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Publications

TBA
Amato SM and Brynildsen MP.
Stress and Environmental Control of Gene Expression in Bacteria, (in press)

TBA
Robinson JL and Brynildsen MP.
Stress and Environmental Control of Gene Expression in Bacteria, (in press)

37. Starved Escherichia coli preserve reducing power under nitric oxide stress
      Gowers GF, Robinson JL, and Brynildsen MP.
      Biochem Biophys Res Commun, 2016 May 17.
      http://www.ncbi.nlm.nih.gov/pubmed/27207837

36. Development of Persister-FACSeq: a method to massively parallelize quantification of
       persister physiology and its heterogeneity

      Henry TC and Brynildsen MP.
      Scientific Reports, 2016 May 4;6:25100.
      http://www.ncbi.nlm.nih.gov/pubmed/27142337  

35. Quantifying current events identifies a novel endurance regulator

      Henry TC and Brynildsen MP.
      Trends in Microbiology, 2016 May;24(5):324-6.
      http://www.ncbi.nlm.nih.gov/pubmed/26954590

34. Discovery and dissection of metabolic oscillations in the nitric oxide response network of
       Escherichia coli

      
Robinson JL and Brynildsen MP.
      PNAS, 2016 March 7.
      http://www.ncbi.nlm.nih.gov/pubmed/26951670

33. Construction and experimental validation of a quantitative kinetic model of nitric oxide stress
      in enterohemorrhagic Escherichia coli O157:H7

     
Robinson JL and Brynildsen MP.
     Bioengineering, 2016 February 6, 3(1),9.
     http://www.mdpi.com/2306-5354/3/1/9

32. Persister formation in Escherichia coli can be inhibited by treatment with nitric oxide
     
Orman MA and Brynildsen MP.
     Free Radical Biology and Medicine, 2016 February 2, epub ahead of print.
     http://www.ncbi.nlm.nih.gov/pubmed/26849946

31. Non-monotonic survival of Staphylococcus aureus with respect to ciprofloxacin
       concentration arises from prophage-dependent killing of persisters
      
Sandvik EL, Fazen CH, Henry TC, Mok WW, and Brynildsen MP.
      Pharmaceuticals, 2015 November 17, 8, 778-792.
      http://www.ncbi.nlm.nih.gov/pubmed/26593926

30. RNA futile cycling in model persisters derived from MazF accumulation
     
Mok WW, Park JO, Rabinowitz JD, and Brynildsen MP.
     mBio, 2015 November 17, 6(6):e01588-15.
     http://www.ncbi.nlm.nih.gov/pubmed/26578677

29. Analyzing persister physiology with fluorescence-activated cell sorting
     
Orman MA, Henry TC, DeCoste CJ, and Brynildsen MP.
     Methods in Molecular Biology, 2016;1333:83-100.
     http://www.ncbi.nlm.nih.gov/pubmed/26468102

28. A kinetic platform to determine the fate of hydrogen peroxide in Escherichia coli
     
Adolfsen KJ and Brynildsen MP.
     PLoS Comp Biol., 2015 Nov 6;11(11).
     http://www.ncbi.nlm.nih.gov/pubmed/26545295

27. Stationary-phase persisters to ofloxacin sustain DNA damage and require repair systems
       only during recovery
      
Volzing KG and Brynildsen MP.
      mBio, 2015 September 1; 6(5):e00731-15.
      http://www.ncbi.nlm.nih.gov/pubmed/26330511

26. Persister heterogeneity arising from a single metabolic stress
     
Amato SM and Brynildsen MP.
     Current Biology, 2015 August 17; 25:1-9.
     http://www.ncbi.nlm.nih.gov/pubmed/26255847

25. Inhibition of stationary phase respiration impairs persister formation in E. coli
     
Orman MA and Brynildsen MP.
     Nature Communications, 2015 August 6; 6:7983.
     
http://www.ncbi.nlm.nih.gov/pubmed/26246187

24. An ensemble-guided approach identifies ClpP as a major regulator of transcript levels in nitric
      oxide-stressed Escherichia coli
     
Robinson JL and Brynildsen MP.
     Metabolic Engineering, 2015 June 22;31:22-34.
     http://www.ncbi.nlm.nih.gov/pubmed/26112956

23. Futile cycling increases sensitivity toward oxidative stress in Escherichia coli
     
Adolfsen KJ and Brynildsen MP.
     Metabolic Engineering, 2015 May;29:26-35.
     http://www.ncbi.nlm.nih.gov/pubmed/25732623

22. Impacts of global transcriptional regulators on persister metabolism
     
Mok WW, Orman MA, and Brynildsen MP.
     Antimicrob Agents Chemother, 2015 May;59(5):2713-9.
     http://www.ncbi.nlm.nih.gov/pubmed/25712354

21. Aminoglycoside-enabled elucidation of bacterial persister metabolism
     
Orman MA, Mok WW, and Brynildsen MP.
     Current Protocols in Microbiology, 2015 Feb 2;36:17.9.1-17.9.14.
     http://www.ncbi.nlm.nih.gov/pubmed/25641098

20. Model-driven identification of dosing regimens that maximize the antimicrobial activity of nitric
       oxide
      
Robinson JL, Miller RV, and Brynildsen MP.
      Metabolic Engineering Communications, 2014 Dec; 1:12-18.
      http://www.sciencedirect.com/science/article/pii/S2214030114000030

