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Items: 1 to 20 of 56


Large-Effect Beneficial Synonymous Mutations Mediate Rapid and Parallel Adaptation in a Bacterium.

Agashe D, Sane M, Phalnikar K, Diwan GD, Habibullah A, Martinez-Gomez NC, Sahasrabuddhe V, Polachek W, Wang J, Chubiz LM, Marx CJ.

Mol Biol Evol. 2016 Feb 23. pii: msw035. [Epub ahead of print]


Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation.

Houser JR, Barnhart C, Boutz DR, Carroll SM, Dasgupta A, Michener JK, Needham BD, Papoulas O, Sridhara V, Sydykova DK, Marx CJ, Trent MS, Barrick JE, Marcotte EM, Wilke CO.

PLoS Comput Biol. 2015 Aug 14;11(8):e1004400. doi: 10.1371/journal.pcbi.1004400. eCollection 2015 Aug.


Transhydrogenase promotes the robustness and evolvability of E. coli deficient in NADPH production.

Chou HH, Marx CJ, Sauer U.

PLoS Genet. 2015 Feb 25;11(2):e1005007. doi: 10.1371/journal.pgen.1005007. eCollection 2015.


Galactose metabolic genes in yeast respond to a ratio of galactose and glucose.

Escalante-Chong R, Savir Y, Carroll SM, Ingraham JB, Wang J, Marx CJ, Springer M.

Proc Natl Acad Sci U S A. 2015 Feb 3;112(5):1636-41. doi: 10.1073/pnas.1418058112. Epub 2015 Jan 20.


Effective use of a horizontally-transferred pathway for dichloromethane catabolism requires post-transfer refinement.

Michener JK, Camargo Neves AA, Vuilleumier S, Bringel F, Marx CJ.

Elife. 2014 Nov 24;3. doi: 10.7554/eLife.04279.


Genetic and phenotypic comparison of facultative methylotrophy between Methylobacterium extorquens strains PA1 and AM1.

Nayak DD, Marx CJ.

PLoS One. 2014 Sep 18;9(9):e107887. doi: 10.1371/journal.pone.0107887. eCollection 2014.


Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics.

Harcombe WR, Riehl WJ, Dukovski I, Granger BR, Betts A, Lang AH, Bonilla G, Kar A, Leiby N, Mehta P, Marx CJ, Segrè D.

Cell Rep. 2014 May 22;7(4):1104-15. doi: 10.1016/j.celrep.2014.03.070. Epub 2014 May 1.


Phylogeny poorly predicts the utility of a challenging horizontally transferred gene in Methylobacterium strains.

Michener JK, Vuilleumier S, Bringel F, Marx CJ.

J Bacteriol. 2014 Jun;196(11):2101-7. doi: 10.1128/JB.00034-14. Epub 2014 Mar 28.


Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli.

Plucain J, Hindré T, Le Gac M, Tenaillon O, Cruveiller S, Médigue C, Leiby N, Harcombe WR, Marx CJ, Lenski RE, Schneider D.

Science. 2014 Mar 21;343(6177):1366-9. doi: 10.1126/science.1248688. Epub 2014 Mar 6.


Mapping the fitness landscape of gene expression uncovers the cause of antagonism and sign epistasis between adaptive mutations.

Chou HH, Delaney NF, Draghi JA, Marx CJ.

PLoS Genet. 2014 Feb 27;10(2):e1004149. doi: 10.1371/journal.pgen.1004149. eCollection 2014 Feb.


Metabolic erosion primarily through mutation accumulation, and not tradeoffs, drives limited evolution of substrate specificity in Escherichia coli.

Leiby N, Marx CJ.

PLoS Biol. 2014 Feb 18;12(2):e1001789. doi: 10.1371/journal.pbio.1001789. eCollection 2014 Feb.


Sign epistasis limits evolutionary trade-offs at the confluence of single- and multi-carbon metabolism in Methylobacterium extorquens AM1.

Carroll SM, Lee MC, Marx CJ.

Evolution. 2014 Mar;68(3):760-71. doi: 10.1111/evo.12301. Epub 2013 Nov 20.


The ability of flux balance analysis to predict evolution of central metabolism scales with the initial distance to the optimum.

Harcombe WR, Delaney NF, Leiby N, Klitgord N, Marx CJ.

PLoS Comput Biol. 2013;9(6):e1003091. doi: 10.1371/journal.pcbi.1003091. Epub 2013 Jun 20.


A novel pair of inducible expression vectors for use in Methylobacterium extorquens.

Chubiz LM, Purswani J, Carroll SM, Marx CJ.

BMC Res Notes. 2013 May 6;6:183. doi: 10.1186/1756-0500-6-183.


Development of an optimized medium, strain and high-throughput culturing methods for Methylobacterium extorquens.

Delaney NF, Kaczmarek ME, Ward LM, Swanson PK, Lee MC, Marx CJ.

PLoS One. 2013 Apr 30;8(4):e62957. doi: 10.1371/journal.pone.0062957. Print 2013.


Evolution after introduction of a novel metabolic pathway consistently leads to restoration of wild-type physiology.

Carroll SM, Marx CJ.

PLoS Genet. 2013 Apr;9(4):e1003427. doi: 10.1371/journal.pgen.1003427. Epub 2013 Apr 4.


Massive mitochondrial gene transfer in a parasitic flowering plant clade.

Xi Z, Wang Y, Bradley RK, Sugumaran M, Marx CJ, Rest JS, Davis CC.

PLoS Genet. 2013;9(2):e1003265. doi: 10.1371/journal.pgen.1003265. Epub 2013 Feb 14.


Can you sequence ecology? Metagenomics of adaptive diversification.

Marx CJ.

PLoS Biol. 2013;11(2):e1001487. doi: 10.1371/journal.pbio.1001487. Epub 2013 Feb 19.

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