Trends Immunol. 2008

J Bacteriol. 2008

PLoS Comput Biol. 2006

Nat Rev Mol Cell Biol. 2005

Trends Biochem Sci. 2004

Gianchandani E.P., A.K. Chavali, J.A. Papin. 2009. The applications of flux balance analysis in systems biology. Wiley Interdisciplinary Reviews: Systems Biology and Medicine. [Abstract]

Oberhardt M.A., B.O. Palsson, J.A. Papin. 2009. Applications of genome-scale metabolic reconstructions. Molecular Systems Biology 5: 320 [Pubmed]

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, J.A. Papin. 2009. Metabolic network analysis integrated with transcript verification for sequenced genomes. Nature Methods 2009 Aug;6(8):589-592 [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 Computational Biology. In press.

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

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

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 beta-arrestin 1 in glioblastomas.  Journal of Neuropathology and Experimental Neurology, 2009 May;68(5):535-41. [PubMed]

Oberhardt MA, Chavali AK, Papin JA. 2009. Flux balance analysis: interrogating genome-scale metabolic networks. Methods Mol. Biol, 2009;500:61-80. [PubMed]

Glass, G., J.A. Papin, J.W. Mandell. 2009. SIMPLE: A Sequential Immunoperoxidase Labeling and Erasing Method. Journal of Histochemistry & Cytochemistry, 2009 Oct;57(10):899-905. [PubMed]

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 2009 Jul;103(4):796-807. [PubMed]

*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]

Puchalka, J., M.A. Oberhardt, M. Godinho, A. Bielecka, D. Regenhardt, K. Timmis, J.A. Papin, and V.M. dos Santos. 2008. Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. PLoS Computational Biology, 4: e1000210. [PubMed | Abstract | 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: 2384-90. [PubMed | Abstract | 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: e1000086. [PubMed | Abstract | 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 | Abstract | Full Text | PDF | UVa School of Medicine Press Release | UVa News Office Press Release | Medical News Today | Asian News International]

*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, 190: 2790-803. [PubMed | Abstract | Full Text | PDF | UVa School of Medicine Press Release | 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 from internal state measurements. BMC Bioinformatics, 9: 43.  [PubMed | Abstract | 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 | Abstract | 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: 2561-75. [PubMed | Abstract | PDF | UVa Press Release]

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.O. Palsson.  2006.  Matrix formalism to describe functional states of transcriptional regulatory systems.  PLoS Computational Biology, 2: e101. [PubMed | Abstract | 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: 140-50. [PubMed | Abstract | 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: 284-91. [PubMed | Full Text]

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.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]

*Papin, J.A., J.L. Reed, and B.O. Palsson.  2004.  Hierarchical thinking in network biology:  the unbiased modularization of biochemical networks.  Trends in Biochemical Sciences, 29: 641-647. [PubMed | Full Text]

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

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

Papin, J.A., and B.O. Palsson.  2004.  Topological analysis of signaling networks: a scalable framework to obtain emergent properties including crosstalk.  Journal of Theoretical Biology, 227: 283-297. [PubMed | Full Text]

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

Papin, J.A., N.D. Price, and B.O. 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.O. Palsson.  2003.  Network-based analysis of metabolic regulation in the human red blood cell.  Journal of Theoretical Biology, 225: 1985-1994. [PubMed | Full Text]

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

Palsson, B.O., 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: 195-198. [PubMed | Full Text]

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

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

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

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

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

*Featured on journal cover.