Journal of Bacteriology, 2014; click for full text
J Bacteriol.
2014
Trends in Immunology, 2008; click for full text
Trends Immunol.
2008
Journal of Bacteriology, 2008; click for full text
J Bacteriol.
2008
PLoS Computational Biology, 2006; click for full text
PLoS Comput Biol.
2006
Nature Reviews Molecular Cell Biology, 2005; click for full text
Nat Rev Mol Cell Biol.
2005
Trends in Biochemical Sciences, 2004; click for full text
Trends Biochem Sci.
2004

Jensen, Paul A., Jason A. Papin. 2014. MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data. Bioinformatics. [Pubmed | Full Text | PDF]

Bartell Jennifer A., Phillip Yen, John J. Varga, Joanna B. Goldberg, and Jason A. Papin. 2014. Comparative Metabolic Systems Analysis of Pathogenic Burkholderia. Journal of Bacteriology. [Pubmed | Full Text | PDF]

Walters Dustin M., Jayme B. Stokes, Sara J Adair, Edward B. Stelow, Cheryl A. Borgman, Bryce T. Lowrey, Wenjun Xin, Edik M. Blais, Jae K. Lee, Jason A. Papin, J. Thomas Parsons, and Todd W. Bauer. 2013. Clinical, Molecular and Genetic Validation of a Murine Orthotopic Xenograft Model of Pancreatic Adenocarcinoma Using Fresh Human Specimens. PLOS One. [Full Text ]

Biggs Matthew B., and Jason A. Papin. 2013. Novel multiscale modeling tool applied to Pseudomonas aeruginosa biofilm formation. PLOS One .[Full Text ]

Koskimaki, Jacob E., Anna S. Blazier, Andres F. Clarens, and Jason A. Papin. 2013. Computational Models of Algae Metabolism for Industrial Applications. Industrial Biotechnology .[Full Text | PDF]

D’Auria, Kevin M., Glynis L. Kolling, Gina M. Donato, Cirle A. Warren, Mary C. Gray, Erik L. Hewlett, and Jason A. Papin. 2013. In Vivo Physiological and Transcriptional Profiling Reveals Host Responses to Clostridium Difficile Toxin A and Toxin B. Infection and Immunity. [Pubmed | Full Text | PDF]

Walpole, J., J.A. Papin, and S.M. Perice. 2013. Multiscale computational models of complex biological systems. Annual Reviews in Biomedical Engineering. [Pubmed | Full Text | PDF]

Blais, E.M., A.K. Chavali, and J.A. Papin. 2013. Linking genome-scale metabolic modeling and genome annotation, in: Systems Metabolic Engineering: Methods and Protocols, ed. Hal S. Alper. [Pubmed | Full Text | PDF]

Thiele, I., N. Swainston, R.M.T. Fleming, A. Hoppe, S. Sahoo, M.K. Aurich, H. Haraldsdottir, M.L. Mo, O. Rolfsson, M.D. Stobbe, S.G. Thorleifsson, R. Agren, C. Bolling, S. Bordel, A.K. Chavali, P. Dobson, W.B. Dunn, L. Endler, D. Hala, M. Hucka, D. Hull, D. Jameson, N. Jamshidi, J.J. Jonsson, N. Juty, S. Keating, I. Nookaew, N. Le Novere, N. Malys, A. Mazein, J.A. Papin, N.D. Price, E. Selkov Sr., M.I. Sigurdsson, E. Simeonidis, N. Sonnenschein, K. Smallbone, A. Sorokin, J.H.G.M van Beek, D. Weichart, I. Goryanin, J. Nielsen, H.V. Westerhoff, D.B. Kell, P. Mendes and B.O. Palsson. 2013. A community-driven global reconstruction of human metabolism. Nature Biotechnology. [Full Text | PDF]

