Areas of Interest
Matthew O'Meara received his Ph.D. in 2013 in computer science from UNC Chapel Hill supervised by Jack Snoeyink (CS) and Brian Kuhlman (Biochemistry) developing computational tools for data driven optimization of the forcefield for the Rosetta protein structure and design software. As a postdoc in Brian Shoichet's lab in the Department of Pharmaceutical Chemistry at UCSF through 2019, he worked on developing a ligand-centric view of systems pharmacology and virtual screening with applications in psychiatric disease and metabolite signaling.
Matt's recent interests are in developing statistical and machine learning methods to model complex experimental design problems for pharmacology and biochemistry. Recent breakthroughs in experimental methods and rich simulation based models in the biological sciences promise to enable new insights and discoveries. However, as these methods scale, an increasing bottleneck is expert synthesis to plan highly informative experiments. By modeling experiments probabilistically, it is possible to holistically capture the assumptions and data, the decisions, and the outcomes. This rigor enables navigating the space of experimental designs to maximize the information gain and making new discoveries. Excitingly, recent breakthroughs in statistics and machine learning for building and fitting structured probabilistic models make it now practical to apply these models at scale.
To apply modeling experimental design to problems in pharmacology and biochemistry, Matt is collaborating with a fantastic and diverse set of researchers, including developing chemical probes for eukaryotic pathogens with Teresa O'Meara and Vern Carruthers in the Department of Microbiology and Immunology and Michigan Drug Discovery here at the University of Michigan; biotherapeutic design with Molly Shoichet at the University of Toronto and Marian Hettiaratchi at the University of Oregon; midbrain neuropharmacology with Elissa Margolis UCSF and Brian Athey's lab here in the DCM&B, and cancer drug discovery with James Fraser and Robert Blelloch at UCSF.