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Publications

TBA
Adolfsen KJ and Brynildsen MP.
Metabolic Engineering, (accepted)

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

T
BA
Orman MA, Henry TC, DeCoste CJ, and Brynildsen MP.
Methods in Molecular Biology, (accepted)

TBA
Orman MA, Mok WW, and Brynildsen MP.
Current Protocols in Microbiology, (in press)

Model-driven identification of dosing regimens that maximize the antimicrobial activity of nitric oxide
Robinson JL, Miller RV, and Brynildsen MP.
Metabolic Engineering Communications, 2015 Jan; 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.sciencedirect.com/science/article/pii/S1369527414000654

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