Schmidt, B.J., J.A. Papin, and C.J. Musante. 2012. Mechanistic systems modeling to guide drug discovery and development. Drug Discovery Today. 00:00/ [Pubmed | Full Text | PDF]

Blazier, A.S. and J.A. Papin. 2012. Integration of expression data in genome-scale metabolic network reconstructions. Frontiers in Computational Physiology and Medicine, 3:299. [Pubmed | Full Text | PDF]

Tilghman, R.W., E.M. Blais, C.R. Cowan, N.E. Sherman, P.R. Grigera, E.D. Jeffrey, J.W. Fox, B.R. Blackman, D.J. Tschumperlin, J.A. Papin, and J.T. Parsons. 2012. Matrix rigidity regulates cancer cell growth by modulating cellular metabolism and protein synthesis. PLoS ONE, 7:5. [Pubmed | Full Text | PDF]

Chavali, A.K., A.S. Blazier, J.L. Tlaxca, P.A. Jensen, R.D. Pearson, and J.A. Papin. 2012. Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease. BMC Systems Biology, 6:27. [Pubmed | Full Text | PDF]

D'Auria, K.M., G.M. Donato, M.C. Gray, G.L. Kolling, C.A. Warren, L.M. Cave, M.D. Solga, J.A. Lannigan, J.A. Papin, and E.L. Hewlett. 2012. Systems analysis of the transcriptional response of human ileocecal epithelial cells to Clostridium difficile toxins and effects on cell cycle control. BMC Systems Biology, 6:2. [Pubmed | Full Text | PDF]

Chavali, A.K., K.M. D'Auria, E.L. Hewlett, R.D. Pearson, and J.A. Papin. 2012. A metabolic network approach for the identification and prioritization of antimicrobial drug targets. Trends in Microbiology, 20:3. [Pubmed | Full Text | PDF]

Haggart, C.R., J.A. Bartell, J.J. Saucerman, and J.A. Papin. 2011. Whole-genome metabolic network reconstruction and constraint-based modeling, in: Methods in Enzymology, ed. Daniel Jameson, Malkhey Verma, and Hans V. Westerhoff. [Pubmed | Full Text | PDF]

Jensen, P.A., K.A. Lutz, and J.A. Papin. 2011. TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks. BMC Systems Biology, 5:147. [Pubmed | Full Text | PDF]

Chang, R.L., L. Ghamsari, A. Manichaikul, E.F.Y. Hom, S. Balaji, W. Fu, Y. Shen, T. Hao, B.Ø. Palsson, K. Salehi-Ashtiani, and J.A. Papin. 2011. Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism. Molecular Systems Biology, 7(518):1-13. [PubMed | Full Text | PDF]

Ghamsari, L., S. Balaji, Y. Shen, X. Yang, D. Balcha, C. Fan, T. Hao, H. Yu, J.A. Papin, and K. Salehi-Ashtiani. 2011. Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii. BMC Genomics, 12(Suppl 1):S4. [Pubmed | Full Text | PDF]

Molhoek, K.R., A.L. Shada, M. Smolkin, S. Chowbina, J.A. Papin, D.L. Brautigan, and C.L. Slingluff. 2011. Comprehensive analysis of receptor tyrosine kinase activation in human melanomas reveals autocrine signaling through IGF-1R. Melanoma Research, 21(274-284). [PubMed | Full Text | PDF]

Oberhardt, M.A., J. Puchalka, V.A. Martins dos Santos, and J.A. Papin. 2011. Reconciliation of genome-scale metabolic reconstructions for comparative systems analysis. PLoS Computational Biology, 7(3):e1001116. [PubMed | Full Text | PDF]

Jensen, P.A. and J.A. Papin. 2011. Functional integration of a metabolic network model and expression data without arbitrary thresholding. Bioinformatics, 27(4):541-547. [PubMed | Full Text | PDF]

