Ph.D., Bioengineering, University of California, San Diego, 2004

Department of Biomedical Engineering
University of Virginia
Box 800759 Health System
Charlottesville, VA 22908

papin@virginia.edu

Laboratory web site

Research Interests

The completed sequences of multiple genomes have catalyzed a phase transition in bioengineering research. Systems analysis has become a requirement for making sense of high-throughput data and for characterizing properties of biological networks. In order to extend these recent developments to medical applications, there is a pressing need for reconstructing and analyzing the biochemical networks that direct cellular processes. The subsequent analysis of these networks requires high-performance computing and sophisticated mathematical techniques.

Our research goals consist of the construction and analysis of large-scale biochemical networks and their application to human disease. Currently, we are working to develop methods for incorporating high-throughput data with integrated signaling, metabolic, and regulatory network reconstructions, and we are using these tools to study fundamental problems in infectious disease, cancer, and bioenergy.

The development and application of computational methods to analyze large biological networks will revolutionize medical research and lead to the characterization of novel therapeutic targets that would be impossible otherwise.

Recent Publications

Oberhardt MA, Palsson BØ, Papin JA
Applications of genome-scale metabolic reconstructions.

Manichaikul A, Ghamsari L, Hom EF, Lin C, Murray RR, Chang RL, Balaji S, Hao T, Shen Y, Chavali AK, Thiele I, Yang X, Fan C, Mello E, Hill DE, Vidal M, Salehi-Ashtiani K, Papin JA
Metabolic network analysis integrated with transcript verification for sequenced genomes.

Gianchandani EP, Joyce AR, Palsson BØ, Papin JA
Functional states of the genome-scale Escherichia coli transcriptional regulatory system.

Roberts SB, Robichaux JL, Chavali AK, Manque PA, Lee V, Lara AM, Papin JA, Buck GA
Proteomic and network analysis characterize stage-specific metabolism in Trypanosoma cruzi.

Mandell JW, Glass G, Gianchandani EP, Locke CN, Amos S, Bourne TD, Schiff D, Papin JA
Dephosphorylation of beta-arrestin 1 in glioblastomas.

More Publications