; PMCID: PMC2862546. [PDF] [PubMed]
van Steensel B*, Braunschweig U*, Filion GJ, Chen M, van Bemmel JG, Ideker T. Bayesian network analysis of targeting interactions in chromatin. Genome Res. 2010 Feb;20(2):190-200. doi: 10.1101/gr.098822.109. Epub 2009 Dec 9. PMID: 20007327; PMCID: PMC2813475. *Equal Contribution [PDF] [PubMed]
Targeting Interactions in Chromatin. [Data]
Bandyopadhyay, S. and Ideker T. Integrative systems biology. Nature Genetics 42(12) (2010). [Poster] (Review)
Chuang HY, Hofree M, Ideker T. A decade of systems biology. Annu Rev Cell Dev Biol. 2010;26:721-44. doi: 10.1146/annurev-cellbio-100109-104122. PMID: 20604711; PMCID: PMC3371392. [PDF] [PubMed] (Review)
Hannum G*, Srivas R*, Guénolé A, van Attikum H, Krogan NJ, Karp RM, Ideker T. Genome-wide association data reveal a global map of genetic interactions among protein complexes. PLoS Genet. 2009 Dec;5(12):e1000782. doi: 10.1371/journal.pgen.1000782. Epub 2009 Dec 24. PMID: 20041197; PMCID: PMC2788232. *Equal Contribution [PDF] [PubMed]
Gersten M, Alirezaei M, Marcondes MC, Flynn C, Ravasi T, Ideker T, Fox HS. An integrated systems analysis implicates EGR1 downregulation in SIVE-induced neural dysfunction. J Neurosci. 2009 Oct 7;29(40):12467-76. doi: 10.1523/JNEUROSCI.3180-09.2009. PMID: 19812322; PMCID: PMC2802851. [PDF] [PubMed]
RNA from duplicate hippocampal samples taken from nine control monkeys and nine monkeys with evidence of SIV encephalitis were hybridized to Affymetrix arrays. [Data Set]
Fossum E, Friedel CC, Rajagopala SV, Titz B, Baiker A, Schmidt T, Kraus T, Stellberger T, Rutenberg C, Suthram S, Bandyopadhyay S, Rose D, von Brunn A, Uhlmann M, Zeretzke C, Dong YA, Boulet H, Koegl M, Bailer SM, Koszinowski U, Ideker T, Uetz P, Zimmer R, Haas J. Evolutionarily conserved herpesviral protein interaction networks. PLoS Pathog. 2009 Sep;5(9):e1000570. doi: 10.1371/journal.ppat.1000570. Epub 2009 Sep 4. PMID: 19730696; PMCID: PMC2731838. [PDF] [PubMed]
Kelley R, Ideker T. Genome-wide fitness and expression profiling implicate Mga2 in adaptation to hydrogen peroxide. PLoS Genet. 2009 May;5(5):e1000488. doi: 10.1371/journal.pgen.1000488. Epub 2009 May 29. PMID: 19503593; PMCID: PMC2676504. [PDF] [PubMed]
Enrichment Summary: Differentially expressed or sensitive members of each significantly over-represented condition or transcription factor target set mentioned in the study. [Data Set]
Expression Table: Log ratios and p-values for all micro-array expression profiling experiments conducted in this study. [Data Set]
Fitness Table: P-values for acute and adaptive screens conducted in this study. [Data Set]
TFs Table: Table containing all of the transcription factor target sets used in this study. [Data Set]
Bushman FD, Malani N, Fernandes J, D’Orso I, Cagney G, Diamond TL, Zhou H, Hazuda DJ, Espeseth AS, König R, Bandyopadhyay S, Ideker T, Goff SP, Krogan NJ, Frankel AD, Young JA, Chanda SK. Host cell factors in HIV replication: meta-analysis of genome-wide studies. PLoS Pathog. 2009 May;5(5):e1000437. doi: 10.1371/journal.ppat.1000437. Epub 2009 May 29. PMID: 19478882; PMCID: PMC2682202. [PDF] [PubMed]
