Feb 23, 2024
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?
Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders
Yuan Mei, et al. Nature Genet. 2025
The Hallmarks of Predictive Oncology
Akshat Singhal, et al. Cancer Discovery 2025
State of the interactomes: an evaluation of molecular networks for generating biological insights.
Sarah Wright, et al. Mole Syst Biol. 2025
A multilineage screen identifies actionable synthetic lethal interactions in human cancers
Samson Fong, et al. Nature Genet. 2024
Prediction of immunotherapy response using mutations to cancer protein assemblies
JungHo Kong, et al. Sciences Advances 2024
Get to know the individuals behind the Ideker Lab. Discover available positions within our lab and explore career opportunities in bioinformatics, cancer cell research, and related disciplines at other organizations.
What the Ideker Lab is reading . . . The Network Biology journal club was established by the Ideker Lab in 2016 to review and evaluate scientific papers in the area of systems biology. All UCSD trainees and research scientists are welcome to attend these meetings, click link below to view upcoming meeting schedule and past papers.
Dr. Trey Ideker and Zane Koch discuss their publication, "Somatic mutation as an explanation for epigenetic aging" (Koch, et al, Nature Aging. 2025) [PubMed] [PDF]
Drs. Trey Ideker and Xiaoyu Zhou discuss their publication, "Cancer mutations converge on a collection of protein assemblies to predict resistance to replication stress." (Zhao, Singhal, et al. Cancer Discovery. 2024) [PubMed] [PDF]
Video Interview: “Inside the Lab: Researcher Spotlight with Dr. Trey Ideker.” UC San Diego Moores Cancer Center’s Researcher Spotlight Series. (Jan 7, 2025) [Vimeo]
Congratulations to Dr. Trey Ideker for his continued recognition as a 2024 Highly Cited Researcher.
UC San Diego ranks 9th in the world for Most Influential Researchers — with 56 recognitions— on the 2024 list.
UC San Diego Today
November 26, 2024
Infusion of Artificial Intelligence in Biology
With deep learning methods revolutionizing life sciences, researchers bet on de novo proteins and cell mapping models to deliver customized precision medicines.
Feb 23, 2024
Congratulations to Dr. Yue Qin! Yue was selected to join the Forbes 30 Under 30, Class of 2023 and also awarded the 2023 UCSD Chancellor’s Dissertation Medal for the Jacobs School of Engineering.
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)
Artificial intelligence is on its way to transforming how we understand and treat disease.
Nicole Mlynaryk
UC San Diego Today
May 18, 2023
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. 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
The Ideker Lab is recruiting exceptional bioinformatics graduate students, postdocs, and senior research scientists to work across multiple laboratory projects. Prior to submitting an inquiry on available positions, please click the link below to learn more about how to apply.