Benedict, K.F., F. Mac Gabhann, R.K. Amanfu, A.K. Chavali, E.P. Gianchandani, L.S. Glaw, M.A. Oberhardt, B.C. Thorne, J.H. Yang, J.A. Papin, S.M. Peirce, J.J. Saucerman, and T.C. Skalak. 2011. Systems analysis of small signaling modules relevant to eight human diseases. Annals of Biomedical Engineering, 39(2):621-635. [PubMed | Full Text | PDF]

Oberhardt, M.A., J.B. Goldberg, M. Hogardt, and J.A. Papin. 2010. Metabolic network analysis of Pseudomonas aeruginosa during chronic cystic fibrosis lung infection. Journal of Bacteriology, 192(20):5534-5548. [PubMed | Full Text | PDF]

Ruppin, E., J.A. Papin, L.F. de Figueiredo, and S. Schuster. 2010. Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks. Current Opinion in Biotechnology, 21(4):502-510. [PubMed | Full Text | PDF]

Schmidt, B.J., X. Lin-Schmidt, A. Chamberlin, K. Salehi-Ashtiani, and J.A. Papin. 2010. Metabolic systems analysis to advance algal biotechnology. Biotechnology Journal, 5(7):660-670. [PubMed | Full Text | PDF]

Sefcik L.S., J.L. Wilson, J.A. Papin, and E.A. Botchwey. 2010. Harnessing systems biology approaches to engineer functional microvascular networks. Tissue Engineering Part B: Reviews, 16(3):361-370. [PubMed | Full Text | PDF]

Gianchandani E.P., A.K. Chavali, and J.A. Papin. 2010. The applications of flux balance analysis in systems biology. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 2(3):372-382. [PubMed]

Schmidt B.J., J.A. Papin, and M.B. Lawrence. 2009. Nano-motion dynamics are determined by surface-tethered selectin mechanokinetics and bond formation. PLoS Compututational Biology, 5(12):e1000612. [PubMed | Full Text | PDF]

Oberhardt M.A., B.Ø. Palsson, and J.A. Papin. 2009. Applications of genome-scale metabolic reconstructions. Molecular Systems Biology, 5:320. [Pubmed | Full Text | PDF]

Manichaikul A., L. Ghamsari, E.F.Y. Hom, C. Lin, R.R. Murray, R.L. Chang, S. Balaji, T. Hao, Y. Shen, A.K. Chavali, I. Thiele, X. Yang, C. Fan, E. Mello, D.E. Hill, M. Vidal, K. Salehi-Ashtiani, and J.A. Papin. 2009. Metabolic network analysis integrated with transcript verification for sequenced genomes. Nature Methods, 6(8):589-592. [PubMed | Full Text | PDF]

Gianchandani, E.P., A.R. Joyce, B.Ø. Palsson, and J.A. Papin. 2009. Functional states of the genome-scale Escherichia coli transcriptional regulatory system. PLoS Computational Biology, 5(6):e1000403. [PubMed | Full Text | PDF]

Roberts, S.B., J.L. Robichaux, A.K. Chavali, P.A. Manque, V. Lee, A.M. Lara, J.A. Papin, and G.A. Buck. 2009. Proteomic and network analysis characterize stage-specific metabolism in Trypanosoma cruzi. BMC Systems Biology, 3:52. [PubMed | Full Text | PDF]

Mandell, J.W., G.F. Glass, E.P. Gianchandani, C.N. Locke, S. Amos, T.D. Bourne, D. Schiff, and J.A. Papin. 2009. Dephosphorylation of β-arrestin 1 in glioblastomas. Journal of Neuropathology and Experimental Neurology, 68(5):535-541. [PubMed]

Oberhardt, M.A., A.K. Chavali, and J.A. Papin. 2009. Flux balance analysis: interrogating genome-scale metabolic networks. Methods in Molecular Biology, 500(2):61-80. [PubMed | Full Text | PDF]

