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Microbial phenotypic heterogeneity in response to a metabolic toxin: Continuous, dynamically shifting distribution of formaldehyde tolerance in Methylobacterium extorquens populations.

Lee JA, Riazi S, Nemati S, Bazurto JV, Vasdekis AE, Ridenhour BJ, Remien CH, Marx CJ.

PLoS Genet. 2019 Nov 11;15(11):e1008458. doi: 10.1371/journal.pgen.1008458. [Epub ahead of print]


Align to Define: Ecologically Meaningful Populations from Genomes.

Stolyar S, Marx CJ.

Cell. 2019 Aug 8;178(4):767-768. doi: 10.1016/j.cell.2019.07.026.


Tales from the crypt(ic).

Lee JA, Marx CJ.

Science. 2019 Jul 26;365(6451):318-319. doi: 10.1126/science.aay2727. No abstract available.


Experimental Evolution of Methylobacterium: 15 Years of Planned Experiments and Surprise Findings.

Marx CJ.

Curr Issues Mol Biol. 2019 Jun 5;33:249-266. doi: 10.21775/cimb.033.249. [Epub ahead of print]


Evolution of bidirectional costly mutualism from byproduct consumption.

Harcombe WR, Chacón JM, Adamowicz EM, Chubiz LM, Marx CJ.

Proc Natl Acad Sci U S A. 2018 Nov 20;115(47):12000-12004. doi: 10.1073/pnas.1810949115. Epub 2018 Oct 22.


A decade of genome sequencing has revolutionized studies of experimental evolution.

Bruger EL, Marx CJ.

Curr Opin Microbiol. 2018 Oct;45:149-155. doi: 10.1016/j.mib.2018.03.002. Epub 2018 Jun 4. Review.


Multiplex Genome Editing by Natural Transformation (MuGENT) for Synthetic Biology in Vibrio natriegens.

Dalia TN, Hayes CA, Stolyar S, Marx CJ, McKinlay JB, Dalia AB.

ACS Synth Biol. 2017 Sep 15;6(9):1650-1655. doi: 10.1021/acssynbio.7b00116. Epub 2017 Jun 6.


Identification of the potentiating mutations and synergistic epistasis that enabled the evolution of inter-species cooperation.

Douglas SM, Chubiz LM, Harcombe WR, Marx CJ.

PLoS One. 2017 May 11;12(5):e0174345. doi: 10.1371/journal.pone.0174345. eCollection 2017.


The E. coli molecular phenotype under different growth conditions.

Caglar MU, Houser JR, Barnhart CS, Boutz DR, Carroll SM, Dasgupta A, Lenoir WF, Smith BL, Sridhara V, Sydykova DK, Vander Wood D, Marx CJ, Marcotte EM, Barrick JE, Wilke CO.

Sci Rep. 2017 Apr 18;7:45303. doi: 10.1038/srep45303.


A transdisciplinary approach to the initial validation of a single cell protein as an alternative protein source for use in aquafeeds.

Tlusty M, Rhyne A, Szczebak JT, Bourque B, Bowen JL, Burr G, Marx CJ, Feinberg L.

PeerJ. 2017 Apr 11;5:e3170. doi: 10.7717/peerj.3170. eCollection 2017.


Hopanoid-free Methylobacterium extorquens DM4 overproduces carotenoids and has widespread growth impairment.

Bradley AS, Swanson PK, Muller EE, Bringel F, Caroll SM, Pearson A, Vuilleumier S, Marx CJ.

PLoS One. 2017 Mar 20;12(3):e0173323. doi: 10.1371/journal.pone.0173323. eCollection 2017.


Growth Trade-Offs Accompany the Emergence of Glycolytic Metabolism in Shewanella oneidensis MR-1.

Chubiz LM, Marx CJ.

J Bacteriol. 2017 May 9;199(11). pii: e00827-16. doi: 10.1128/JB.00827-16. Print 2017 Jun 1.


Parallel Mutations Result in a Wide Range of Cooperation and Community Consequences in a Two-Species Bacterial Consortium.

Douglas SM, Chubiz LM, Harcombe WR, Ytreberg FM, Marx CJ.

PLoS One. 2016 Sep 12;11(9):e0161837. doi: 10.1371/journal.pone.0161837. eCollection 2016.


Transfer of a Catabolic Pathway for Chloromethane in Methylobacterium Strains Highlights Different Limitations for Growth with Chloromethane or with Dichloromethane.

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

Front Microbiol. 2016 Jul 19;7:1116. doi: 10.3389/fmicb.2016.01116. eCollection 2016.


Adding biotic complexity alters the metabolic benefits of mutualism.

Harcombe WR, Betts A, Shapiro JW, Marx CJ.

