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TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks.
Jensen PA, Lutz KA, Papin JA. Jensen PA, et al. Among authors: papin ja. BMC Syst Biol. 2011 Sep 23;5:147. doi: 10.1186/1752-0509-5-147. BMC Syst Biol. 2011. PMID: 21943338 Free PMC article.
Systems analyses characterize integrated functions of biochemical networks.
Gianchandani EP, Brautigan DL, Papin JA. Gianchandani EP, et al. Among authors: papin ja. Trends Biochem Sci. 2006 May;31(5):284-91. doi: 10.1016/j.tibs.2006.03.007. Epub 2006 Apr 17. Trends Biochem Sci. 2006. PMID: 16616498 Review.
Flux balance analysis in the era of metabolomics.
Lee JM, Gianchandani EP, Papin JA. Lee JM, et al. Among authors: papin ja. Brief Bioinform. 2006 Jun;7(2):140-50. doi: 10.1093/bib/bbl007. Epub 2006 Apr 26. Brief Bioinform. 2006. PMID: 16772264 Review.
Matrix formalism to describe functional states of transcriptional regulatory systems.
Gianchandani EP, Papin JA, Price ND, Joyce AR, Palsson BO. Gianchandani EP, et al. Among authors: papin ja. PLoS Comput Biol. 2006 Aug 11;2(8):e101. doi: 10.1371/journal.pcbi.0020101. PLoS Comput Biol. 2006. PMID: 16895435 Free PMC article.
Mechanistic exploration of phthalimide neovascular factor 1 using network analysis tools.
Wieghaus KA, Gianchandani EP, Brown ML, Papin JA, Botchwey EA. Wieghaus KA, et al. Among authors: papin ja. Tissue Eng. 2007 Oct;13(10):2561-75. doi: 10.1089/ten.2007.0023. Tissue Eng. 2007. PMID: 17723106 Free PMC article.
Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior.
Robertson SH, Smith CK, Langhans AL, McLinden SE, Oberhardt MA, Jakab KR, Dzamba B, DeSimone DW, Papin JA, Peirce SM. Robertson SH, et al. Among authors: papin ja. BMC Syst Biol. 2007 Oct 22;1:46. doi: 10.1186/1752-0509-1-46. BMC Syst Biol. 2007. PMID: 17953751 Free PMC article.
Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1.
Oberhardt MA, Puchałka J, Fryer KE, Martins dos Santos VA, Papin JA. Oberhardt MA, et al. Among authors: papin ja. J Bacteriol. 2008 Apr;190(8):2790-803. doi: 10.1128/JB.01583-07. Epub 2008 Jan 11. J Bacteriol. 2008. PMID: 18192387 Free PMC article.
Predicting biological system objectives de novo from internal state measurements.
Gianchandani EP, Oberhardt MA, Burgard AP, Maranas CD, Papin JA. Gianchandani EP, et al. Among authors: papin ja. BMC Bioinformatics. 2008 Jan 24;9:43. doi: 10.1186/1471-2105-9-43. BMC Bioinformatics. 2008. PMID: 18218092 Free PMC article.
Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major.
Chavali AK, Whittemore JD, Eddy JA, Williams KT, Papin JA. Chavali AK, et al. Among authors: papin ja. Mol Syst Biol. 2008;4:177. doi: 10.1038/msb.2008.15. Epub 2008 Mar 25. Mol Syst Biol. 2008. PMID: 18364711 Free PMC article.
Dynamic analysis of integrated signaling, metabolic, and regulatory networks.
Lee JM, Gianchandani EP, Eddy JA, Papin JA. Lee JM, et al. Among authors: papin ja. PLoS Comput Biol. 2008 May 23;4(5):e1000086. doi: 10.1371/journal.pcbi.1000086. PLoS Comput Biol. 2008. PMID: 18483615 Free PMC article.
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