Moxley JF*, Jewett MC*, Antoniewicz MR*, Villas-Boas SG*, Alper H, Wheeler RT, Tong L, Hinnebusch AG, 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. 2009 Apr 21;106(16):6477-82. doi: 10.1073/pnas.0811091106. Epub 2009 Apr 3. PMID: 19346491; PMCID: PMC2672541. *Equal Contribution [PDF] [PubMed]
Mak HC, Pillus L, Ideker T. Dynamic reprogramming of transcription factors to and from the subtelomere. Genome Res. 2009 Jun;19(6):1014-25. doi: 10.1101/gr.084178.108. Epub 2009 Apr 16. PMID: 19372386; PMCID: PMC2694488. [PDF] [PubMed]
Schwartz AS, Yu J, Gardenour KR, Finley RL Jr, Ideker T. Cost-effective strategies for completing the interactome. Nat Methods. 2009 Jan;6(1):55-61. doi: 10.1038/nmeth.1283. Epub 2008 Dec 14. PMID: 19079254; PMCID: PMC2613168. [PDF] [PubMed]
Ideker T. Book Review: “Wetware: A Computer in Every Living Cell” by Dennis Bray. Cell 138: 820-821 (2009) (Review)
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. Nat Protoc. 2007;2(10):2366-82. doi: 10.1038/nprot.2007.324. PMID: 17947979; PMCID: PMC3685583. †Co-Corresponding Authors [PDF] [PubMed]
Chuang HY*, Lee E*, Liu YT, Lee D, Ideker T. Network-based classification of breast cancer metastasis. Mol Syst Biol. 2007;3:140. doi: 10.1038/msb4100180. Epub 2007 Oct 16. PMID: 17940530; PMCID: PMC2063581. *Equal Contribution [PDF] [PubMed]
Ourfali O, Shlomi T, Ideker T, Ruppin E, Sharan R. SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. Bioinformatics. 2007 Jul 1;23(13):i359-66. doi: 10.1093/bioinformatics/btm170. PMID: 17646318. [PDF] [PubMed]
Parrish JR, Yu J, Liu G, Hines JA, Chan JE, Mangiola BA, Zhang H, Pacifico S, Fotouhi F, Dirita VJ, Ideker T, Andrews P, Finley RL Jr. A proteome-wide protein interaction map for Campylobacter jejuni. Genome Biol. 2007;8(7):R130. doi: 10.1186/gb-2007-8-7-r130. PMID: 17615063; PMCID: PMC2323224. [PDF] [PubMed]
Tan K, Shlomi T, Feizi H, Ideker T, Sharan R. Transcriptional regulation of protein complexes within and across species. Proc Natl Acad Sci U S A. 2007 Jan 23;104(4):1283-8. doi: 10.1073/pnas.0606914104. Epub 2007 Jan 16. PMID: 17227853; PMCID: PMC1783126. [PDF] [PubMed]
Mak HC*, Daly M*, Gruebel B, Ideker T. CellCircuits: a database of protein network models. Nucleic Acids Res. 2007 Jan;35(Database issue):D538-45. doi: 10.1093/nar/gkl937. Epub 2006 Nov 29. PMID: 17135207; PMCID: PMC1751555. *Equal Contribution [PDF] [PubMed]
Ideker T, Bafna V, Lemberger T. Integrating scientific cultures. Mol Syst Biol. 2007;3:105. doi: 10.1038/msb4100145. Epub 2007 Apr 17. PMID: 17437030; PMCID: PMC1865587. [PDF] [PubMed] (Editorial)
Beyer A, Bandyopadhyay S, Ideker T. Integrating physical and genetic maps: from genomes to interaction networks. Nat Rev Genet. 2007 Sep;8(9):699-710. doi: 10.1038/nrg2144. PMID: 17703239; PMCID: PMC2811081. [PDF] [PubMed](Review)
Ideker T. Network genomics. Ernst Schering Res Found Workshop. 2007;(61):89-115. doi: 10.1007/978-3-540-31339-7_5. PMID: 17249498. [PDF] [PubMed] (Review)
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)
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. Nat Protoc. 2007;2(10):2366-82. doi: 10.1038/nprot.2007.324. PMID: 17947979; PMCID: PMC3685583. †Co-Corresponding Authors [PDF] [PubMed]
