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]

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]

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)

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]

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 Discov. 2024 Mar 1;14(3):508-523. doi: 10.1158/2159-8290.CD-23-0641. PMID: 38236062  *Equal Contribution [PubMed] [PDF]

• Related Press: “AI Harnesses Tumor Genetics to Predict Treatment Response“. features Trey Ideker, PhD, and Xiaoyu Zhao, Postdoctoral Scholar.

• See also: Interesting Engineering, Innovators Magazine, Inside Precision Medicine, The UCSD Guardian, and the National Cancer Institute (NIH)

Qin Y, Huttlin EL, Winsnes CF, Gosztyla ML, Wacheul L, Kelly MR, Blue SM, Zheng F, Chen M, Schaffer LV, Licon K, Bäckström A, Vaites LP, Lee JJ, Ouyang W, Liu SN, Zhang T, Silva E, Park J, Pitea A, Kreisberg JF, Gygi SP, Ma J, Harper JW, Yeo GW, Lafontaine DLJ, Lundberg E, Ideker T. A multi-scale map of cell structure fusing protein images and interactions. Nature. 2021 Nov 24. doi: 10.1038/s41586-021-04115-9. Online ahead of print. PMID: 34819669 [PubMed] [PDF]

• Related press: “We Might Not Know Half of What’s in Our Cells, New AI Technique Reveals,” features Trey Ideker, PhD, and Yue Qin, grad student. 

• See also: GEN, SciTech Daily, ScienceDaily, The Medical News, Neuroscience News, Science Blog, Laboratory Equipment, La Jolla Light, Times of San Diego and Patch

Zheng F*, Kelly MR*, Ramms DJ, Heintschel ML, Tao K, Tutuncuoglu B, Lee JJ, Ono K, Foussard H, Chen M, Herrington KA, Silva E, Liu SN, Chen J, Churas C, Wilson N, Kratz A, Pillich RT, Patel DN, Park J, Kuenzi B, Yu MK, Licon K, Pratt D, Kreisberg JF, Kim M, Swaney DL, Nan X, Fraley SI, Gutkind JS, Krogan NJ†, Ideker T†. Interpretation of cancer mutations using a multiscale map of protein systems. Science. 2021 Oct;374(6563):eabf3067. doi: 10.1126/science.abf3067. Epub 2021 Oct 1. PMID: 34591613 *Equal Contribution, †Co-Corresponding Authors [PubMed] [PDF]

• Related press: “Looking Beyond DNA to See Cancer with New Clarity,” features Trey Ideker, PhD. 

• See also FierceBiotech, MSN, San Francisco Chronicle and Times of San Diego

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]

• Related Press: UCSD Health, AZoLifeSciences, Med India, Health IT Analytics and ScienceDaily.

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: Here’s a better way to convert dog years to human years, scientists say. Science Magazine (15 Nov 2019).

• See also: Scientific American, BBC, NPR, Washington Post, Discover Magazine, Smithsonian, New York Post, (and more) 

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 

• Cover Art: Nature Methods “About the Cover”

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Zhang W*, Bojorquez-Gomez A*, Velez DO, Xu G, Sanchez KS, Shen JP, Chen K, Licon K, Melton C, Olson KM, Yu MK, Huang JK, Carter H, Farley EK, Snyder M, Fraley SI, Kreisberg JF, Ideker T. A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. Nat Genet. 2018 Apr 2. doi: 10.1038/s41588-018-0091-2. PMID: 29610481 *Equal Contribution [PDF] [PubMed]

• Related Press: Even DNA that Doesn’t Encode Genes Can Drive Cancer 

• See also: Researchers Identify Hundreds of Mutations outside of Coding Genes that Influence Tumor Gene Expression

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]

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

• Cover Art: Artwork by first author Michael Yu

• Related Press: Just the FAQs: Connecting Connecting Genotype to Phenotype with “Ontotype”

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]

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]

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

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]

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]

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 USA. 2005 Feb 8;102(6):1974-9. doi: 10.1073/pnas.0409522102. Epub 2005 Feb 1. PMID: 15687504; PMCID: PMC548573. [PDF] [PubMed] *Cover Article

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]