19. Deciphering nitric oxide stress in bacteria with quantitative modeling
      
Robinson JL, Adolfsen KJ, and Brynildsen MP.
      Curr Opin Microbiol., 2014 June; 19:16-24.
      http://www.ncbi.nlm.nih.gov/pubmed/24983704

18. Nutrient transitions are a source of persisters in Esherichia coli biofilms
      
Amato SM and Brynildsen MP.
      PLoS One, 2014 Mar 25;9(3):e93110.
      
http://www.ncbi.nlm.nih.gov/pubmed/24667358

17. The role of metabolism in bacterial persistence
      Amato SM, Fazen CH, Henry TC, Mok WW, Orman MA, Sandvik EL, Volzing KG, and Brynildsen MP.
      Frontiers in Microbiology, 2014 Mar 3;5:70.
      http://www.ncbi.nlm.nih.gov/pubmed/24624123

16. Establishment of a method to rapidly assay bacterial persister metabolism
      Orman MA and Brynildsen MP. 
      Antimicrob Agents Chemother,
2013 Sep;57(9):4398-409.
      http://www.ncbi.nlm.nih.gov/pubmed/23817376

15. Dormancy is not necessary or sufficient for bacterial persistence
       Orman MA and Brynildsen MP. 
       Antimicrob Agents Chemother,
2013 Jul;57(7):3230-9.
       http://www.ncbi.nlm.nih.gov/pubmed/23629720

14. Metabolic control of persister formation in Escherichia coli
      Amato SM, Orman MA, and Brynildsen MP.
      Molecular Cell
, 2013 May 23; 50: 1-13.
      http://www.ncbi.nlm.nih.gov/pubmed/23665232

13. A kinetic platform to determine the fate of nitric oxide in Escherichia coli

      Robinson JL and Brynildsen MP. 
      PLoS Comp Biol
, 2013 May 2; 9(5).
      http://www.ncbi.nlm.nih.gov/pubmed/23658508

12. Potentiating antibacterial activity by predictably enhancing endogenous microbial ROS
       production

       Brynildsen MP, Winkler JA, Spina CS, MacDonald IC, and Collins JJ.
       Nature Biotech
, 2013 Feb;31(2):160-5.
       http://www.ncbi.nlm.nih.gov/pubmed/23292609

11. Heterogeneous bacterial persisters and engineering approaches to eliminate them
      Allison KR, Brynildsen MP, and Collins JJ. 
      Curr Opin Microbiol
. 2011 Oct;14(5):593-8.
      http://www.ncbi.nlm.nih.gov/pubmed/21937262

10. Metabolite-enabled eradication of bacterial persisters by aminoglycosides
      Allison KR, Brynildsen MP, and Collins JJ. 
      Nature
, 2011 May 12; 473(7346):216-20.
      http://www.ncbi.nlm.nih.gov/pubmed/21562562

9. Systems biology makes it personal
    Brynildsen MP and Collins JJ. 
    Molecular Cell
., 2009 Apr 24;34(2):137-8.
    http://www.ncbi.nlm.nih.gov/pubmed/19394290

8. An integrated network approach identifies the isobutanol response network of Escherichia
    coli

    Brynildsen MP and Liao JC. 
    Mol Syst Biol
., 2009; 5:277.
    http://www.ncbi.nlm.nih.gov/pubmed/19536200

7. Metabolic engineering of Escherichia coli for 1-butanol production
    Atsumi S, Cann AF, Connor MR, Shen CR, Smith KM, Brynildsen MP, Chou KJ, Hanai T, and Liao
    JC. 
    Metabolic Engineering
, 2008 Nov;10(6):305-11.
    http://www.ncbi.nlm.nih.gov/pubmed/17942358

6. Biological network mapping and source signal deduction
    Brynildsen MP, Wu TY, Jang SS, and Liao JC. 
    Bioinformatics
, 2007 Jul 15;23(14):1783-91.
    http://www.ncbi.nlm.nih.gov/pubmed/17495996

5. A Gibbs sampler for the identification of gene expression and network connectivity
    consistency

    Brynildsen MP, Tran LM, and Liao JC. 
    Bioinformatics
, 2006 Dec 15;22(24):3040-6.
    http://www.ncbi.nlm.nih.gov/pubmed/17060361

4. Versatility and connectivity efficiency of bipartite transcription networks
    Brynildsen MP, Tran LM,and  Liao JC. 
    Biophys J
, 2006 Oct 15;91(8):2749-59.
    http://www.ncbi.nlm.nih.gov/pubmed/16815895

3. Transcriptional regulation and metabolism
    Brynildsen MP, Wong WW, and Liao JC. 
    Biochem Soc Trans
, 2005 Dec;33(Pt 6):1423-6.
    http://www.ncbi.nlm.nih.gov/pubmed/16246136

2. Inferring yeast cell cycle regulators and interactions using transcription factor activities
   
Yang YL, Suen J, Brynildsen MP, Galbraith S, and Liao JC.
    BMC Genomics
, 2005 Jun 10;6(1):90.
    http://www.ncbi.nlm.nih.gov/pubmed/15949038

1. gNCA: A framework for determining transcription factor activity based on transcriptome:
    Identifiability and numerical implementation

    Tran LM, Brynildsen MP, Kao KC, Suen JK, and Liao JC. 
    Metabolic Engineering
, 2005 Mar;7(2):128-41.
    http://www.ncbi.nlm.nih.gov/pubmed/15781421