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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. BMC Syst Biol. 2011 Sep 23;5:147. doi: 10.1186/1752-0509-5-147. BMC Syst Biol. 2011. PMID: 21943338 Free PMC article.
MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data.
Jensen PA, Papin JA. Jensen PA, et al. Bioinformatics. 2014 May 1;30(9):1327-8. doi: 10.1093/bioinformatics/btt758. Epub 2014 Jan 9. Bioinformatics. 2014. PMID: 24413519 Free PMC article.
Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease.
Chavali AK, Blazier AS, Tlaxca JL, Jensen PA, Pearson RD, Papin JA. Chavali AK, et al. Among authors: jensen pa. BMC Syst Biol. 2012 Apr 27;6:27. doi: 10.1186/1752-0509-6-27. BMC Syst Biol. 2012. PMID: 22540944 Free PMC article.
A scalable systems analysis approach for regulated metabolic networks.
Jensen PA, Papin JA. Jensen PA, et al. Annu Int Conf IEEE Eng Med Biol Soc. 2009;2009:5464-5. doi: 10.1109/IEMBS.2009.5334060. Annu Int Conf IEEE Eng Med Biol Soc. 2009. PMID: 19964682
Functional integration of a metabolic network model and expression data without arbitrary thresholding.
Jensen PA, Papin JA. Jensen PA, et al. Bioinformatics. 2011 Feb 15;27(4):541-7. doi: 10.1093/bioinformatics/btq702. Epub 2010 Dec 20. Bioinformatics. 2011. PMID: 21172910 Free PMC article.
Coupling Fluxes, Enzymes, and Regulation in Genome-Scale Metabolic Models.
Jensen PA. Jensen PA. Methods Mol Biol. 2018;1716:337-351. doi: 10.1007/978-1-4939-7528-0_15. Methods Mol Biol. 2018. PMID: 29222761 Review.
Miniaturized plate readers for low-cost, high-throughput phenotypic screening.
Jensen PA, Dougherty BV, Moutinho TJ Jr, Papin JA. Jensen PA, et al. J Lab Autom. 2015 Feb;20(1):51-5. doi: 10.1177/2211068214555414. Epub 2014 Nov 3. J Lab Autom. 2015. PMID: 25366331 Free PMC article.
Antibiotics Disrupt Coordination between Transcriptional and Phenotypic Stress Responses in Pathogenic Bacteria.
Jensen PA, Zhu Z, van Opijnen T. Jensen PA, et al. Cell Rep. 2017 Aug 15;20(7):1705-1716. doi: 10.1016/j.celrep.2017.07.062. Cell Rep. 2017. PMID: 28813680 Free PMC article.
Gapsplit: efficient random sampling for non-convex constraint-based models.
Keaty TC, Jensen PA. Keaty TC, et al. Among authors: jensen pa. Bioinformatics. 2020 Apr 15;36(8):2623-2625. doi: 10.1093/bioinformatics/btz971. Bioinformatics. 2020. PMID: 31913465
Droplet Tn-Seq combines microfluidics with Tn-Seq for identifying complex single-cell phenotypes.
Thibault D, Jensen PA, Wood S, Qabar C, Clark S, Shainheit MG, Isberg RR, van Opijnen T. Thibault D, et al. Among authors: jensen pa. Nat Commun. 2019 Dec 16;10(1):5729. doi: 10.1038/s41467-019-13719-9. Nat Commun. 2019. PMID: 31844066 Free PMC article.
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