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.

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.

Thumb Thumb

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.

View More

Integrative genome-scale metabolic model of GABAergic neurons reveals metabolic signatures across the mild cognitive impairment – Alzheimer disease continuum

INTRODUCTION: Mild cognitive impairment (MCI) represents a prodromal stage of Alzheimer’s disease (AD), but the metabolic mechanisms underlying early neuronal dysfunction remain incompletely understood. GABAergic neurons, which maintain excitatory-inhibitory balance and network stability, exhibit early vulnerability during neurodegeneration, although the metabolic alterations associated with their dysfunction remain poorly characterized.METHODS: We developed a context-specific genome-scale metabolic […]

Read More

Benchmarking biochemical networks generated by large language models

Computational models of biochemical networks provide frameworks for predicting how molecular cues guide cell decisions. These models are typically limited by the time-intensive manual curation required to extract network mechanisms from incomplete literature. Here, we test whether general-purpose large language models (LLMs) can generate accurate models of signaling and metabolic networks. We find that general-purpose […]

Read More

Integrating multi-omics data with network modeling to characterize Pseudomonas aeruginosa persister cell metabolism

Pseudomonas aeruginosa is a gram-negative bacterial pathogen capable of forming antimicrobial-tolerant subpopulations known as persister cells. These cells are transient phenotypic variants that can tolerate antimicrobial treatment and have been associated with chronic infections and the development of antibiotic resistance. While persister cells are classically associated with reduced metabolic activity, the characteristics of their metabolism […]

Read More
Location

415 Lane Road, Room 2041
Charlottesville, VA 22903

Contact Information

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

Send a Message

papinlab@virginia.edu

Logo

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: papinlab@virginia.edu
  • Phone (434) 924-8195