Publications

Publication list (in reverse chronological order; lab members in bold; “*” = co-first authors):

 

Harcombe, W. R., N. F. Delaney, N. Leiby, N. Klitgord, and C. J. Marx.

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

PLoS Computational Biology. 9:e1003091 (2013). [pdf]


Chubiz, L. M., J. Purswani, S. M. Carroll, and C. J. Marx.

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

BMC Research Notes. 6:183 (2013).[Recommended by Faculty of 1000]


Delaney, N. F., M. E. Kaczmarek, L. M. Ward, P. K. Swanson, M.-C. Lee, and C. J. Marx.

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

PLoS One. 8:e62957 (2013). [pdf]


Carroll, S. M. and C. J. Marx.

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

PLoS Genetics. 9:e1003427 (2013). [pdf]


Lee, M.-C. and C. J. Marx.

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

Genetics. 193:943-952 (2013). [Highlighted article][Recommended by Faculty of 1000]


Marx, C. J.

Can you sequence ecology? Metagenomics of adaptive diversification.

PLoS Biology. 11:e1001487 (2013). [Primer]


Xi. Z., Y. Wang, R. K. Bradley, M. Sugumaran, C. J. Marx, J. S. Rest, and C. C. Davis.

Massive mitochondrial gene transfer in a parasitic flowering plant clade.

PLoS Genetics. 9:1003265 (2013). [pdf]


Agashe, D., N. C. Martinez-Gomez, D. A. Drummond, and C. J. Marx.

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

Molecular Biology and Evolution. 30:549-560 (2013). [pdf] [Recommended by Faculty of 1000]


*Chubiz, L. M., *M.-C. Lee, N. F. Delaney, and C. J. Marx.

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

PLoS One. 7:e47959. (2012). [pdf]


*Delaney, N. F., *J. I. Rojas Echenique, and C. J. Marx.

Clarity: An open source manager for laboratory automation.

Journal of Laboratory Automation. OnlineFirst: doi:10.1177/2211068212457161.(2012). [pdf]


Leiby, N., W. R. Harcombe, and C. J. Marx.

Multiple long-term, experimentally-evolved populations of Escherichia coli acquire dependence upon citrate as an iron chelator for optimal growth on glucose.

BMC Evolutionary Biology. 12:151 (2012). [pdf]


*Robinson, D. G., *M.-C. Lee, and C. J. Marx.

OASIS: An automated program for global investigation of Bacterial and Archaeal insertion sequences.

Nucleic Acids Research. 40:e174 (2012). [pdf]


Chiu, H.-C., C. J. Marx, and D. Segrè.

Epistasis from functional dependence of fitness on underlying traits.

Proceedings of the Royal Society B. 279:4156-4164 (2012). [pdf]


Marx, C. J., F. Bringel, L. Chistoserdova, L. Moulin, M. F. Ul Haque, D. E. Fleischman, C. Gruffaz, P. Jourand, C. Kneif, Lee, M.-C. , E. E. L. Muller, T. Nadalig, R. Peyraud, S. Roselli, L. Russ, L. A Goodwin, N. Ivanova, N. Kyrpides, A. Lajus, M. L. Land, C. Médigue, N. Mikhailova, M. Nolan, T. Woyke, S. Stolyar, J. A. Vorholt, and S. Vuilleumier.

Complete genome sequences of six strains of the genus Methylobacterium.

Journal of Bacteriology. 194:4746-4748 (2012). [pdf]


Marx, C. J.

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

BMC Evolutionary Biology.12:109. (2012). [pdf]


Lee, M.-C. and C. J. Marx.

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

PLoS Genetics. 8:e1002651 (2012). [pdf]


Delaney, N.F., S. Balenger, C. Bonneaud, C. J. Marx, G. E. Hill, N. Ferguson-Noel, P. Tsai, A. Rodrigo, and S. V. Edwards.

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

PLoS Genetics. 8:e1002511 (2012). [pdf]


Chou, H.-H. and C. J. Marx.

Optimization of gene expression through divergent mutational paths.

Cell Reports. 1:133-140 (2012). [pdf]


Marx, C. J.

Regulatory Revolution: Evolving the “Anti-Lacl” Repressor.

Cell. 146:350-352 (2011).[pdf]


Chou, H.-H., H.-C. Chiu, N. F. Delaney, D. Segrè, and C. J. Marx.

Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation.

Science. 332:1190-1192 (2011).[pdf]


Marx, C. J.

Evolution as an experimental tool in microbiology: “Bacterium, improve thyself!”

Environmental Microbiology Reports. 3:12-14 (2011). [Perspective]


Bradley, A. S., A. Pearson, J. P. Sáenz, C. J. Marx.

Adenosylhopane: the first intermediate in hopanoid side chain biosynthesis.

Organic Geochemistry (2010). [pdf]


Segrè, D and C. J. Marx.

Introduction to Focus Issue: Genetic Interactions.

Chaos. 20:026101 (2010). [Introduction] [pdf]


Gudelj, I., J. S. Weitz, T. Ferenci, M. C. Horner-Devine, C. J. Marx, J. R. Meyer, and S. E. Forde.

An integrative approach to understanding microbial diversity: from intracellular mechanisms to community structure.

Ecology Letters. 13:1073-1084 (2010). [Idea and Perspective] [pdf]


Chou, H-H, J. Berthet, and C. J. Marx.

Fast Growth Increases the Selective Advantage of a Mutation Arising Recurrently during Evolution under Metal Limitation.

PLoS Genetics 5:e1000652 (2009). [pdf], [supplemental] or [summary]


Lee, M-C, H-H Chou, and C. J. Marx.

Assymetric, bi-modal tradeoffs during adaptation of Methylobacterium to distinct growth substrates.       

