Matthew Morris – Rochester General Hospital

Matthew Morris – Rochester General Hospital

Matt is a research scientist in Systems Biology at Rochester Regional Health with an interdisciplinary skill set that spans applied computation and cellular and molecular biology. He holds a PhD in Genetics, Bioinformatics, and Computational Biology from Virginia Tech and is teaching and advising students at the Rochester Institute of Technology. Previously he has studied intracellular signaling networks and pediatric immunology. In partnership with Elsevier, he is currently active in developing network models of chronic diseases and host-pathogen interactions for discovery of novel mechanisms.


Sequential Literature-informed Refinement of Mechanistic Hypotheses in Biology and Medicine


Natural Language Processing now make it possible to extract statements about mechanistic relationships directly from the research community’s understanding of biological processes. By integrating experimental and clinical data with these statements, we can model these processes as logical decision-making circuits. Analysis of the differences in competing candidate models helps identify maximally informative experiments. Recently we developed a model of immune response to upper respiratory infection based on regulatory mechanisms documented in over 20,000 journal publications. We identified 35 candidate models consistent with available data. However, different behaviors were predicted from one model to the next.  Consensus among the family of competing models identified the immune mediators IL-4 and CXCL8 as maximally informative measurements. By performing these measurements, the set of feasible models was reduced from 35 to 11. Casting existing data in the context of documented regulatory mechanisms efficiently focuses experimentation in an advance over conventional design of experiments.