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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Spatial transcriptome-guided multi-scale framework connects P. aeruginosa metabolic states to oxidative stress biofilm microenvironment

PLoS Comput Biol. 2024 Apr 26;20(4):e1012031. doi: 10.1371/journal.pcbi.1012031. eCollection 2024 Apr.ABSTRACTWith the generation of spatially resolved transcriptomics of microbial biofilms, computational tools can be used to integrate this data to elucidate the multi-scale mechanisms controlling heterogeneous biofilm metabolism. This work presents a Multi-scale model of Metabolism In Cellular Systems (MiMICS) which is a computational framework […]

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Identifying metabolic adaptations characteristic of cardiotoxicity using paired transcriptomics and metabolomics data integrated with a computational model of heart metabolism

PLoS Comput Biol. 2024 Feb 29;20(2):e1011919. doi: 10.1371/journal.pcbi.1011919. Online ahead of print. ABSTRACT Improvements in the diagnosis and treatment of cancer have revealed long-term side effects of chemotherapeutics, particularly cardiotoxicity. Here, we present paired transcriptomics and metabolomics data characterizing in vitro cardiotoxicity to three compounds: 5-fluorouracil, acetaminophen, and doxorubicin. Standard gene enrichment and metabolomics approaches […]

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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. ABSTRACT Bacterial 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, […]

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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