Skip over navigation


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

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

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

Impacts of global transcriptional regulators on persister metabolism
Mok WW, Orman MA, and Brynildsen MP.
Antimicrob Agents Chemother, 2015 Feb 23.

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.

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.

Deciphering nitric oxide stress in bacteria with quantitative modeling
Robinson JL, Adolfsen KJ, and Brynildsen MP.
Curr Opin Microbiol., 2014 June; 19:16-24.

Nutrient transitions are a source of persisters in Esherichia coli biofilms
Amato SM and Brynildsen MP.
PLoS One, 2014 Mar 25;9(3):e93110.

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.

Establishment of a method to rapidly assay bacterial persister metabolism. 
Orman MA and Brynildsen MP. 
Antimicrob Agents Chemother,
2013 Sep;57(9):4398-409.

Dormancy is not necessary or sufficient for bacterial persistence.
Orman MA and Brynildsen MP. 
Antimicrob Agents Chemother,
2013 Jul;57(7):3230-9.

Metabolic control of persister formation in Escherichia coli.
Amato SM, Orman MA, and Brynildsen MP.
Molecular Cell
, 2013 May 23; 50: 1-13.

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).

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.

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.

Metabolite-enabled eradication of bacterial persisters by aminoglycosides.
Allison KR, Brynildsen MP, and Collins JJ. 
, 2011 May 12; 473(7346):216-20.

Systems biology makes it personal. 
Brynildsen MP and Collins JJ. 
Molecular Cell
., 2009 Apr 24;34(2):137-8.

An integrated network approach identifies the isobutanol response network of Escherichia coli.
Brynildsen MP and Liao JC. 
Mol Syst Biol
., 2009; 5:277.

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.

Biological network mapping and source signal deduction.
Brynildsen MP, Wu TY, Jang SS, and Liao JC. 
, 2007 Jul 15;23(14):1783-91.

A Gibbs sampler for the identification of gene expression and network connectivity consistency.
Brynildsen MP, Tran LM, and Liao JC. 
, 2006 Dec 15;22(24):3040-6.

Versatility and connectivity efficiency of bipartite transcription networks.
Brynildsen MP, Tran LM,and  Liao JC. 
Biophys J
, 2006 Oct 15;91(8):2749-59.

Transcriptional regulation and metabolism.
Brynildsen MP, Wong WW, and Liao JC. 
Biochem Soc Trans
, 2005 Dec;33(Pt 6):1423-6.

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.

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.