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112 results
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MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data.
Jensen PA, Papin JA. Jensen PA, et al. Among authors: papin ja. Bioinformatics. 2014 May 1;30(9):1327-8. doi: 10.1093/bioinformatics/btt758. Epub 2014 Jan 9. Bioinformatics. 2014. PMID: 24413519 Free PMC article.
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.
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.
Novel pathway compendium analysis elucidates mechanism of pro-angiogenic synthetic small molecule.
Wieghaus KA, Gianchandani EP, Paige MA, Brown ML, Botchwey EA, Papin JA. Wieghaus KA, et al. Among authors: papin ja. Bioinformatics. 2008 Oct 15;24(20):2384-90. doi: 10.1093/bioinformatics/btn451. Epub 2008 Aug 21. Bioinformatics. 2008. PMID: 18718940 Free PMC article.
Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology.
Puchałka J, Oberhardt MA, Godinho M, Bielecka A, Regenhardt D, Timmis KN, Papin JA, Martins dos Santos VA. Puchałka J, et al. Among authors: papin ja. PLoS Comput Biol. 2008 Oct;4(10):e1000210. doi: 10.1371/journal.pcbi.1000210. Epub 2008 Oct 31. PLoS Comput Biol. 2008. PMID: 18974823 Free PMC article.
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