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Mark Brynildsen

Selected Publications

For a complete listing of downloadable publications, click here.

  1. Mok WWK, Orman MA, Brynildsen MP. Impacts of global transcriptional regulators on persister metabolism. Antimicrob Agents Chemother, accepted.
  2. Amato SM, Brynildsen MP. Mechanisms of stress-activated persister formation in Escherichia coli. Stress and Environmental Control of Gene Expression in Bacteria, accepted.
  3. Adolfsen KJ, Brynildsen MP. Futile cycling increases sensitivity toward oxidative stress in Escherichia coli. Metab Eng, accepted.
  4. Orman MA, Henry TC, DeCoste CJ, Brynildsen MP. Analyzing persister physiology with fluorescence activated cell sorting. Methods in Molecular Biology, accepted.
  5. Orman MA, Mok WWK, Brynildsen MP. Aminoglycoside-enabled elucidation of bacterial persister metabolism. Curr. Protoc. Microbiol. 2015 Feb; 36:17.9.1-17.9.14.
  6. Robinson JL, Miller RV, Brynildsen MP. Model-driven identification of dosing regimens that maximize the antimicrobial activity of nitric oxide. Metab Eng Comm. 2014 Dec; 1:12-18.
  7. Robinson JL, Adolfsen KJ, Brynildsen MP. Deciphering nitric oxide stress in bacteria with quantitative modeling. Curr Opin Microbiol. 2014 Jun; 19C:16-24.
  8.  Amato SM, Brynildsen MP. Nutrient transitions are a source of persisters in Escherichia coli biofilms. PLoS One, 2014 Mar 25;9(3):e93110.
  9. Amato SM, Fazen CH, Henry T, Mok WWK, Orman MA, Sandvik EL, Volzing KG, Brynildsen MP. The role of metabolism in bacterial persistence. Frontiers in Microbiology, 2014 Mar 3;5:70.
  10. Orman MA, Brynildsen MP. Establishment of a method to rapidly assay bacterial persister metabolism. Antimicrob Agents Chemother., 2013 Sep;57(9):4398-409.
  11. Orman MA, Brynildsen MP. Dormancy is not necessary or sufficient for bacterial persistence. Antimicrob Agents Chemother., 2013 Jul;57(7):3230-9.
  12. Robinson JL, Brynildsen MP. A kinetic platform to determine the fate of nitric oxide in Escherichia coli. PLoS Comput Biol., 2013 May;9(5):e1003049.
  13. Amato SM, Orman MA, Brynildsen MP. Metabolic control of persister formation in Escherichia coli. Molecular Cell, 2013 May 23;50(4):475-87.
  14. Brynildsen MP, Winkler JA, Spina K, MacDonald IC, Collins JJ. Potentiating antibacterial activity by predictably enhancing endogenous microbial ROS production. Nature Biotechnology, 2013 Feb; 31(2):160-5.
  15. Allison KR, Brynildsen MP, Collins JJ. Heterogeneous bacterial persisters and engineering approaches to eliminate them. Curr Opin Microbiol., 2011 Oct;14(5):593-8.
  16. Allison KR, Brynildsen MP, Collins JJ. Metabolite-enabled eradication of bacterial persisters by aminoglycosides . Nature, 2011 May 12; 473(7346):216-20.
  17. Brynildsen MP, Liao JC. An integrated network approach identifies the isobutanol response network of Escherichia coli. Mol Syst Biol, 2009; 5:277.
  18. Brynildsen MP, Collins JJ. Systems biology makes it personal. Molecular Cell, 2009 Apr 24;34(2):137-8.
  19. Atsumi S, Cann AF, Connor MR, Shen CR, Smith KM, Brynildsen MP, Chou KJ, Hanai T, Liao JC. Metabolic engineering of Escherichia coli for 1-butanol production. Metab Eng, 2008 Nov;10(6):305-11.
  20. Brynildsen MP, Wu TY, Jang SS, Liao JC. Biological network mapping and source signal deduction. Bioinformatics, 2007 Jul 15;23(14):1783-91.
  21. Brynildsen MP, Tran LM, Liao JC. A Gibbs sampler for the identification of gene expression and network connectivity consistency. Bioinformatics, 2006 Dec 15;22(24):3040-6.
  22. Brynildsen MP, Tran LM, Liao JC. Versatility and connectivity efficiency of bipartite transcription networks. Biophys J, 2006 Oct 15;91(8):2749-59.                 
  23. Brynildsen MP, Wong WW, Liao JC. Transcriptional regulation and metabolism. Biochem Soc Trans, 2005 Dec;33(Pt 6):1423-6.
  24. Yang YL, Suen J, Brynildsen MP, Galbraith S, Liao JC. Inferring yeast cell cycle regulators and interactions using transcription factor activities. BMC Genomics, 2005 Jun 10;6(1):90.Tran LM,
  25. Brynildsen MP, Kao KC, Suen JK, Liao JC. gNCA: A framework for determining transcription factor activity based on transcriptome: Identifiability and numerical implementation. Metab Eng, 2005 Mar;7(2):128-41.