Glass, G., J.A. Papin, and J.W. Mandell. 2009. SIMPLE: A sequential immunoperoxidase labeling and erasing method. Journal of Histochemistry & Cytochemistry, 57(10):899-905. [PubMed | Full Text | PDF]

Wieghaus, K.A., E.P. Gianchandani, R.A. Neal, M.A. Paige, M.L. Brown, J.A. Papin, and E.A. Botchwey. 2009. Phthalimide neovascular factor 1 (PNF1) modulates MT1-MMP activity in human microvascular endothelial cells. Biotechnology & Bioengineering, 103(4):796-807. [PubMed | Full Text | PDF]

*Chavali, A.K., E.P. Gianchandani, K.S. Tung, M.B. Lawrence, S.M. Peirce-Cottler, and J.A. Papin. 2008. Characterizing emergent properties of immunological systems with multi-cellular rule-based computational modeling. Trends in Immunology, 29:589-599. [PubMed | Full Text | PDF]

Puchalka, J., M.A. Oberhardt, M. Godinho, A. Bielecka, D. Regenhardt, K. Timmis, J.A. Papin, and V.A. Martins dos Santos. 2008. Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. PLoSComputational Biology, 4(10):e1000210. [PubMed | Full Text | PDF]

Wieghaus, K.A., E.P. Gianchandani, M.A. Paige, M.L. Brown, E.A. Botchwey, and J.A. Papin. 2008. Novel pathway compendium analysis elucidates mechanism of pro-angiogenic synthetic small molecule. Bioinformatics, 24(20):2384-2390. [PubMed | Full Text | PDF]

Lee, J.M., E.P. Gianchandani, J.A. Eddy, and J.A. Papin. 2008. Dynamic analysis of integrated signaling, metabolic, and regulatory networks. PLoS Computational Biology, 4(5): e1000086. [PubMed | Full Text | PDF]

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, 4:177. [PubMed| Full Text | PDF| UVa News Office Press Release | Medical News Today | Asian News International]

*Oberhardt, M.A., J. Puchalka, K. Fryer, V.A. Martins dos Santos, and J.A. Papin. 2008. Genome-scale network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1. Journal of Bacteriology, 190(8):2790-2803. [PubMed| Full Text | PDF | UVa News Office Press Release | Medical News Today | Asian News International]

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

Robertson, S.H., C.K. Smith, A.L. Langhans, S.E. McLinden, M.A. Oberhardt, K.R. Jakab, B. Dzamba, D.W. DeSimone, J.A. Papin, and S.M. Peirce. 2007. Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior. BMC Systems Biology, 1:46. [PubMed | Full Text | PDF]

Wieghaus, K.A., E.P. Gianchandani, M.L. Brown, J.A. Papin, and E.A. Botchwey. 2007. Mechanistic exploration of phthalimide neovascular factor 1 (PNF1) using network analysis tools. Tissue Engineering,13:2561-2575. [PubMed | PDF]

Peirce-Cottler, S.M., T.S. Skalak, and J.A. Papin. 2006. Multi-scale systems integration from cells to tissues: Coupling intracellular network analysis with tissue-patterning simulations. IBM Journal of Research and Development. [Full Text | PDF]

*Gianchandani, E.P., J.A. Papin, N.D. Price, A.R. Joyce, and B.Ø. Palsson. 2006. Matrix formalism to describe functional states of transcriptional regulatory systems. PLoS Computational Biology, 2(8):e101. [PubMed | Full Text | PDF]

Lee, J.M., E.P. Gianchandani, and J.A. Papin. 2006. Flux balance analysis in the era of metabolomics. Briefings in Bioinformatics, 7(2):140-150. [PubMed | Full Text | PDF]

Gianchandani, E.P., D.L. Brautigan, and J.A. Papin. 2006. Systems analyses characterize integrated functions of biochemical networks. Trends in Biochemical Sciences, 31(5):284-291. [PubMed | Full Text | PDF]

