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.

Principle 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

Debi Luzader

dh3bj@virginia.edu
0000-0002-7453-406X
CV

Debi is a Postdoctoral Fellow being co-mentored by Dr. Sean Moore in the Department of Pediatrics. Her research interests are aimed at understanding how host age and circadian rhythms influence the microbiota and the role this plays in bacterial infection. Debi received her BS in Genetics, Cell and Developmental Biology with a minor in Mathematics from Arizona State University and her PhD in Microbiology from the University of Virginia. Debi enjoys baking and running outdoors.


Graduate Students

Matthew Biggs

mb3ad@virginia.edu
0000-0001-6492-8180
LinkedIn

Matt is a fourth-year graduate student. He received his degree in Bioinformatics from Brigham Young University. In his spare time, Matt loves playing soccer, enjoys reading, hiking and other outdoorsy things with his wife and two kids.

Anna Blazier

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

Anna is a second-year 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.

Maureen Carey

mac9jc@virginia.edu
0000-0003-2890-5445

Maureen is a third year microbiology graduate student, working jointly with Dr. Papin and Dr. Jenny G├╝ler. She studies the metabolic network of Plasmodium falciparum in order to investigate antimalarial drug resistance. She received her B.S. in biology from Lafayette College, and likes hiking and going to the farmer's market.

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

Laura is a second-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

Greg is a third-year graduate student. He graduated from the University of Washington in 2014, where he studied bioengineering. He is currently developing models to understand community metabolism within the human gut microbiome. Outside the lab, he enjoys powerlifting and playing tennis.

Thomas Moutinho

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

Tom is a second-year graduate student studying microbial community metabolism related to human health and disease. 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 current third year graduate student 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 trying new restaurants, puzzling, and learning to cook new things.

Phillip Yen

py4wg@virginia.edu
0000-0002-0234-7791

Phillip is a senior graduate student. He has previously been involved in developing metabolic reconstructions of pathogenic Burkholderia species. Currently, he is studying the development of multi-drug resistance in Pseudomonas aeruginosa through adaptive evolution. He did his undergraduate studies in biomedical engineering at Johns Hopkins University. In his leisure time, Phillip likes to bike and play tennis.

Undergraduates

Amanda Elfman

ase3we@virginia.edu

Amanda is a fourth-year undergraduate student, majoring in Biomedical Engineering and minoring in Computer Science. She currently acts as the lab manager and contributes to engineering the co-culture device to study the metabolomics of interacting bacterial populations. In her free time she enjoys playing tennis, hiking, and traveling.

J.C. Panagides

jcp4ay@virginia.edu

J.C. is a third-year undergraduate student majoring in Biomedical Engineering. He is currently working with Matt, Greg, and Tom on engineering a co-culture device to study the metabolomics of diverse bacterial populations. When he's not in the lab, J.C. can be found training to be an EMT, playing piano, or running all over Grounds.

Ana Untaroiu

amu4pv@virginia.edu

Ana is a third-year student majoring in Biomedical Engineering. She is working with Maureen on characterizing transcriptional and metabolic changes in antimalarial-resistant parasites. She enjoys hiking and playing tennis.

Dennis McDuffie

dgm5ha@virginia.edu

Dennis is a third-year undergraduate majoring in Biomedical Engineering and minoring in Spanish. He currently acts as lab manager and is working with Greg in studying bacterial interactions in the gut microbiome. In his free time, he enjoys running, hiking, and golfing.

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?