Meet our team members

Jason Papin Ph.D.

Principal Investigator

Mohammad Mazharul Islam Ph.D.

Postdoctoral Research Associate

Mariska Batavia Ph.D.

Postdoctoral Research Associate

Lillian Dillard Ph.D.

Postdoctoral Research Associate

Deborah Powers

Graduate Student

Joseph Ficarrotta

Graduate Student

Emma Glass

Graduate Student

Connor Moore

Graduate Student

Will Shao

Graduate Student

Alumni: Post-Doctoral Fellows

Matthew Jenior (8/17 – 6/22):

Project: Metabolic networks of microbial communities

Previous: PhD Microbiology, University of Michigan

Post-lab: Scientist at Zymergen (www.zymergen.com)

Deborah Luzader (1/17 – 1/18) (co-advised by Sean Moore, MD):

Project: Intersection of microbial metabolism and gut epithelial circadian rhythms

Previous: PhD Microbiology, University of Virginia

Post-lab: Scientist at FDA

Jacob Koskimaki (11/12 – 8/13):

Project: Systems analysis of rat metabolism for toxicology studies.

Previous: Ph.D. Biomedical Engineering, Johns Hopkins University

Post-lab: Associate Director of Data Analytics at the American Society of Clinical Oncology

Arvind Chavali (7/11 – 7/12):

Project: Reconstruction of intracellular metabolic network of Leishmania major and immune response.

Previous: Ph.D. Biomedical Engineering, University of Virginia

Post-lab:  Consultant with ZS Associates.

Charles Haggart (7/10 – 10/11)  (Joint with Dr. Jeff Saucerman):

Project: Reconstruction and analysis of a human cardiomyocyte-specific metabolic network.

Previous: Ph.D. Biomedical Engineering, Columbia University

Post-lab:  Scientist at FDA

Brian Schmidt (5/09 – 10/09):

Project: Reconstruction of metabolic network of cardiac myocyte under Type 2 diabetes; machine learning approaches applied to cancer profiling data.

Previous: Ph.D. Biomedical Engineering, University of Virginia

Current Status: Scientist at Bristol-Myers Squibb

Ani Manichaikul (1/08 – 9/09):

Project: Validation of genome annotation through network reconstruction and analysis of Chlamydomonas reinhardtii metabolism with hydrogen production applications

Previous: Ph.D. Biostatistics, Johns Hopkins University

Current Status: Associate Professor, Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia (see people.virginia.edu/~am3xa/)

Jong-Min Lee (7/05 – 7/06):

Project: Genome-scale dynamic analysis of cellular signaling.

Previous:  Ph.D. Chemical Engineering, Georgia Institute of Technology

Current Status: Associate Professor, Department of Chemical Engineering, Seoul National University (see http://epel.snu.ac.kr/)

Alumni: Graduate Students

Lillian Dillard (2/20 – 8/23):

Project: Metabolic network analysis of the vaginal microbiome.

Awards: Appointment to Biotechnology Training Grant; 2nd Place Poster UVA GBS Research Day (2022); NSF ADVANCE appointment (2022-2023); 1st Place (Tied) Poster GBS Symposium (2023); 1 of 5 finalists for the DSM Kirk Apt North American Biotech Student Award (2023)

Dawson Payne (12/19 – 12/21):

Project: Mucin-modulated metabolism of Pseudomonas aeruginosa.

Current Status: Scientist at Genomatica, Inc. (www.genomatica.com)

Thomas Moutinho (8/15 – 8/21):

Project: Metabolism of microbial co-cultures.

Awards: NSF Graduate Research Fellowship (2016-2019)

Current Status: Bioinformatician at Conagen, Inc. (www.conagen.com)

Laura Dunphy (1/16 – 11/20):

Project: Pseudomonas drug resistance.

Awards: NSF Graduate Research Fellowship (2016-2019)

Current Status: Scientist at Applied Physics Lab (www.jhuapl.edu)

Bonnie Dougherty (1/16 – 11/20):

Project: Toxicology metabolism.

Awards: Cardiovascular Training Grant appointment (2016 – present), NSF Graduate Research Fellowship (2017-2020)

Current Status: Scientist at Tempus (www.tempus.com)

Kris Rawls (12/14 – 12/19):

Project: Rat metabolic network.

