Jason Papin


Primary Appointment

Professor, Biomedical Engineering


  • PhD, Bioengineering, University of California, San Diego

Research Disciplines

Biochemistry, Bioinformatics and Genomics, Biomedical Engineering, Biophysics, Biotechnology, Cardiovascular Biology, Computational Biology, Experimental Pathology, Infectious Diseases/Biodefense, Metabolism, Microbiology, Physiology, Structural Biology

Research Interests

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

Research Description

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 network reconstructions, and we are using these tools to study fundamental problems in infectious disease, cancer, toxicology, and metabolic engineering.


  • Basic Cardiovascular Research Training Grant
  • Biodefense & Infectious Diseases Short-Term Training to Increase Diversity in Biomedical Sciences
  • Biotechnology Training Grant
  • Cancer Research Training in Molecular Biology
  • Global Biothreats Training Program
  • Infectious Diseases Training Program
  • Training in Cell and Molecular Biology
  • Training in Molecular Biophysics

Selected Publications

Newhook TE, Blais EM, Lindberg JM, Adair SJ, Xin W, Lee JK, Papin JA, Parsons JT, Bauer TW, A thirteen-gene expression signature predicts survival of patients with pancreatic cancer and identifies new genes of interest., 2014; PloS one. 9(9) e105631. PMID: 25180633 | PMCID: PMC4152146

Bartell JA, Yen P, Varga JJ, Goldberg JB, Papin JA, Comparative metabolic systems analysis of pathogenic Burkholderia., 2013; Journal of bacteriology. 196(2) 210-26. PMID: 24163337 | PMCID: PMC3911241

D'Auria KM, Donato GM, Gray MC, Kolling GL, Warren CA, Cave LM, Solga MD, Lannigan JA, Papin JA, Hewlett EL, Systems analysis of the transcriptional response of human ileocecal epithelial cells to Clostridium difficile toxins and effects on cell cycle control., 2012; BMC systems biology. 6() 2. PMID: 22225989 | PMCID: PMC3266197

Chavali AK, D'Auria KM, Hewlett EL, Pearson RD, Papin JA, A metabolic network approach for the identification and prioritization of antimicrobial drug targets., 2012; Trends in microbiology. 20(3) 113-23. PMID: 22300758 | PMCID: PMC3299924

Chavali AK, Blazier AS, Tlaxca JL, Jensen PA, Pearson RD, Papin JA, Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease., 2012; BMC systems biology. 6() 27. PMID: 22540944 | PMCID: PMC3388006

Tilghman RW, Blais EM, Cowan CR, Sherman NE, Grigera PR, Jeffery ED, Fox JW, Blackman BR, Tschumperlin DJ, Papin JA, Parsons JT, Matrix rigidity regulates cancer cell growth by modulating cellular metabolism and protein synthesis., 2012; PloS one. 7(5) e37231. PMID: 22623999 | PMCID: PMC3356407

Blazier AS, Papin JA, Integration of expression data in genome-scale metabolic network reconstructions., 2012; Frontiers in physiology. 3() 299. PMID: 22934050 | PMCID: PMC3429070

Jensen PA, Lutz KA, Papin JA, TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks., 2011; BMC systems biology. 5() 147. PMID: 21943338 | PMCID: PMC3224351

Oberhardt MA, PuchaÅka J, Martins dos Santos VA, Papin JA, Reconciliation of genome-scale metabolic reconstructions for comparative systems analysis., 2011; PLoS computational biology. 7(3) e1001116. PMID: 21483480 | PMCID: PMC3068926

Molhoek KR, Shada AL, Smolkin M, Chowbina S, Papin J, Brautigan DL, Slingluff CL, Comprehensive analysis of receptor tyrosine kinase activation in human melanomas reveals autocrine signaling through IGF-1R., 2011; Melanoma research. 21(4) 274-84. PMID: 21654344 | PMCID: PMC3131461

Haggart CR, Bartell JA, Saucerman JJ, Papin JA, Whole-genome metabolic network reconstruction and constraint-based modeling., 2011; Methods in enzymology. 500() 411-33. PMID: 21943909 | PMCID: PMC3361743

Wieghaus KA, Gianchandani EP, Neal RA, Paige MA, Brown ML, Papin JA, Botchwey EA, Phthalimide neovascular factor 1 (PNF1) modulates MT1-MMP activity in human microvascular endothelial cells., 2009; Biotechnology and bioengineering. 103(4) 796-807. PMID: 19326468 | PMCID: PMC2711776

Glass G, Papin JA, Mandell JW, SIMPLE: a sequential immunoperoxidase labeling and erasing method., 2009; The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society. 57(10) 899-905. PMID: 19365090 | PMCID: PMC2746723

Schmidt BJ, Papin JA, Lawrence MB, Nano-motion dynamics are determined by surface-tethered selectin mechanokinetics and bond formation., 2009; PLoS computational biology. 5(12) e1000612. PMID: 20019797 | PMCID: PMC2787012

Oberhardt MA, Palsson BÃ, Papin JA, Applications of genome-scale metabolic reconstructions., 2009; Molecular systems biology. 5() 320. PMID: 19888215 | PMCID: PMC2795471

Gianchandani EP, Oberhardt MA, Burgard AP, Maranas CD, Papin JA, Predicting biological system objectives de novo from internal state measurements., 2008; BMC bioinformatics. 9() 43. PMID: 18218092 | PMCID: PMC2258290

Lee JM, Min Lee J, Gianchandani EP, Eddy JA, Papin JA, Dynamic analysis of integrated signaling, metabolic, and regulatory networks., 2008; PLoS computational biology. 4(5) e1000086. PMID: 18483615 | PMCID: PMC2377155

Wieghaus KA, Gianchandani EP, Paige MA, Brown ML, Botchwey EA, Papin JA, Novel pathway compendium analysis elucidates mechanism of pro-angiogenic synthetic small molecule., 2008; Bioinformatics (Oxford, England). 24(20) 2384-90. PMID: 18718940 | PMCID: PMC2562016

Robertson SH, Smith CK, Langhans AL, McLinden SE, Oberhardt MA, Jakab KR, Dzamba B, DeSimone DW, Papin JA, Peirce SM, Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior., 2007; BMC systems biology. 1() 46. PMID: 17953751 | PMCID: PMC2190763

Gianchandani EP, Papin JA, Price ND, Joyce AR, Palsson BO, Matrix formalism to describe functional states of transcriptional regulatory systems., 2006; PLoS computational biology. 2(8) e101. PMID: 16895435 | PMCID: PMC1534074

Gianchandani EP, Brautigan DL, Papin JA, Systems analyses characterize integrated functions of biochemical networks., 2006; Trends in biochemical sciences. 31(5) 284-91. PMID: 16616498