Chuang HY*, Lee E*, Liu YT, Lee D, Ideker T. Network-based classification of breast cancer metastasis. Mol Syst Biol. 2007;3:140. doi: 10.1038/msb4100180. Epub 2007 Oct 16. PMID: 17940530; PMCID: PMC2063581. *Equal Contribution [PDF] [PubMed]
Ourfali O, Shlomi T, Ideker T, Ruppin E, Sharan R. SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. Bioinformatics. 2007 Jul 1;23(13):i359-66. doi: 10.1093/bioinformatics/btm170. PMID: 17646318. [PDF] [PubMed]
Parrish JR, Yu J, Liu G, Hines JA, Chan JE, Mangiola BA, Zhang H, Pacifico S, Fotouhi F, Dirita VJ, Ideker T, Andrews P, Finley RL Jr. A proteome-wide protein interaction map for Campylobacter jejuni. Genome Biol. 2007;8(7):R130. doi: 10.1186/gb-2007-8-7-r130. PMID: 17615063; PMCID: PMC2323224. [PDF] [PubMed]
Tan K, Shlomi T, Feizi H, Ideker T, Sharan R. Transcriptional regulation of protein complexes within and across species. Proc Natl Acad Sci U S A. 2007 Jan 23;104(4):1283-8. doi: 10.1073/pnas.0606914104. Epub 2007 Jan 16. PMID: 17227853; PMCID: PMC1783126. [PDF] [PubMed]
Mak HC*, Daly M*, Gruebel B, Ideker T. CellCircuits: a database of protein network models. Nucleic Acids Res. 2007 Jan;35(Database issue):D538-45. doi: 10.1093/nar/gkl937. Epub 2006 Nov 29. PMID: 17135207; PMCID: PMC1751555. *Equal Contribution [PDF] [PubMed]
Ideker T, Bafna V, Lemberger T. Integrating scientific cultures. Mol Syst Biol. 2007;3:105. doi: 10.1038/msb4100145. Epub 2007 Apr 17. PMID: 17437030; PMCID: PMC1865587. [PDF] [PubMed] (Editorial)
Beyer A, Bandyopadhyay S, Ideker T. Integrating physical and genetic maps: from genomes to interaction networks. Nat Rev Genet. 2007 Sep;8(9):699-710. doi: 10.1038/nrg2144. PMID: 17703239; PMCID: PMC2811081. [PDF] [PubMed](Review)
Ideker T. Network genomics. Ernst Schering Res Found Workshop. 2007;(61):89-115. doi: 10.1007/978-3-540-31339-7_5. PMID: 17249498. [PDF] [PubMed] (Review)
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)
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]
Bandyopadhyay S, Kelley R, Ideker T. Discovering Regulated Networks During HIV-1 Latency and Reactivation. Pac Symp Biocomput. 2006:354-66. PMID: 17094252; PMCID: PMC5224933. [PDF] [PubMed]
Suthram S, Shlomi T, Ruppin E, Sharan R, Ideker T. A direct comparison of protein interaction confidence assignment schemes. BMC Bioinformatics. 2006 Jul 26;7:360. doi: 10.1186/1471-2105-7-360. PMID: 16872496; PMCID: PMC1550431. [PDF] [PubMed]
Reguly T*, Breitkreutz A*, Boucher L*, Breitkreutz BJ*, Hon GC, Myers CL, Parsons A, Friesen H, Oughtred R, Tong A, Stark C, Ho Y, Botstein D, Andrews B, Boone C, Troyanskya OG, Ideker T, Dolinski K, Batada NN*, Tyers M. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J Biol. 2006;5(4):11. doi: 10.1186/jbiol36. Epub 2006 Jun 8. PMID: 16762047; PMCID: PMC1561585. *Equal Contribution [PDF] [PubMed]
Beyer A, Workman C, Hollunder J, Radke D, Möller U, Wilhelm T, Ideker T. Integrated assessment and prediction of transcription factor binding. PLoS Comput Biol. 2006 Jun 16;2(6):e70. doi: 10.1371/journal.pcbi.0020070. Epub 2006 Jun 16. PMID: 16789814; PMCID: PMC1479087. [PDF] [PubMed]
