Jason Papin


  • PhD, University of California, San Diego

Primary Appointment

  • Professor, Biomedical Engineering


Research Interest(s)

Systems biology, infectious disease, cancer, toxicology, metabolic engineering

Research Description

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, toxicology, and metabolic engineering.

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

  • Newhook T, Blais E, Lindberg J, Adair S, Xin W, Lee J, Papin J, Parsons J, Bauer T. A thirteen-gene expression signature predicts survival of patients with pancreatic cancer and identifies new genes of interest. PloS one. 2014;9(9): e105631. PMID: 25180633 | PMCID: PMC4152146
  • Bartell J, Yen P, Varga J, Goldberg J, Papin J. Comparative metabolic systems analysis of pathogenic Burkholderia. Journal of bacteriology. 2013;196(2): 210-26. PMID: 24163337 | PMCID: PMC3911241
  • Blazier A, Papin J. Integration of expression data in genome-scale metabolic network reconstructions. Frontiers in physiology. 2012;3 299. PMID: 22934050 | PMCID: PMC3429070
  • Chavali A, Blazier A, Tlaxca J, Jensen P, Pearson R, Papin J. Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease. BMC systems biology. 2012;6 27. PMID: 22540944 | PMCID: PMC3388006
  • Chavali A, D'Auria K, Hewlett E, Pearson R, Papin J. A metabolic network approach for the identification and prioritization of antimicrobial drug targets. Trends in microbiology. 2012;20(3): 113-23. PMID: 22300758 | PMCID: PMC3299924
  • D'Auria K, Donato G, Gray M, Kolling G, Warren C, Cave L, Solga M, Lannigan J, Papin J, Hewlett E. Systems analysis of the transcriptional response of human ileocecal epithelial cells to Clostridium difficile toxins and effects on cell cycle control. BMC systems biology. 2012;6 2. PMID: 22225989 | PMCID: PMC3266197
  • Tilghman R, Blais E, Cowan C, Sherman N, Grigera P, Jeffery E, Fox J, Blackman B, Tschumperlin D, Papin J, Parsons J. Matrix rigidity regulates cancer cell growth by modulating cellular metabolism and protein synthesis. PloS one. 2012;7(5): e37231. PMID: 22623999 | PMCID: PMC3356407
  • Haggart C, Bartell J, Saucerman J, Papin J. Whole-genome metabolic network reconstruction and constraint-based modeling. Methods in enzymology. 2011;500 411-33. PMID: 21943909 | PMCID: PMC3361743
  • Jensen P, Lutz K, Papin J. TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks. BMC systems biology. 2011;5 147. PMID: 21943338 | PMCID: PMC3224351
  • Molhoek K, Shada A, Smolkin M, Chowbina S, Papin J, Brautigan D, Slingluff C. Comprehensive analysis of receptor tyrosine kinase activation in human melanomas reveals autocrine signaling through IGF-1R. Melanoma research. 2011;21(4): 274-84. PMID: 21654344 | PMCID: PMC3131461
  • Oberhardt M, Puchałka J, Martins dos Santos V, Papin J. Reconciliation of genome-scale metabolic reconstructions for comparative systems analysis. PLoS computational biology. 2011;7(3): e1001116. PMID: 21483480 | PMCID: PMC3068926
  • Glass G, Papin J, Mandell J. SIMPLE: a sequential immunoperoxidase labeling and erasing method. The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society. 2009;57(10): 899-905. PMID: 19365090 | PMCID: PMC2746723
  • Oberhardt M, Palsson B, Papin J. Applications of genome-scale metabolic reconstructions. Molecular systems biology. 2009;5 320. PMID: 19888215 | PMCID: PMC2795471
  • Schmidt B, Papin J, Lawrence M. Nano-motion dynamics are determined by surface-tethered selectin mechanokinetics and bond formation. PLoS computational biology. 2009;5(12): e1000612. PMID: 20019797 | PMCID: PMC2787012
  • Wieghaus K, Gianchandani E, Neal R, Paige M, Brown M, Papin J, Botchwey E. Phthalimide neovascular factor 1 (PNF1) modulates MT1-MMP activity in human microvascular endothelial cells. Biotechnology and bioengineering. 2009;103(4): 796-807. PMID: 19326468 | PMCID: PMC2711776
  • Gianchandani E, Oberhardt M, Burgard A, Maranas C, Papin J. Predicting biological system objectives de novo from internal state measurements. BMC bioinformatics. 2008;9 43. PMID: 18218092 | PMCID: PMC2258290
  • Lee J, Min Lee J, Gianchandani E, Eddy J, Papin J. Dynamic analysis of integrated signaling, metabolic, and regulatory networks. PLoS computational biology. 2008;4(5): e1000086. PMID: 18483615 | PMCID: PMC2377155
  • Wieghaus K, Gianchandani E, Paige M, Brown M, Botchwey E, Papin J. Novel pathway compendium analysis elucidates mechanism of pro-angiogenic synthetic small molecule. Bioinformatics (Oxford, England). 2008;24(20): 2384-90. PMID: 18718940 | PMCID: PMC2562016
  • Robertson S, Smith C, Langhans A, McLinden S, Oberhardt M, Jakab K, Dzamba B, DeSimone D, Papin J, Peirce S. Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior. BMC systems biology. 2007;1 46. PMID: 17953751 | PMCID: PMC2190763
  • Gianchandani E, Brautigan D, Papin J. Systems analyses characterize integrated functions of biochemical networks. Trends in biochemical sciences. 2006;31(5): 284-91. PMID: 16616498
  • Gianchandani E, Papin J, Price N, Joyce A, Palsson B. Matrix formalism to describe functional states of transcriptional regulatory systems. PLoS computational biology. 2006;2(8): e101. PMID: 16895435 | PMCID: PMC1534074