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Jason Papin

Assistant Professor of Biomedical Engineering

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.

Selected Publications

Chavali, A.K., J.D. Whittemore, J.A. Eddy, K.T. Williams, and J.A. Papin. 2008. Systems analysis of metabolism in the pathogenic Trypanosomatid Leishmania major. Nature/EMBO Molecular Systems Biology, in press.

Oberhardt, M.A., J. Puchalka, K. Fryer, V.M. dos Santos, and J.A. Papin. 2008. Genome-scale network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1. Journal of Bacteriology, in press. Cover illustration. [PubMed | Abstract | PDF]

Gianchandani, E.P., M.A. Oberhardt, A.P. Burgard, C.D. Maranas, and J.A. Papin. 2008. Predicting biological system objectives from internal state measurements. BMC Bioinformatics, 9: 43. [PubMed | Abstract | PDF]

Gianchandani, E.P., J.A. Papin, N.D. Price, A.R. Joyce, and B.O. Palsson. 2006. Matrix formalism to describe functional states of transcriptional regulatory systems. PLoS Computational Biology, 2: e101. Cover illustration. [PubMed | Abstract | Full Text | PDF]

Papin, J.A., T. Hunter, B.O. Palsson, and S. Subramaniam. 2005. Reconstruction of cellular signalling networks and analysis of their properties. Nature Reviews Molecular Cell Biology, 6: 1-13.[PubMed | Abstract | Full Text | PDF]

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