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.

Biology is Now a Data Science - a new training grant matches computation and modeling to experimental design
@sepiddsh @NIH @papinsysbio @janeslab @UVAEngineers

Enterococci enhance Clostridioides difficile pathogenesis @Nature

Excellent example of why community context (i.e. who & what else is there) matters in the #microbiome

@papinsysbio is the latest @UVABME lab to get GOLD Green Labs Certification! They took some impressive steps towards being a more sustainable lab including a major overhaul of their cold storage inventories.

#LabTuesdays #LabSustainability #UVAGreenLabs

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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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Enterococci enhance Clostridioides difficile pathogenesis

Nature. 2022 Nov 16. doi: 10.1038/s41586-022-05438-x. Online ahead of print. ABSTRACT Enteric pathogens are exposed to a dynamic polymicrobial environment in the gastrointestinal tract1. This microbial community has been shown to be important during infection, but there are few examples illustrating how microbial interactions can influence the virulence of invading pathogens2. Here we show that […]

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Genome-scale metabolic modeling reveals increased reliance on valine catabolism in clinical isolates of Klebsiella pneumoniae

NPJ Syst Biol Appl. 2022 Oct 28;8(1):41. doi: 10.1038/s41540-022-00252-7. ABSTRACT Infections due to carbapenem-resistant Enterobacteriaceae have recently emerged as one of the most urgent threats to hospitalized patients within the United States and Europe. By far the most common etiological agent of these infections is Klebsiella pneumoniae, frequently manifesting in hospital-acquired pneumonia with a mortality […]

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New perspectives into the vaginal microbiome with systems biology

Trends Microbiol. 2022 Oct 19:S0966-842X(22)00257-8. doi: 10.1016/j.tim.2022.09.011. Online ahead of print. ABSTRACT The vaginal microbiome (VMB) is critical to female reproductive health; however, the mechanisms associated with optimal and non-optimal states remain poorly understood due to the complex community structure and dynamic nature. Quantitative systems biology techniques applied to the VMB have improved understanding of […]

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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