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

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.


Graduate Students

Matthew biggs

mb3ad@virginia.edu

Matt is a third-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, and trying new restaurants with his wife, Jessica.

Edik Blais

emb8ab@virginia.edu

Edik is a senior graduate student analyzing the effects of drugs on mammalian metabolism within the contexts of toxicology and cancer. He grew up in Seattle and studied bioengineering at the University of Washington. He enjoys snowboarding, hiking, and listening to the Rebirth Brass Band.

Anna Blazier

asb9v@virginia.edu

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

Maureen is a first 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.

Greg Medlock

glm5uh@virginia.edu

Greg is a first-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

Tom is a first-year graduate student interested in studying human microbiome ecological interactions. He graduated from Worcester Polytechnic Institute in 2015, where he majored in biomedical engineering. For leisure, Tom enjoys hiking, biking, archery and cooking.

Kristopher Rawls

kr2up@virginia.edu

Kris is a current first year graduate student studying the metabolic networks of the rat liver, kidney, and heart. 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, walking, and occasionally playing video games.

Phillip Yen

py4wg@virginia.edu

Phillip is a fourth-year 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.

Lab Technicians

Bonnie Dougherty

bvd5nq@virginia.edu

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.

Undergraduates

Amanda Elfman

ase3we@virginia.edu

Amanda is a third-year undergraduate student, majoring in Biomedical Engineering and minoring in Computer Science. She currently acts as the lab manager for the Papin lab. In her free time she enjoys playing tennis, hiking, and traveling.

Andrew Kubiak

adk9nc@virginia.edu

Andrew is a fourth-year undergraduate student, majoring in Biomedical Engineering with a minor in Computer Science. Andrew is working with Julius Ha on analyzing the metabolic network of P. falciparum. He enjoys playing soccer and has a keen interest in computing technologies and games.

Issac Li

zl5cy@virginia.edu

Issac is a fourth-year undergraduate student, majoring in Biomedical Engineering. Issac is helping Edik on the rat reconstruction, studying the effects of a drug called Nitrofurantoin on the rat liver. He will also work on improving and validating the new rat reconstruction.

Angela Liu

al5sn@virginia.edu

Angela is a fourth year student majoring in Biomedical Engineering and minoring in Engineering Business. Angela is assisting Matt in reconstructing the metabolic networks of several bacteria that are known to exist in the human ileum. In her free time, Angela likes to travel and enjoy the outdoors.

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?