Professor and Department Chair, Biomolecular Engineering Department
Jack Baskin Endowed Chair of Biomolecular Engineering
Faculty Affiliate, UC Santa Cruz Genomics Institute
Alfred P. Sloan Fellow, 2005-2012
Lab Webpage
Curriculum Vitae

1156 High Street
Mail Stop: SOE2
UC Santa Cruz
Santa Cruz, CA 95066
831 459 1344 (office)
831 459 4829 (fax)

Research Interests

Dr. Stuart has expertise in developing computational models to integrate multiple sources of information and a background in machine-learning applied to high-throughput datasets. He has recently developed pathway-based models to integrate multiple sources of gene activity to predict alterations and clinical outcomes in tumor samples. He co-leads the Pan-Cancer working groups for the Cancer Genome Atlas project and the International Cancer Genomics Consortium, co-directs the UCSC-Buck institute genome data analysis center, directs a big data resource for NCI to develop high-level information from CGHub raw DNA/RNA sequence data, and leads the pathway analysis for a prostate cancer Stand Up To Cancer and Prostate Cancer Foundation “Dream Team.” 

  • Discovering pathways underlying carcinogenesis. Work with David Haussler
  • Open competitions to identify the best methods for cancer analysis with DREAM.

List Publications


  • BME 211 - Computational Systems Biology.
  • BME 200 - Research and Teaching in Bioinformatics.
  • BME 230 - Computational Genomics. (with David Haussler)
  • BME 60 - Programming for Biologists and Biochemists.
  • BME 210 - Application and Analysis of Microarrays (with Todd Lowe)
  • BME 280b - Bioinformatics Graduate Seminar