The Scientist
Meenakshi Prabhune, PhD
Feb 23, 2024
Meenakshi Prabhune, PhD
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?
Mapping a human cell gives researchers a view of subcellular architecture and sheds light on how cancer develops
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
Mapping a human cell gives researchers a view of subcellular architecture and sheds light on how cancer develops.
Related Research:
* Schaffer, et al. Multimodal cell maps as a foundation for structural and functional genomics. Nature (2025) [PDF]
* View U2OS Cell Map
May 20, 2025
Researchers at UC San Diego are included in a $142 million initiative from ARPA-H with the goal of creating adaptive and personalized cancer treatments. The six-year project will create new technology to match patients with breast, lung or colon cancer to optimal courses of therapy.
Related Press Release: ARPA-H pioneers game-changing cancer care designed to adapt throughout treatment (ARPA-H ADAPT Program)
April 25, 2025
A high-resolution map of how protein organization inside the cell provides a platform for interrogating the way cancer mutations disrupt entire protein assemblies
Related Research:
* Schaffer, et al. Multimodal cell maps as a foundation for structural and functional genomics. Nature (2025) [PDF]
* View U2OS Cell Map
Jan 27, 2025
What do your genes have to do with growing old? Quite a lot. But is it due to the actual DNA, or the way those genes are expressed? KPBS sci-tech reporter Thomas Fudge has more on new research that raises a question that’s key to treating age-related conditions.
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]
Jan 18, 2024
The team published a study in Cancer Discovery that uses artificial intelligence to predict the best treatment for cancer patients.
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: “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
With deep learning methods revolutionizing life sciences, researchers bet on de novo proteins and cell mapping models to deliver customized precision medicines.
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.
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.
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.