Jason Papin, Ph.D.

Professor, Biomedical Engineering Harrison Distinguished Teaching Professor

Contact

papin@virginia.edu

Office

(434) 924-8195

Location

MR-5 2041a

Box 800759, Health System
Charlottesville, VA 22908

Google Scholar Papin Lab

About

Jason Papin develops computational models of cellular networks and performs high-throughput experiments to characterize biological systems relevant to human disease. After his training in Bioengineering at the University of California, San Diego, Jason Papin joined the faculty at the University of Virginia in 2005. He is now a Professor in the Department of Biomedical Engineering.

His lab works on problems in systems biology, metabolic network analysis, infectious disease, toxicology, heart disease, and cancer, developing computational approaches for integrating high-throughput data into predictive computational models. He manages a lab with both experimental and computational activities and his research group has had continuous support with funding from the National Institutes of Health, National Science Foundation (including as a CAREER award recipient), Department of Defense, Department of Energy, and several private foundations and companies. Jason is an elected fellow of the Biomedical Engineering Society and the American Institute of Medical and Biological Engineering.

Jason serves as the Co-Editor-in-Chief of PLOS Computational Biology as well as on the editorial board of other journals. His service to the scientific community also includes effort as a past elected member of the Board of Directors of the Biomedical Engineering Society, previously as a standing member of the Biodata Management and Analysis (BDMA) NIH study section, and numerous other review panels of federal funding agencies.

His teaching and mentoring have been recognized with receipt of awards for excellence in undergraduate, graduate, and postdoctoral training. He is the past director of the Biomedical Engineering graduate program at the University of Virginia.

Jason’s work also involves many translational activities with recognition as an inventor on several issued patents and consulting with biotechology companies.

Education

Ph.D. University of California, San Diego 2005

M.S. University of California, San Diego 2002

B.S. University of California, San Diego 2000

There is a pressing need for reconstructing and analyzing the biochemical networks that orchestrate cellular processes. Understanding how these biochemical networks function (and malfunction) will lead to revolutionary advances in medicine, biotechnology, and the understanding of fundamental biological processes.

JASON PAPIN, PHD

Research Interests

Biomedical Data Sciences

Computational Systems Biology

Quantitative Biosciences

Biotechnology and Biomolecular Engineering Biomolecular Design, Cellular and Molecular Bioengineering

Selected Publications

Network analysis of toxin production in Clostridioides difficile identifies key metabolic dependencies. PLOS Computational Biology. D.A. Powers, M.L. Jenior, G.L. Kolling, J.A. Papin

Abstract

Reconstructor: a COBRApy compatible tool for automated genome-scale metabolic network reconstruction with parsimonious flux-based gap-filling. Bioinformatics. M. L. Jenior, E.M. Glass, J.A. Papin

Abstract

Identifying functional metabolic shifts in heart failure with the integration of omics data and a heart-specific, genome-scale model. Cell Reports. B.V. Dougherty, K.D. Rawls, G.L. Kolling, K.C. Vinnakota, A. Wallqvist, J.A. Papin

Abstract

Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models. PLOS Computational Biology. M.A. Carey , G.L. Medlock, M. Stolarczyk, W.A. Petri Jr., J.L. Guler, J.A. Papin

Abstract

Integrated Experimental and Computational Analyses Reveal Differential Metabolic Functionality in Antibiotic-Resistant Pseudomonas aeruginosa. Cell Systems. L.J. Dunphy, P. Yen, J.A. Papin

Abstract

Courses Taught

BME 4380 Microbial Biomedical Engineering

BME 4315/6315 Systems Bioengineering

Awards

Biomedical Engineering Society Fellow (2018)

American Institute of Medical and Biological Engineering College of Fellows (2016)

National Science Foundation CAREER Award (2007-2012)

University of Virginia Research Collaboration Award (2022), Distinguished Career Development Award (2014)

University of Virginia School of Medicine Dean’s Award for Research Excellence in Team Science (2020), Robert J. Kadner Award for Outstanding Graduate Teaching (2017),

UVA Biomedical Engineering Department Outstanding Postdoctoral Student Advisor (2020), Award for Excellence in Biomedical Engineering Undergraduate Education (2012, 2007), Most Helpful Mentor Award (2012),

Featured Grants & Projects

National Institutes of Health T32GM145443 Systems and Biomolecular Data Science Training Program (SBDS) The overarching goal of the Systems and Biomolecular Data Science training program (SBDS) is to prepare the next generation of transdiciplinary biomedical scientists at the interface of quantitative biology, systems biology, machine learning and informatics.

SBDS Website

National Institutes of Health KL2TR003016 iTHRIV Scholars Program The iTHRIV Scholars Program is a mentored, career development award that prepares Scholars to excel in a biomedical research environment in which digital data drives health care hypotheses, interventions, and health quality evaluation.The program contributes to the growth of team science culture with a strong emphasis on clinical translational science.

iTHRIV Website

Computational Systems Biology Laboratory (CSBL) We use computational and experimental approaches to characterize biological systems relevant to human disease. In particular, we reconstruct integrated cellular networks and develop tools to analyze their properties. The analysis of these networks requires sophisticated computing capabilities, experimental methods, and mathematical techniques.

Lab Website