Publication Highlights

PUBLICATION HIGHLIGHTS

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 15, 3636 (2024). https://doi.org/10.1038/s41467-024-47120-y. [PubMed] [PDF]
- Related Press: Drug Discovery News, UC San Diego Today, list23, International The News, Scitechdaily

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

Spotlight on the Cancer Cell Map Initiative with three simultaneous publications in Science (Oct 2021)
- Zheng F*, Kelly MR*, Ramms DJ, Heintschel ML, Tao K, Tutuncuoglu B, Lee JJ, Ono K, Foussard H, Chen M, Herrington KA, Silva E, Liu SN, Chen J, Churas C, Wilson N, Kratz A, Pillich RT, Patel DN, Park J, Kuenzi B, Yu MK, Licon K, Pratt D, Kreisberg JF, Kim M, Swaney DL, Nan X, Fraley SI, Gutkind JS, Krogan NJ†, Ideker T†. Interpretation of cancer mutations using a multiscale map of protein systems. Science. 2021 Oct;374(6563):eabf3067. doi: 10.1126/science.abf3067. Epub 2021 Oct 1. PMID: 34591613 *Equal Contribution, †Co-Corresponding Authors [PubMed] [PDF]
  - Related press: “Looking Beyond DNA to See Cancer with New Clarity,” features Trey Ideker, PhD.
  - See also FierceBiotech, MSN, San Francisco Chronicle and Times of San Diego

- Swaney DL, Ramms DJ, Wang Z, Park J, Goto Y, Soucheray M, Bhola N, Kim K, Zheng F, Zeng Y, McGregor M, Herrington KA, O’Keefe R, Jin N, VanLandingham NK, Foussard H, Von Dollen J, Bouhaddou M, Jimenez-Morales D, Obernier K, Kreisberg JF, Kim M, Johnson DE, Jura N, Grandis JR, Gutkind JS, Ideker T†, Krogan NJ†. A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity. Science. 2021 Oct;374(6563):eabf2911. doi: 10.1126/science.abf2911. Epub 2021 Oct 1. PMID: 34591642 †Co-Corresponding Authors [PubMed] [PDF]

- 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]

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)

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)

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”
- Related Press: Cracking Open the Black Box of AI with Cell Biology
- See also: How a Yeast Cell Helps Crack Open the “Black Box” Behind Artificial Intelligence
- See also: Deep Learning-Based Cell Model May Predict Patient Tumor Cell Growth Someday

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

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]
- Data: [Dataset] [GitHub]

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

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
- 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]
- Supplemental Data: Supporting Online Material for Rewiring of Genetic Networks in Response to DNA Damage
- Differential epistasis mapping (dE-MAP) [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]
- Human TF interactions [Data]
- Mouse TF interactions [Data]

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]

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]

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]
- Supplemental Information: The Plasmodium protein network diverges from those of other eukaryotes

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

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]
- Supplemental Data: Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network