The Ideker Laboratory is in the Division of Human Genetics and Precision Medicine at UC San Diego School of Medicine. We are a vibrant research team of 30-40 staff, postdocs, graduate students, and undergraduate students known for its dynamic and collaborative environment. We perform bioinformatics research coupled with wet-lab investigations, working in the areas of network biology, data-driven hierarchical modeling, and machine learning applied to biomedicine. We also support multiple open-source software projects, some with 100K+ users.
The Ideker Laboratory at UC San Diego is recruiting a Senior Director of BioMachine Learning (BioML) to lead machine learning research and development at the Center for Dynamic Digital Tumors, a recently launched national precision oncology initiative. This center forms the central AI prediction hub of the ARPA-H ADAPT program.
The overall goal of the project is to use advanced AI/ML technologies to deliver the right therapy to the right patients at the right time. The project will revolutionize cancer treatment via interpretable AI/ML models which learn to predict patient drug responses, enabling dynamical cancer treatment strategies and personalized therapies for patients with metastatic cancers. This position will oversee AI/ML research projects and objectives toward the successful completion of the APRA-H ADAPT program goals.
In particular, the position will:
Direct a team of 6-8 talented AI/ML professionals and trainees in the design and implementation of a drug recommender system for cancer.
Foster interdisciplinary collaborations among biologists, oncologists, statisticians, and other computational/ML scientists to translate computational findings into therapeutic strategies.
Design, debug, and optimize algorithms and computational techniques to analyze and fuse complex, multimodal datasets, including genomic, transcriptomic and proteomic data from various sources for biomarker discovery and therapy recommendation.
Create and validate computational tools to track tumor changes and adapt therapy plans in real-time using insights from clinical data.
Oversee creation of a central benchmarking platform for standardizing AI/ML models.
Contribute to the creation and maintenance of a central cancer treatment and analysis platform, ensuring accurate and timely data availability for clinicians and researchers.
Provide mentorship and guidance to junior researchers, including PhD students and postdocs, fostering expertise in bioML and its applications in oncology.
Prepare detailed reports, publications, and presentations showcasing progress on ADAPT program goals, and represent the lab at national and international conferences.
Collaborate closely with the Ideker Lab’s Program Director to identify and pursue new funding opportunities, align lab objectives with emerging trends in precision medicine, and contribute to grant proposals to support long-term research initiatives.
In addition to the main ADAPT initiative, we expect that this position will work on and potentially lead other projects within the Ideker Lab research portfolio as needed.
Qualifications: PhD or equivalent degree in Computer Science, Statistics, Mathematics, Bioinformatics, or a related discipline, with 3+ years relevant work experience. Experience in deep learning is essential, including but not limited to transformer models, transfer and meta-learning, and multi-modal data fusion approaches. Prior experience in bioinformatics and cancer biology is not required but preferred.
To apply: Send a cover letter and CV to our Program Director, Dr. Jillian Parker at jillianparker@health.ucsd.edu
Ideker Lab develops bioinformatic resources for network analysis that are widely used by the biological and biomedical research community. The best known is Cytoscape, a collaborative open-source platform for visualizing and analyzing complex networks. Cytoscape is widely used, with tens of thousands of downloads per month and more than 25,000 citations from research papers. NDEx, the Network Data Exchange, is another major project. NDEx is a public web resource for sharing, storing, accessing, and publishing biological networks on the cloud. For more information about the Cytoscape Ecosystem & NDEx Network Cloud, visit the Software & Platforms page.
The Ideker Laboratory is currently recruiting a Research Software Developer, please apply via link below. Inquires about positions with our Software Development Team may be directed to Jing Chen at jic002@health.ucsd
The Ideker Lab is in open recruitment for exceptional graduate students, postdocs, and senior research scientists to work across multiple laboratory projects. Prior to submitting an inquiry on available research positions, please watch Dr. Ideker’s recorded talk from AACR 2021, his keynote from the First IDSI Conference 2022, and most importantly, review our Research Projects and Publications relevant to the work that interests you. We have also posted a partial list of open projects.
Postdocs & Senior Research Scientists
Applicants for computational studies must have a PhD in bioinformatics, computer science or a related discipline, a strong background in machine learning and bioinformatics. Applicants for experimental ‘omics studies must have a PhD in the biological sciences with a strong background in genetics and genomics. All applicants must have a history of productive publication. If interested in applying for a position, submit your cover letter, CV, and three professional references to idekeradmin@ucsd.edu
Graduate Students (PhD)
Dr. Ideker is affiliated with the following graduate programs at UC San Diego:
If you have been admitted to a UCSD PhD program and are interested in a Graduate Student Researcher position (including rotations) in the Ideker Lab, please submit your CV and professional references to idekeradmin@ucsd.edu
Graduate Students (MS)
The Ideker lab typically holds interviews for Master of Science (MS) students twice yearly, during the first week of Fall and Spring Quarters. If interested in interviewing, please submit a brief summary of your relevant research interests, your CV, and professional references to idekeradmin@ucsd.edu
**As of Fall 2025, we do not currently have any openings for MS students.
Prospective UCSD Students
Admission to UC San Diego is determined by the university, not individual labs. Only students admitted to a relevant graduate program may be considered for joining our group. More information about graduate admissions can be found here: https://grad.ucsd.edu/admissions/