Biology Seminar | Paul Denis Thomas - Tuesday, May 2, 2023 - 4 pm

Date: Tuesday, May 2, 2023

Reception: 3:30 pm

Seminar: 4 pm

Location: Chen 100

Speaker: Paul Denis Thomas

Professor of Population and Public Health Sciences

Keck School of Medicine - University of Southern California

Faculty Host: Paul Sternberg

Title: Big Knowledge in Biology: using phylogenetics and data science to create a human gene "functionome"

Abstract: Understanding the human functionome – the complete set of functions performed by the macromolecules encoded by all genes of the human genome – has been a longstanding goal of biomedical research. It is clear that much progress has been made, but quantifying that progress has remained a challenge. I will describe the approach and results from a multi-year effort by the Gene Ontology Consortium to create a complete, draft human functionome, as determined from a comprehensive synthesis of functional knowledge from ~175,000 published papers in the Gene Ontology knowledgebase. Our approach relies on expert manual curation on top of semantic integration using the ontology, and evolutionary modeling, using gene phylogenies to integrate knowledge for human genes and their homologs in model organisms. The resulting draft functionome specifies at least one functional characteristic for >80% of human protein-coding genes, with 20-40% of genes being functionally well characterized. Our work provides a tool for exploring the human genome, and a quantitative estimate of the contributions of experimental studies in both humans and non-human models to our current understanding of the functions of human genes.