The long-term objective of the Ideker Lab is to create artificially intelligent, mechanistic models of cancer and neurodegenerative diseases for translation of patient data to precision diagnosis and treatment. We seek to advance this goal by addressing fundamental questions in the field: What are the genetic and molecular networks that promote disease, and how do we best chart these? How do we use knowledge of these networks in intelligent systems for predicting the effects of genotype on phenotype?
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Meet the Team
The Ideker Laboratory has welcomed many distinguished researchers over the years — ranging from undergraduates to visiting scientists. Click buttons below to view Dr. Ideker’s profile and meet our past and present lab members.
Open Projects and Positions
The Ideker Laboratory is in continual open recruitment for excellent postdoctoral scholars, graduate students, and software engineers.
News
Proceedings of the National Academy of Sciences
Epigenetic age can fluctuate by five years in a single day
“It’s a study I’ve been waiting to see for a long time.” – Trey Ideker
Epigenetic changes—in particular, DNA methylation, which can regulate gene expression—are thought to accumulate over years or decades, “but not over short periods,” says Art Petronis, a chrono-epigeneticist with dual appointments at the University of Toronto, Canada, and Vilnius University in Lithuania. But in a recent study in Aging Cell, Petronis and coauthors found that epigenetic age actually fluctuates throughout the course of a day.
Amy McDermott
May 3, 2024
Simulated Chemistry: New AI Platform Designs Tomorrow’s Cancer Drugs
The new platform helped UC San Diego scientists synthesize 32 potential multi-target cancer drug
Explore the advancements at UC San Diego where our innovative AI platform is revolutionizing cancer drug development. Dive deeper into how this technology is setting new standards in drug design and pharmaceutical sciences.
Learn more about our work here.
“AI-guided drug discovery has become a very active area in industry, but unlike the methods being developed in companies, we’re making our technology open source and accessible to anybody who wants to use it.”
–Trey Ideker, Ph.D.
Spotlight
UC San Diego School of Medicine uses AI to predict which drugs to use to treat cancer patients
Discover our recent publication highlighted by four simultaneous news coverage articles. Delve into an informative interview with Dr. Ideker and Abbie Black from CBS News.
Related Press:
- UC San Diego Today, Interesting Engineering, Inside Precision Medicine, Innovators Magazine, The UCSD Guardian, National Cancer Institute (NIH)
- “Hundreds of proteins work together in complex arrangements to replicate DNA. Mutations in any one part of this system can change how the entire tumor responds to chemotherapy.”
Spotlight on Cancer Cell Map Initiative
A New Map
Smartly Done
Forbes 30 Under 30 Class of 2023
Yue Qin, et al. A multi-scale map of cell structure fusing protein images and interactions. Nature. 2021. [PubMed] [PDF]
Recent press: “Studies Delve Deep into the Protein Machinery of Cancer Cells.” NCI (4 Nov 2021)
A New Map Reveals the Complicated World in Which Cells Seek to Repair Damaged DNA.
Scott LaFee, UC San Diego Today. (2023 May 22) [PDF]
Nicole Mlynaryk, UC San Diego Today. (2023 May 18)
Congratulations to Dr. Yue Qin, Ideker Lab Graduate, for getting two major awards! Yue was selected to join the Forbes 30 Under 30, Class of 2023 (read more here and here) and also awarded the 2023 UCSD Chancellor’s Dissertation Medal for the Jacobs School of Engineering.
Yue Qin, et al. A multi-scale map of cell structure fusing protein images and interactions. Nature. 2021. [PubMed] [PDF]
Recent press: We Might Not Know Half of What’s in Our Cells, New AI Technique Reveals.
Tina Wang, et al. Quantitative Translation of Dog-to-Human Aging by Conserved Remodeling of the DNA Methylome. Cell Systems (2020 Aug). [PDF] [PubMed]
Recent Press: Old Dogs, New Research and the Secrets of Aging. New York Times (2020)
Brent M. Kuenzi, Jisoo Park, et al. Predicting Drug Response and Synergy Using a Deep Learning Model of Human Cancer Cells. Cancer Cell (2020 Oct). [PDF] [PubMed]
Recent Press: DrugCell: New Experimental AI Platform Matches Tumor to Best Drug Combo.
Dr. Ideker is a Clarivate Highly Cited Researcher two years in a row, in both 2020 and 2021. This highly anticipated annual list identifies researchers who demonstrated significant influence in their chosen field or fields through the publication of multiple highly cited papers during the last decade. View the complete 2021 Highly Cited Researchers list.
Research Centers & Affiliates