Awards: Vice President National Society of Black Engineers (2016), Updike Award for BME Department Service (2019)

Current Status: Computational biologist for Hemoshear Therapeutics (www.hemoshear.com)

Greg Medlock (12/14 – 5/19):

Project: Microbiome dynamics.

Awards: NSF Graduate Research Fellowship Honorable Mention (2016), Hungerford Prize (2019), Grand Challenges Grant from Gates Foundation (2019)

Post-lab: Assistant Professor, University of Virginia, Department of Pediatrics; Director of Research at Vedanta Biosciences (www.vedantabio.com)

Anna Blazier (8/13 – 4/19):

Project: Persistence in microbial pathogens.

Awards: Updike Award for BME Department Service (2016)

Current Status: Scientist at Casma Therapeutics (https://www.casmatx.com/)

Maureen Carey (1/15 – 10/18):

Project: Plasmodium falciparum metabolism.

Awards: PhRMA Fellowship (2018)

Current Status: Assistant Professor, University of Virginia, Department of Medicine

Matthew Biggs (8/12 – 2/17):

Project: Network analysis of pathogenicity in P. aeruginosa.

Awards: Presidential Fellowship in Data Science (2014-2015)

Current Status:  Bioinformatics scientist at AgBiome (www.agbiome.com)

Phillip Yen (8/11 – 12/17):

Project: Network analysis of pathogenicity in P. aeruginosa.

Awards: Huskey Research Symposium – 1st place in division (2016), Top prize ASM student poster competition (2016)

Current Status:  Scientist at Arzeda (www.arzeda.com)

Edik Blais (1/11 – 8/16):

Project: Network analysis of cancer metabolism.

Awards: Appointment on Cancer Training Grant.

Current Status:  Computational biologist at Perthera (www.perthera.com)

Jennifer Bartell (1/11 – 5/15):

Project: Systems analysis of pathogenesis in Burkolderia cenocepacia.

Awards: Sture G. Olsson Fellowship (University of Virginia) 2012, Whitaker International Post-Doctoral Fellowship 2015

Post-lab:  Post-doctoral fellow at Denmark Technical University (DTU)

Kevin D’Auria (8/09 – 7/14):

Project: Systems analysis of Clostridium difficile toxins.

Awards: Infectious Disease Training Grant Annual Symposium, Presenter Award (2013)

Current Status:  Scientist at Counsyl (www.counsyl.com)

Paul Jensen (8/08 – 12/13):

Project: Network analysis of pathogenicity in P. aeruginosa and network analysis methods.

Awards:  NSF Graduate Research Fellowship (2010-2013), Double Hoo Research Award ($5000), Department of Biomedical Engineering, Most Outstanding Student (2013)

Current status: Assistant Professor, Bioengineering, University of Illinois

Arvind Chavali (8/06 – 5/11):

Project: Reconstruction of intracellular metabolic network of Leishmania major and immune response.

Awards: Award for Excellence in the Sciences and Engineering, University of Virginia (2009), Grand Prize Winner, University-wide research poster competition, University of Virginia Presidential Inauguration (2011)

Current Status: Consultant with ZS Associates

Matthew Oberhardt (11/05 – 8/10):

Project: Analysis of metabolic networks in opportunistic pathogen Pseudomonas aeruginosa.

Awards: Hungerford Prize (For most outstanding graduate research in the University of Virginia Biomedical Sciences graduate programs 2010), Dan David Prize 2010, Whitaker International Fellowship 2010, Department of Biomedical Engineering Most Outstanding Student 2010, Award for Excellence in the Sciences and Engineering, University of Virginia 2008

Current Status: Data Scientist, Columbia University/Presbyterian Health System, New York

Corinne Locke (11/05 – 12/07):

Graduated with M.S. in Molecular Physiology & Biophysics, 2008

Project: Reconstruction and analysis of signaling networks in gliomas.

Post-lab:  Medical Resident, Physical Med and Rehab, Carolinas Med Center, Charlotte, NC

Erwin Gianchandani (1/05 – 3/09):

Project: Integration of cellular signaling, regulatory, and metabolic networks in Saccharomyces cerevisiae; systems analysis of signaling networks in human cancer.

Awards: AAAS Science Policy Fellowship 2009, Department of Biomedical Engineering Most Outstanding Student 2008, Award for Excellence in the Sciences and Engineering, University of Virginia 2007

Post-lab: Director of Computing Research Association (2009-2012); Director of BMEplanet (2009).

Current Status: Deputy Director, Computing Division, NSF (2013 – present).

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