Trey Ideker

Trey Ideker is a Professor in the Division of Genetics, Department of Medicine at the University of California, San Diego School of Medicine. He also holds adjunct professor appointments in the Departments of Bioengineering and Computer Science. His research spans multiple disciplines including systems biology, computational biology, and bioinformatics, with particular focus on cancer, networks, and genomic technologies. Ideker leads several major NIH-funded research centers including the Cancer Cell Map Initiative and the National Resource for Network Biology.

His educational background includes a BS and MEng in Electrical Engineering & Computer Science from MIT (1994, 1995) and a PhD in Molecular Biotechnology from the University of Washington (2001).

Dr. Ideker's research primarily focuses on developing systems-level approaches to understand biological networks, particularly in cancer and disease contexts. His work integrates computational methods with experimental biology to map and model complex biological systems. Key areas include network biology, systems genetics, and the development of tools for analyzing high-throughput genomic data. His lab has pioneered approaches for mapping protein-protein interaction networks, genetic networks, and multi-omics integration to understand disease mechanisms.

Analysis of his recent publications reveals a strong emphasis on multiscale network analysis across biological systems, with significant contributions to understanding SARS-CoV-2 host interactions, cancer systems biology, and epigenetic mechanisms of aging. His work consistently bridges computational methodology development with biological discovery, often focusing on network-based approaches to integrate diverse data types.

• 2020 Clarivate Web of Science Highly Cited Researcher (top 1% of citations for field and year)
• 2015 Elected Fellow, American Association for the Advancement of Science (AAAS)
• 2014 Elected Fellow, American Institute for Medical and Biological Engineering (AIMBE)
• 2009 Overton Prize, International Society for Computational Biology (ISCB)
• 2009 Distinguished Alumni Award, Duke University Talent Identification Program
• 2009 Member of Faculty of 1000
• 2006 Technology Review Top 10 Innovator
• 2005 Technology Review Top 35 Young Innovator
• 2004 Packard Foundation Fellowship

Dr. Ideker has received substantial grant funding including multiple NIH R01 awards and leadership roles in major centers such as the Cancer Cell Map Initiative (U54CA209891), National Resource for Network Biology (P41GM103504), and the San Diego Center for Systems Biology (P50GM085764). His research has produced influential tools like Cytoscape and NDEx that are widely used in the systems biology community. He serves on multiple editorial boards including Cell, Cell Systems, and Cell Reports, and has advised numerous graduate students and postdocs who have gone on to establish independent research careers.

Dr. Ideker leads the Ideker Lab at UCSD, which focuses on developing computational and experimental methods for mapping biological networks at multiple scales. The lab is central to the Psychiatric Cell Map Initiative and Cancer Cell Map Initiative, large collaborative efforts to create comprehensive molecular maps of disease states. His team combines high-throughput experimental approaches with advanced computational methods to analyze complex biological systems, with particular emphasis on network-based approaches to understand disease mechanisms and identify therapeutic targets.