Workman CT, Mak HC, McCuine S, Tagne JB, Agarwal M, Ozier O, Begley TJ, Samson LD, Ideker T. A Systems Approach to Mapping DNA Damage Response Pathways. Science. 2006 May 19;312(5776):1054-9. doi: 10.1126/science.1122088. PMID: 16709784; PMCID: PMC2811083. [PDF] [PubMed]
Scott J, Ideker T, Karp RM, Sharan R. Efficient algorithms for detecting signaling pathways in protein interaction networks. J Comput Biol. 2006 Mar;13(2):133-44. doi: 10.1089/cmb.2006.13.133. PMID: 16597231. [PDF] [PubMed]
Bandyopadhyay S, Sharan R, Ideker T. Systematic identification of functional orthologs based on protein network comparison. Genome Res. 2006 Mar;16(3):428-35. doi: 10.1101/gr.4526006. PMID: 16510899; PMCID: PMC1415213. [PDF] [PubMed] *Cover Article
Feist AM†, Scholten JC†, Palsson BØ, Brockman FJ, Ideker T. Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Mol Syst Biol. 2006;2:2006.0004. doi: 10.1038/msb4100046. Epub 2006 Jan 31. PMID: 16738551; PMCID: PMC1681478. †Co-Corresponding Authors [PDF] [PubMed]
Ideker T, Valencia A. Bioinformatics in the human interactome project. Bioinformatics. 2006 Dec 15;22(24):2973-4. doi: 10.1093/bioinformatics/btl579. PMID: 17142816. [PDF] [PubMed]
Ideker T, Winslow LR, Lauffenburger DA. Bioengineering and systems biology. Ann Biomed Eng. 2006 Jul;34(7):1226-33. doi: 10.1007/s10439-006-9119-3. PMID: 16929563. [PDF] [PubMed] (Review)
Sharan R, Ideker T. Modeling cellular machinery through biological network comparison. Nat Biotechnol. 2006 Apr;24(4):427-33. doi: 10.1038/nbt1196. PMID: 16601728.[PDF] [PubMed] (Review)
Warner GJ, Adeleye YA, Ideker T. Interactome networks: the state of the science. Genome Biol. 2006;7(1):301. doi: 10.1186/gb-2006-7-1-301. Epub 2006 Jan 23. PMID: 16515723; PMCID: PMC1431712. [PDF] [PubMed]
Suthram S, Sittler T, Ideker T. The Plasmodium protein network diverges from those of other eukaryotes. Nature. 2005 Nov 3;438(7064):108-12. doi: 10.1038/nature04135. PMID: 16267557; PMCID: PMC2830740.[PDF] [PubMed]
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. 2005 Jul-Aug;12(6):835-46. doi: 10.1089/cmb.2005.12.835. PMID: 16108720.[PDF] [PubMed]
Yeang CH, Mak HC, McCuine S, Workman C, Jaakkola T, Ideker T. Validation and refinement of gene-regulatory pathways on a network of physical interactions. Genome Biol. 2005;6(7):R62. doi: 10.1186/gb-2005-6-7-r62. Epub 2005 Jul 1. PMID: 15998451; PMCID: PMC1175993. [PDF] [PubMed]
Hsiao A, Ideker T, Olefsky JM, Subramaniam S. VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W627-32. doi: 10.1093/nar/gki443. PMID: 15980550; PMCID: PMC1160204. [PDF] [PubMed]
Workman CT, Yin Y, Corcoran DL, Ideker T, Stormo GD, Benos PV. enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W389-92. doi: 10.1093/nar/gki439. PMID: 15980495; PMCID: PMC1160200.[PDF] [PubMed]
Kelley, R. and Ideker, T. Systematic interpretation of genetic interactions using protein networks. Nature Biotechnology 23(5):561-566 (2005). [PDF] [PubMed]
