Computational Systems Biology Lab

Principal Investigator: Jason Papin Ph.D.

Our Mission

What do we do?

We aspire to tackle important questions in the study of metabolic networks that underlie challenges in human health & well-being. We perform experiments to understand the systems-level function of cellular metabolic networks and we develop novel computational tools to integrate high-throughput data in order to predict how cells respond to environmental & genetic perturbations. We perform further experiments to validate and improve these computational models. With increased predictive ability, we gain an understanding of mechanisms of metabolism that are critical in public health and identify potential strategies and interventions. Our efforts in this research area are always guided by clear ethical principles.  As we engage in this research, we will make important advances in the health and well-being of society.

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The Papin Lab

Understanding biochemical networks will lead to revolutionary advances in medicine and biotechnology.

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.

The Computational Systems Biology Laboratory (CSBL) at the University of Virginia uses 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.

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Recent Publications

View some of the Papin Lab's most recent published works. A more complete list of our published works can be found below or by visiting Dr. Papin's PubMed page found on the Publications page.

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A computational model of Pseudomonas syringae metabolism unveils a role for branched-chain amino acids in Arabidopsis leaf colonization

PLoS Comput Biol. 2023 Dec 27;19(12):e1011651. doi: 10.1371/journal.pcbi.1011651. Online ahead of print.ABSTRACTBacterial pathogens adapt their metabolism to the plant environment to successfully colonize their hosts. In our efforts to uncover the metabolic pathways that contribute to the colonization of Arabidopsis thaliana leaves by Pseudomonas syringae pv tomato DC3000 (Pst DC3000), we created iPst19, an ensemble […]

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Model-driven characterization of functional diversity of Pseudomonas aeruginosa clinical isolates with broadly representative phenotypes

bioRxiv. 2023 Oct 10:2023.10.08.561426. doi: 10.1101/2023.10.08.561426. Preprint. ABSTRACT Pseudomonas aeruginosa is a leading cause of infections in immunocompromised individuals and in healthcare settings. This study aims to understand the relationships between phenotypic diversity and the functional metabolic landscape of P. aeruginosa clinical isolates. To better understand the metabolic repertoire of P. aeruginosa in infection, we […]

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Systems-ecology designed bacterial consortium protects from severe Clostridioides difficile infection

bioRxiv. 2023 Aug 10:2023.08.08.552483. doi: 10.1101/2023.08.08.552483. Preprint. ABSTRACT Fecal Microbiota Transplant (FMT) is an emerging therapy that has had remarkable success in treatment and prevention of recurrent Clostridioides difficile infection (rCDI). FMT has recently been associated with adverse outcomes such as inadvertent transfer of antimicrobial resistance, necessitating development of more targeted bacteriotherapies. To address this […]

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415 Lane Road, Room 2041
Charlottesville, VA 22903

Contact Information

(434) 924-8195
Computational lab:
(434) 982-6267
Computational lab 2nd line:
(434) 982-6269
Wet lab:
(434) 924-8640

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Computational Systems Biology Laboratory; The research group of Dr. Jason Papin in the Department of Biomedical Engineering at the University of Virginia.

Contact Info

The research group of Dr. Jason Papin in the Department of Biomedical Engineering at the University of Virginia

  • Email:
  • Phone (434) 924-8195