Papin, J.A., E.P. Gianchandani, and S. Subramaniam. 2006. Mapping the genotype-phenotype relationship in cellular signaling networks: Building bridges over the unknown, in: Networks and Models for Systems Biology, ed. Isidore Rigoutsos and Gregory Stephanopoulos. [Purchase Textbook]

*Papin, J.A., T. Hunter, B.Ø. Palsson, and S. Subramaniam. 2005. Reconstruction of cellular signalling networks and analysis of their properties. Nature Reviews Molecular Cell Biology, 6(2): 99-111. [PubMed | Full Text | PDF]

*Papin, J.A., J.L. Reed, B.Ø. Palsson. 2004. Hierarchical thinking in network biology: The unbiased modularization of biochemical networks. Trends in Biochemical Sciences, 29(12):641-647. [PubMed | Full Text | PDF]

Papin, J.A., J. Stelling, N.D. Price, S. Klamt, S. Schuster, and B.Ø. Palsson. 2004. Comparison of network-based pathway analysis methods. Trends in Biotechnology, 22(8):400-405. [PubMed | Full Text | PDF]

Papin, J.A. and B.Ø. Palsson. 2004. The JAK-STAT signaling network in the human B-cell: An extreme signaling pathway analysis. Biophysical Journal, 87(1):37-46. [PubMed | Full Text | PDF]

Papin, J.A. and B.Ø.Palsson. 2004. Topological analysis of signaling networks: A scalable framework to obtain emergent properties including crosstalk. Journal of Theoretical Biology, 227(2):283-297. [PubMed | FullText | PDF]

Papin, J.A. and S. Subramaniam. 2004. Bioinformatics and cellular signaling. Current Opinion in Biotechnology, 15(1):78-81. [PubMed | Full Text | PDF]

Papin, J.A., N.D. Price, and B.Ø. Palsson. 2004. In silico cells: studying genotype-phenotype relationships using constraints-based models, in: Metabolic Engineering in the Post-Genomic Era, eds. Hans Westerhoff and Boris Kholodenko. [Purchase Textbook]

Price, N.D., J.L. Reed, J.A. Papin, S.J. Wiback, and B.Ø. Palsson. 2003. Network-based analysis of metabolic regulation in the human red blood cell. Journal of Theoretical Biology, 225(2):1985-1994. [PubMed | Full Text | PDF]

Papin, J.A., N.D. Price, S.J. Wiback, D.A. Fell, and B.Ø. Palsson. 2003. Metabolic pathways in the post-genome era. Trends in Biochemical Sciences, 28(5):250-258. [PubMed | Full Text | PDF]

Palsson, B.Ø., N.D. Price, and J.A. Papin. 2003. Development of network-based pathway definitions: The need to analyze real metabolic networks. Letter to the Editor, Trends in Biotechnology, 21(5):195-198. [PubMed | Full Text | PDF]

Price, N.D., J.A. Papin, C.H. Schilling, and B.Ø. Palsson. 2003. Genome-scale microbial in silico models: the constraints-based approach. Trends in Biotechnology, 21(4):162-169. [PubMed | Full Text | PDF]

Price, N.D., J.L. Reed, J.A. Papin, I. Famili, and B.Ø. Palsson. 2003. Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices. Biophysical Journal, 84(2):794-804. [PubMed | Full Text | PDF]

Papin, J.A., N.D. Price, and B.Ø. Palsson. 2002. Extreme pathway lengths and reaction participation in genome-scale metabolic networks. Genome Research, 12(12):1889-1900. [PubMed | Full Text | PDF]

Papin, J.A., N.D. Price, J.S. Edwards, and B.Ø. Palsson. 2002. The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy. Journal of Theoretical Biology, 215(1):67-82. [PubMed | Full Text | PDF]

Price, N.D., J.A. Papin, and B.Ø. Palsson. 2002. Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis. Genome Research, 12(5):760-769. [PubMed | Full Text | PDF]

*Featured on journal cover.