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Mark Brynildsen

Selected Publications

For a complete listing of downloadable publications, click here.

TBA
Robinson JL and Brynildsen MP.
PNAS, (accepted)

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)

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

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

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

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

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

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

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


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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