Sharan R, Suthram S, Kelley RM, Kuhn T, McCuine S, Uetz P, Sittler T, Karp RM, Ideker T. Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci U S A. 2005 Feb 8;102(6):1974-9. doi: 10.1073/pnas.0409522102. Epub 2005 Feb 1. PMID: 15687504; PMCID: PMC548573. [PDF] [PubMed] *Cover Article
Scott J, Ideker T, Karp RM, 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. 2006 Mar;13(2):133-44. doi: 10.1089/cmb.2006.13.133. PMID: 16597231. [PDF] [PubMed]
Ideker, T. “Data collection and analysis in systems biology.” Wiley Encyclopedia of Genetics, Genomics, Proteomics, and Bioinformatics, Dunn, M.J., Jorde, L.B., Little, P.F.R., Subramaniam, S. (Eds). 0-470-84974-6 (2005) [Book]
Ideker, T., Tan, K., Uetz, P. “Visualization and Integration of Protein Interaction Networks”, in Protein-Protein Interactions Second Edition: A Molecular Cloning Manual, E. Golemis and P. Adams eds. CSHL Press, Cold Spring Harbor, N.Y. 7(42):839-856 (2005) [Book chapter]
Haugen AC, Kelley R, Collins JB, Tucker CJ, Deng C, Afshari CA, Brown JM, Ideker T, Van Houten B. Integrating phenotypic and expression profiles to map arsenic-response networks. Genome Biol. 2004;5(12):R95. doi: 10.1186/gb-2004-5-12-r95. Epub 2004 Nov 29. PMID: 15575969; PMCID: PMC545798. [PDF] [PubMed]
Yeang CH, Ideker T, Jaakkola T. Physical network models. J Comput Biol. 2004;11(2-3):243-62. doi: 10.1089/1066527041410382. PMID: 15285891. [PDF] [PubMed]
Kelley BP, Yuan B, Lewitter F, Sharan R, Stockwell BR, Ideker T. PathBLAST: a tool for alignment of protein interaction networks. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W83-8. doi: 10.1093/nar/gkh411. PMID: 15215356; PMCID: PMC441549. [PDF] [PubMed]
Begley TJ, Rosenbach AS, Ideker T, Samson LD. Hot spots for modulating toxicity identified by genomic phenotyping and localization mapping. Mol Cell. 2004 Oct 8;16(1):117-25. doi: 10.1016/j.molcel.2004.09.005. PMID: 15469827. [PDF] [PubMed]
Sharan R, Ideker T, Kelley B, Shamir R, Karp RM. 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). J Comput Biol. 2005 Jul-Aug;12(6):835-46. doi: 10.1089/cmb.2005.12.835. PMID: 16108720. [PDF] [PubMed]
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. 2004;547:21-30. doi: 10.1007/978-1-4419-8861-4_3. PMID: 15230090. [PDF][PubMed] (Review)
Ideker T. Systems biology 101–what you need to know. Nat Biotechnol. 2004 Apr;22(4):473-5. doi: 10.1038/nbt0404-473. PMID: 15085805. [PDF] [PubMed]
Kelley BP, Sharan R, Karp RM, Sittler T, Root DE, Stockwell BR, Ideker T. Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11394-9. doi: 10.1073/pnas.1534710100. Epub 2003 Sep 22. PMID: 14504397; PMCID: PMC208768. [PDF] [PubMed] [PathBLAST Website]
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 2003 Nov;13(11):2498-504. doi: 10.1101/gr.1239303. PMID: 14597658; PMCID: PMC403769. [PDF] [PubMed]
Ozier O, Amin N, Ideker T. Global architecture of genetic interactions on the protein interaction network. Nat Biotechnol. 2003 May;21(5):490-1. doi: 10.1038/nbt0503-490. PMID: 12721566. [PDF] [PubMed]
Young ET, Dombek KM, Tachibana C, Ideker T. Multiple pathways are co-regulated by the protein kinase Snf1 and the transcription factors Adr1 and Cat8. JJ Biol Chem. 2003 Jul 11;278(28):26146-58. doi: 10.1074/jbc.M301981200. Epub 2003 Apr 3. PMID: 12676948. [PDF] [PubMed]
