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.

Last week we welcomed 102 #COBRA community members from 48 institutions from all across the 🌎 in sunny #Galway for #COBRAcon2022. Thank you all for making this conference a huge success! @ines_thiele @GalwayCMNHS @Pharmabiotic @RyanInstitute @ERC_Research @GalwayBayHotel

Important work enabling sex-specific modelling in drug toxicological responses, also addressing the historical underrepresentation of women in clinical studies. @papinsysbio @UVABME #COBRAcon2022

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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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Histone deacetylase inhibition by gut microbe-generated short chain fatty acids entrains intestinal epithelial circadian rhythms

Gastroenterology. 2022 Aug 4:S0016-5085(22)00827-7. doi: 10.1053/j.gastro.2022.07.051. Online ahead of print. ABSTRACT BACKGROUND & AIMS: The circadian clock orchestrates ∼24-hour oscillations of gastrointestinal epithelial structure and function that drive diurnal rhythms in gut microbiota. Here, we use experimental and computational approaches in intestinal organoids to reveal reciprocal effects of gut microbial metabolites on epithelial timekeeping by […]

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Leveraging metabolic modeling to identify functional metabolic alterations associated with COVID-19 disease severity

Metabolomics. 2022 Jul 11;18(7):51. doi: 10.1007/s11306-022-01904-9. ABSTRACT OBJECTIVE: Since the COVID-19 pandemic began in early 2020, SARS-CoV2 has claimed more than six million lives world-wide, with over 510 million cases to date. To reduce healthcare burden, we must investigate how to prevent non-acute disease from progressing to severe infection requiring hospitalization. METHODS: To achieve this […]

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Fecal sphingolipids predict parenteral nutrition associated cholestasis in the neonatal intensive care unit

JPEN J Parenter Enteral Nutr. 2022 Mar 13. doi: 10.1002/jpen.2374. Online ahead of print. ABSTRACT BACKGROUND: Parenteral nutrition associated cholestasis (PNAC) in the neonatal intensive care unit (NICU) causes significant morbidity and associated healthcare costs. Laboratory detection of PNAC currently relies on elevated serum conjugated bilirubin levels in the aftermath of impaired bile flow. Here, […]

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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