About

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 and advanced experimental and mathematical techniques.

People

Meet The research team.

Principal Investigator

Dr. Jason Papin

papin@virginia.edu
0000-0002-2769-5805
CV
Dr. Jason Papin is a Professor of Biomedical Engineering at the University of Virginia. His research interests include the integration of high-throughput data into predictive, computational models that can be used to interrogate metabolic and regulatory networks in microbial pathogens and human disease.



Research Faculty

Dr. Glynis Kolling

GLK3A@hscmail.mcc.virginia.edu
0000-0001-8871-8129

Dr. Glynis Kolling is an Assistant Professor of Research at the University of Virginia. Her research interests are aimed at understanding the how metabolism within the intestinal microbiota affects human health and the role of metabolism in various bacterial physiological states.


Postdoctoral Fellows

Matt Jenior

mljenior@virginia.edu
0000-0003-1884-3543

Matt is a Postdoctoral Fellow who recently obtained his Ph.D. in Microbiology & Immunology from the University of Michigan. Prior to graduate school he graduated with a BA in Biology and a minor in Chemistry from Hiram College. Matt is interested in modeling the metabolism of complex communities of bacteria using next-generation sequencing data in order to better understand context-dependent behavior of microbiome and host during disease. He enjoys walking his dog, playing video games, and eating great food.


Graduate Students

Anna Blazier

asb9v@virginia.edu
0000-0001-5226-0339
Linkedin

Anna is a senior graduate student currently studying therapeutic strategies to combat antibiotic resistance using a genome-scale metabolic network reconstruction of Pseudomonas aeruginosa. She studied both biomedical engineering and religious studies as an undergraduate at the University of Virginia.

Bonnie Dougherty

bvd5nq@virginia.edu
0000-0002-1454-4899

Bonnie recently graduated from the University of Virginia with a degree in biomedical engineering. She is currently working on developing a novel plate reader for use in high-throughput screening of microbial pathogens. In her spare time, Bonnie enjoys spending time outdoors, especially hiking, biking, and skiing, as well as exploring Charlottesville with friends.

Laura Dunphy

ljd6ab@virginia.edu
0000-0003-1797-8403
Linkedin
github

Laura is a fourth-year graduate student studying the relationship between bacterial metabolism and the development of antibiotic resistance. She received her undergraduate degree in Biological Engineering from MIT. In her free time, Laura enjoys paddle boarding, snowboarding, and sailing with friends.

Greg Medlock

glm5uh@virginia.edu
0000-0002-1571-0801
Linkedin
github

Greg is a 5th year PhD student in Biomedical Engineering at the University of Virginia. He develops data-driven methods and computational modeling approaches to better understand metabolism within microbial communities. He graduated from the University of Washington with a BS in Bioengineering. Outside the lab, he enjoys powerlifting and tennis.

Thomas Moutinho

tjm4k@virginia.edu
0000-0002-8940-4970

Tom is a fourth-year graduate student studying Lactobacillus metabolism in the context of the gastrointestinal microbiome. He graduated from Worcester Polytechnic Institute in 2015, where he majored in biomedical engineering. For leisure, Tom enjoys hiking, skiing, and archery.

Kristopher Rawls

kr2up@virginia.edu
0000-0001-5873-0127
LinkedIn

Kris is a 5th year PhD in biomedical engineering studying metabolic modeling of different organ systems in response to toxic compounds. He graduated from North Carolina State University in May 2014 and studied biomedical engineering, with a minor in math. Outside the lab Kris enjoys playing video games, visiting wineries, and learning to cook new things.

Undergraduates

Jessica Mahoney

jem2qb@virginia.edu

Jess is a third-year undergraduate student from Long Island, New York and is majoring in Biomedical Engineering. She currently acts as the lab manager and is working with Laura on using computational modeling to predict the interactions between Pseudomonas aeruginosa and other pathogens that co-infect the lung in cystic fibrosis. Jessica is also a part of the Virginia Dance Team and enjoys taking a hot yoga classes in her free time.

Sophia Xiao

sx5hr@virginia.edu

Sophia is a third-year undergraduate student from Manassas, Virginia double majoring in Systems Engineering and Biomedical Engineering. She is working with Tom to study the metabolic interactions between various bacterial species using coculture plates. Sophia enjoys trying new foods and going to the gym in her free time.

benjamin neubert

bcn6fe@virginia.edu

Ben is a third-year undergraduate student from Philadelphia, Pennsylvania majoring in Biomedical Engineering. He is working with Tom on modeling the metabolism of Lactobacillus strains in order to better understand probiotics. In his free time, Ben enjoys reading and exploring new hiking spots.

Opportunities

Postdoctoral Researchers

We are actively looking for talented post-doctoral fellows. Excellent communication skills and a Ph.D. in bioengineering, bioinformatics, chemical engineering, biochemistry or molecular biology with strong experience in a quantitative field are required. Individuals with computational modeling and experimental systems biology expertise particularly relevant to the current project areas are especially encouraged to apply. If you are interested, please send a CV and brief statement of interest to Dr. Jason Papin.

Graduate Students

We are very interested in talented graduate students interested in working in the field of systems bioengineering. Contact Dr. Jason Papin, if interested.

Undergraduate Students

A variety of research projects are available for undergraduate volunteers in engineering or the life sciences. Contact Dr. Jason Papin, if interested.

Questions?