Ideker T, Lauffenburger D. Building with a scaffold: Emerging strategies for high- to low-level cellular modeling. Trends Biotechnol. 2003 Jun;21(6):255-62. doi: 10.1016/S0167-7799(03)00115-X. PMID: 12788545. [PDF] [PubMed] (Comparative Study)
Ideker T, Ozier O, Schwikowski B, Siegel AF. Discovering regulatory and signaling circuits in molecular interaction networks. Bioinformatics. 2002;18 Suppl 1:S233-40. doi: 10.1093/bioinformatics/18.suppl_1.s233. PMID: 12169552.[PDF] [PubMed]
Begley TJ, Rosenbach AS, Ideker T, Samson LD. Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping. Mol Cancer Res. 2002 Dec;1(2):103-12. PMID: 12496357. [PDF] [PubMed]
Griffin TJ, Gygi SP, Ideker T, Rist B, Eng J, Hood L, Aebersold R. Complementary Profiling of Gene Expression at the Transcriptome and Proteome Levels in S. cerevisiae. Mol Cell Proteomics. 2002 Apr;1(4):323-33. doi: 10.1074/mcp.m200001-mcp200. PMID: 12096114. [PDF] [PubMed]
Smith JJ, Marelli M, Christmas RH, Vizeacoumar FJ, Dilworth DJ, Ideker T, Galitski T, Dimitrov K, Rachubinski RA, Aitchison JD. Transcriptome profiling to identify genes involved in peroxisome assembly and function. J Cell Biol. 2002 Jul 22;158(2):259-71. doi: 10.1083/jcb.200204059. Epub 2002 Jul 22. PMID: 12135984; PMCID: PMC2173120. [PDF] [PubMed]
Ideker T, Grimmond S, Ibarra S. “Hybridization and Post-Hybridization Washing,” in DNA Microarrays: A Molecular Cloning Manual, D. Bowtell and J. Sambrook eds. CSHL Press, Cold Spring Harbor, N.Y. (2002) [Book chapter]
Uetz P, Schwikowski B, Ideker T. “Visualization and Integration of Protein-Protein Interactions”, in Protein-Protein Interactions: A Molecular Cloning Manual, E. Golemis ed. CSHL Press, Cold Spring Harbor, N.Y. (2002). [Book chapter]
Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L. Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network. Science. 2001 May 4;292(5518):929-34. doi: 10.1126/science.292.5518.929. PMID: 11340206. [PDF] [PubMed]
Ideker T, Galitski T, Hood L. A New Approach to Decoding Life: Systems Biology. Annu Rev Genomics Hum Genet. 2001;2:343-72. doi: 10.1146/annurev.genom.2.1.343. PMID: 11701654. [PDF] [PubMed](Review)
Ideker T, Thorsson V, Siegel AF, Hood LE. Testing for Differentially-Expressed Genes by Maximum-Likelihood Analysis of DNA Microarray Data. J Comput Biol. 2000;7(6):805-17. doi: 10.1089/10665270050514945. PMID: 11382363. [PDF] [PubMed]
Ideker TE, Thorsson V, Karp RM. Discovery of Regulatory Interactions Through Perturbation: Inference and Experimental Design. Pac Symp Biocomput. 2000:305-16. doi: 10.1142/9789814447331_0029. PMID: 10902179.[PDF] [PubMed]
Nelson PS, Hawkins V, Schummer M, Bumgarner R, Ng WL, Ideker T, Ferguson C, Hood L. Negative Selection: A Method for Obtaining Low Abundance cDNAs Using High Density cDNA Clone Arrays. Genet Anal. 1999 Dec 15;15(6):209-15. doi: 10.1016/s1050-3862(99)00006-6. PMID: 10609756. [PDF] [PubMed]
Picoult-Newberg L, Ideker TE, Pohl MG, Taylor SL, Donaldson MA, Nickerson DA, Boyce-Jacino M. Mining SNPs from EST databases. Genome Res. 1999 Feb;9(2):167-74. PMID: 10022981; PMCID: PMC310719. [PDF] [PubMed]