Evolution 63:2816-2830 (2009). [pdf],  or [summary]


Marx, C.J.

Getting in Touch with Your Friends.

Science 324: 1150-1151 (2009). [Perspective] [summary] or [full text]


Vuilleumier S, Chistoserdova L, Lee M-C, Bringel F, Lajus A, Zhou Y, Gourion B, Barbe V, Chang J, Cruveiller S, Dossat C, Gillett W, Gruffaz C, Haugen E, Hourcade E, Levy R, Mangenot S, Muller E, Nadalig T, Pangi M, Penny C, Peyraud R, Robinson D, Roche D, Rouy Z, Saenampechek C, Salvignol G, Vallenet D, Wu Z, Marx CJ, Vorholt JA, Olson MV, Kaul R, Weissenbach J, Medigue C, and Lidstrom ME.2009.

Methylobacterium Genome Sequences: A Reference Blueprint to Investigate Microbial Metabolism of C1 Compounds from Natural and Industrial Sources.      

PLoS ONE. 4(5): e5584 (2009). [pdf]


Marx, C.J.

Development of a broad-host-range sacB-based vector for unmarked allelic exchange.

BMC Research Notes 1:1 (2008). [pdf] [link]


Chain, P. S. G., V. J. Denef, K. Konstantinidis, L. M Vergez, L. Agulló, V. Latorre Reyes, L. Hauser, M. Córdova, L. Gómez, M. González, M. Land, V. Lao, F. Larimer, J. J. LiPuma, E. Mahenthiralingam, S. A. Malfatti, C. J. Marx , J. J. Parnell, A. Ramette, P. Richardson, M. Seeger, D. Smith, T. Spilker, W. J. Sul, T. V. Tsoi, L. E. Ulrich, I. B. Zhulin, and J. M. Tiedje.

Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73 Mbp genome shaped for versatility.

Proc. Natl. Acad. Sci. USA (2006) . [pdf]


Kalyuzhnaya, M. G., N. Korotkova, G. Crowther, C. J. Marx , M. E. Lidstrom, and L. Chistoserdova.

Analysis of gene islands involved in methanopterin-linked C 1 transfer reactions, deduction of novel C 1 transfer genes, and new insights into the evolution of “archaeal” genes in bacteria.

J. Bacteriol. 187:4607-4614 (2005). [pdf]


Marx, C. J., S. J. Van Dien, and M. E. Lidstrom.Flux analysis uncovers key role of functional redundancy in formaldehyde pathways.

PLoS Biol. 3:e16 (2005). [abstract] [pdf] [Highlighted in Nature Reviews Microbiology 3:103]


Marx, C. J., J. A. Miller, L. Chistoserdova, and M. E. Lidstrom.

Multiple formaldehyde oxidation pathways in Burkholderia fungorum LB400.

J. Bacteriol. 186:2173-2178 (2004). [pdf] [link]


Chistoserdova, L., C. Jenkins, M. G. Kalyuzhnaya, C. J. Marx, A. Lapidus, J. T. Staley, and M.E. Lidstrom.

The enigmatic Planctomyces may hold a key to the origins of methanogenesis and methylotrophy.

Mol. Biol. Evol. 21:1234-1241 (2004). [pdf] [link]


Marx, C. J., and M. E. Lidstrom.

Development of an insertional vector system for Methylobacterium extorquens AM1 and generation of null mutants lacking mtdA and/or fch.

Microbiology 150:9-19 (2004). [pdf] [link]


Van Dien, S. J., C. J. Marx, B. N. O’Brien, and M. E. Lidstrom.

Genetic characterization of the carotenoid biosynthetic pathway in Methylobacterium extorquens AM1 and isolation of a colorless mutant.

Appl. Environ. Microbiol. 69:7563-7566 (2003). [pdf] [link]


Marx, C. J., L. Chistoserdova, and M. E. Lidstrom.

The formaldehyde detoxifying role of the tetrahydromethanopterin-linked pathway in Methylobacterium extorquens AM1.

J. Bacteriol185:7160-7168 (2003). [pdf] [link]


Marx, C. J., M. Laukel, J. A. Vorholt, and M. E. Lidstrom.

Purification of the formate-tetrahydrofolate ligase from Methylobacterium extorquens AM1 and demonstration of its requirement for methylotrophic growth. 

J. Bacteriol. 185:7169-7175 (2003). [pdf] [link]


Marx, C. J., B. N. O’Brien, J. Breezee, and M. E. Lidstrom.

Novel methylotrophy genes of Methylobacterium extorquens AM1 identified by using transposon mutagenesis including a putative dihydromethanopterin reductase.

J. Bacteriol. 185:669-673 (2003). [pdf] [link]


Marx, C. J., and M. E. Lidstrom.

Broad-host-range cre-lox system for antibiotic marker recycling in Gram-negative bacteria. 

BioTechniques33:1062-1067 (2002). [pdf pt1]  [pdf pt2] [link]


Marx, C. J., and M. E. Lidstrom.

Development of improved versatile broad-host-range vectors for use in methylotrophs and other Gram-negative bacteria.

Microbiology 147:2065-2075 (2001). [pdf] [link]


Vorholt, J. A., C. J. Marx, M. E. Lidstrom, and R. K. Thauer.

Novel formaldehyde-activating enzyme in Methylobacterium extorquens AM1 required for growth on methanol. 

J. Bacteriol. 182:6645-6650 (2000). [pdf] [link]


Cohen-Kupiec, R., C. J. Marx, and J. A. Leigh.

Function and regulation of glnA in the methanogenic archaeon Methanococcus maripaludis.

J. Bacteriol181:256-261 (1999). [pdf] [link]