Assembling Digital Tumor Cells for Precision Oncology

About this Class

Trey Ideker, Ph.D., is a professor of medicine, bioengineering, and computer science, and former chief of genetics at the University of California San Diego (UCSD). Additionally, he is director or co-director of the Bridge2AI Functional Genomics Data Generation Program, the Cancer Cell Map Initiative, the National Resource for Network Biology, and the UCSD Graduate Program in Bioinformatics and Systems Biology—all NIH-funded efforts.

Dr. Ideker received his B.S. and M.Eng. degrees in computer science from the Massachusetts Institute of Technology and a Ph.D. in genome sciences from the University of Washington under Drs. Lee Hood and Dick Karp. He was then a David Baltimore fellow at the Whitehead Institute in Cambridge, MA, before joining the UCSD faculty in 2003. Presently, Dr. Ideker serves on the Board of Scientific Advisors to NCI and, formerly, to the National Human Genome Research Institute. He also serves on the editorial boards of Cell, Cell Systems, PLoS Computational Biology, and Molecular Systems Biology. He was named a Top 10 Innovator by Technology Review, received the 2009 International Society for Computational Biology Overton Prize, and is a fellow of the American Association for the Advancement of Science, American Institute for Medical and Biological Engineering, and International Society for Computational Biology organizations. Since 2020, he has been named a Web of Science Highly Cited Researcher (top 1% by citations).

Dr. Ideker’s research laboratory has led seminal studies establishing the theory and practice of systems biology, including systematic techniques for elucidating human cell architecture and its molecular networks. From 2001 to the present, his laboratory produced numerous maps of protein-protein, transcriptional, and genetic networks in model organisms and humans (in collaboration with trainees and co-investigators), along with widely used Cytoscape network analysis software (with Dr. Gary Bader and others). His studies introduced core concepts in bioinformatics, including generation of transcriptional networks to explain genome-wide expression patterns (with Dr. Leroy Hood), network alignment and evolutionary comparison (with Drs. Richard Karp and Roded Sharan) and network biomarkers, which enable multigenic definitions of patient subtypes and treatment responses. He also introduced experimental mapping techniques, including synthetic-lethal interaction mapping with CRISPR/Cas9 (with Dr. Prashant Mali) and characterization of differential interactions across conditions and time (with Dr. Nevan Krogan). These technologies have broadly informed the mechanisms by which diverse genetic alterations drive cancer, neurological disorders, and drug resistance.

Recently, Drs. Ideker and Emma Lundberg demonstrated an end-to-end pipeline for mapping the structure of human cells over a broad range (10–9 to 10–5 m) based on the fusion of protein networks with immunofluorescence imaging. Dr. Ideker has also recently shown that network maps provide a substrate for deep learning models of cell structure and function, with basic implications for the construction of intelligent systems in precision medicine (with Dr. Jianzhu Ma and co-investigators). Finally, Dr. Ideker and collaborators showed that large parts of the methylome are remodeled with age, leading to the first epigenetic clock and the rapidly expanding field of epigenetic aging.