Evolution. 2016 Aug;70(8):1871-81. doi: 10.1111/evo.12973. Epub 2016 Jun 24.


Selection Maintains Apparently Degenerate Metabolic Pathways due to Tradeoffs in Using Methylamine for Carbon versus Nitrogen.

Nayak DD, Agashe D, Lee MC, Marx CJ.

Curr Biol. 2016 Jun 6;26(11):1416-26. doi: 10.1016/j.cub.2016.04.029. Epub 2016 May 19.


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 Jun;33(6):1542-53. doi: 10.1093/molbev/msw035. Epub 2016 Feb 23.


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.


Parallel and Divergent Evolutionary Solutions for the Optimization of an Engineered Central Metabolism in Methylobacterium extorquens AM1.

Carroll SM, Chubiz LM, Agashe D, Marx CJ.

Microorganisms. 2015 Apr 9;3(2):152-74. doi: 10.3390/microorganisms3020152.


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.


Synchronous waves of failed soft sweeps in the laboratory: remarkably rampant clonal interference of alleles at a single locus.

Lee MC, Marx CJ.

Genetics. 2013 Mar;193(3):943-52. doi: 10.1534/genetics.112.148502. Epub 2013 Jan 10.


Good codons, bad transcript: large reductions in gene expression and fitness arising from synonymous mutations in a key enzyme.

Agashe D, Martinez-Gomez NC, Drummond DA, Marx CJ.

Mol Biol Evol. 2013 Mar;30(3):549-60. doi: 10.1093/molbev/mss273. Epub 2012 Dec 4.


FREQ-Seq: a rapid, cost-effective, sequencing-based method to determine allele frequencies directly from mixed populations.

Chubiz LM, Lee MC, Delaney NF, Marx CJ.

PLoS One. 2012;7(10):e47959. doi: 10.1371/journal.pone.0047959. Epub 2012 Oct 31.


Clarity: an open-source manager for laboratory automation.

Delaney NF, Rojas Echenique JI, Marx CJ.

J Lab Autom. 2013 Apr;18(2):171-7. doi: 10.1177/2211068212460237. Epub 2012 Oct 2.


OASIS: an automated program for global investigation of bacterial and archaeal insertion sequences.

Robinson DG, Lee MC, Marx CJ.

Nucleic Acids Res. 2012 Dec;40(22):e174. doi: 10.1093/nar/gks778. Epub 2012 Aug 16.


Epistasis from functional dependence of fitness on underlying traits.

Chiu HC, Marx CJ, Segrè D.

Proc Biol Sci. 2012 Oct 22;279(1745):4156-64. doi: 10.1098/rspb.2012.1449. Epub 2012 Aug 15.


Complete genome sequences of six strains of the genus Methylobacterium.

Marx CJ, Bringel F, Chistoserdova L, Moulin L, Farhan Ul Haque M, Fleischman DE, Gruffaz C, Jourand P, Knief C, Lee MC, Muller EE, Nadalig T, Peyraud R, Roselli S, Russ L, Goodwin LA, Ivanova N, Kyrpides N, Lajus A, Land ML, Médigue C, Mikhailova N, Nolan M, Woyke T, Stolyar S, Vorholt JA, Vuilleumier S.

J Bacteriol. 2012 Sep;194(17):4746-8. doi: 10.1128/JB.01009-12.


Optimization of gene expression through divergent mutational paths.

Chou HH, Marx CJ.

Cell Rep. 2012 Feb 23;1(2):133-40. doi: 10.1016/j.celrep.2011.12.003. Epub 2012 Feb 2.


Recovering from a bad start: rapid adaptation and tradeoffs to growth below a threshold density.

Marx CJ.

BMC Evol Biol. 2012 Jul 4;12:109. doi: 10.1186/1471-2148-12-109.


Repeated, selection-driven genome reduction of accessory genes in experimental populations.

Lee MC, Marx CJ.

PLoS Genet. 2012;8(5):e1002651. doi: 10.1371/journal.pgen.1002651. Epub 2012 May 10.


Ultrafast evolution and loss of CRISPRs following a host shift in a novel wildlife pathogen, Mycoplasma gallisepticum.

Delaney NF, Balenger S, Bonneaud C, Marx CJ, Hill GE, Ferguson-Noel N, Tsai P, Rodrigo A, Edwards SV.

PLoS Genet. 2012 Feb;8(2):e1002511. doi: 10.1371/journal.pgen.1002511. Epub 2012 Feb 9. Erratum in: PLoS Genet. 2012 Mar;8(3). doi: 10.1371/annotation/b5608bc6-aa54-40a7-b246-51fa7bc4a9db.

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