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Constraint and Contingency Pervade the Emergence of Novel Phenotypes in Complex Metabolic Systems.

Hosseini SR, Wagner A.

Biophys J. 2017 Aug 8;113(3):690-701. doi: 10.1016/j.bpj.2017.06.034.


Recombination-Driven Genome Evolution and Stability of Bacterial Species.

Dixit PD, Pang TY, Maslov S.

Genetics. 2017 Sep;207(1):281-295. doi: 10.1534/genetics.117.300061. Epub 2017 Jul 27.


Culture independent analysis using gnd as a target gene to assess Escherichia coli diversity and community structure.

Cookson AL, Biggs PJ, Marshall JC, Reynolds A, Collis RM, French NP, Brightwell G.

Sci Rep. 2017 Apr 12;7(1):841. doi: 10.1038/s41598-017-00890-6.


Phenotypic innovation through recombination in genome-scale metabolic networks.

Hosseini SR, Martin OC, Wagner A.

Proc Biol Sci. 2016 Sep 28;283(1839). pii: 20161536.


Whole-Genome Multilocus Sequence Typing of Extended-Spectrum-Beta-Lactamase-Producing Enterobacteriaceae.

Kluytmans-van den Bergh MF, Rossen JW, Bruijning-Verhagen PC, Bonten MJ, Friedrich AW, Vandenbroucke-Grauls CM, Willems RJ, Kluytmans JA.

J Clin Microbiol. 2016 Dec;54(12):2919-2927. Epub 2016 Sep 14.


Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants.

Raveh-Sadka T, Firek B, Sharon I, Baker R, Brown CT, Thomas BC, Morowitz MJ, Banfield JF.

ISME J. 2016 Dec;10(12):2817-2830. doi: 10.1038/ismej.2016.83. Epub 2016 Jun 3.


Evolvability of an Optimal Recombination Rate.

Lobkovsky AE, Wolf YI, Koonin EV.

Genome Biol Evol. 2015 Dec 10;8(1):70-7. doi: 10.1093/gbe/evv249.


Synonymous Genetic Variation in Natural Isolates of Escherichia coli Does Not Predict Where Synonymous Substitutions Occur in a Long-Term Experiment.

Maddamsetti R, Hatcher PJ, Cruveiller S, M├ędigue C, Barrick JE, Lenski RE.

Mol Biol Evol. 2015 Nov;32(11):2897-904. doi: 10.1093/molbev/msv161. Epub 2015 Jul 20.


Impermanence of bacterial clones.

Bobay LM, Traverse CC, Ochman H.

Proc Natl Acad Sci U S A. 2015 Jul 21;112(29):8893-900. doi: 10.1073/pnas.1501724112.


Recombinant transfer in the basic genome of Escherichia coli.

Dixit PD, Pang TY, Studier FW, Maslov S.

Proc Natl Acad Sci U S A. 2015 Jul 21;112(29):9070-5. doi: 10.1073/pnas.1510839112. Epub 2015 Jul 7.


Aggressive Emerging Pathovars of Xanthomonas arboricola Represent Widespread Epidemic Clones Distinct from Poorly Pathogenic Strains, as Revealed by Multilocus Sequence Typing.

Fischer-Le Saux M, Bonneau S, Essakhi S, Manceau C, Jacques MA.

Appl Environ Microbiol. 2015 Jul;81(14):4651-68. doi: 10.1128/AEM.00050-15. Epub 2015 May 1.


Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts.

Huang CL, Pu PH, Huang HJ, Sung HM, Liaw HJ, Chen YM, Chen CM, Huang MB, Osada N, Gojobori T, Pai TW, Chen YT, Hwang CC, Chiang TY.

BMC Genomics. 2015 Mar 15;16:188. doi: 10.1186/s12864-015-1369-8.


The unexhausted potential of E. coli.

Blount ZD.

Elife. 2015 Mar 25;4. doi: 10.7554/eLife.05826. Review.


ClonalFrameML: efficient inference of recombination in whole bacterial genomes.

Didelot X, Wilson DJ.

PLoS Comput Biol. 2015 Feb 12;11(2):e1004041. doi: 10.1371/journal.pcbi.1004041. eCollection 2015 Feb.


BorreliaBase: a phylogeny-centered browser of Borrelia genomes.

Di L, Pagan PE, Packer D, Martin CL, Akther S, Ramrattan G, Mongodin EF, Fraser CM, Schutzer SE, Luft BJ, Casjens SR, Qiu WG.

BMC Bioinformatics. 2014 Jul 3;15:233. doi: 10.1186/1471-2105-15-233.


Multilocus sequence analysis of the marine bacterial genus Tenacibaculum suggests parallel evolution of fish pathogenicity and endemic colonization of aquaculture systems.

Habib C, Houel A, Lunazzi A, Bernardet JF, Olsen AB, Nilsen H, Toranzo AE, Castro N, Nicolas P, Duchaud E.

Appl Environ Microbiol. 2014 Sep;80(17):5503-14. doi: 10.1128/AEM.01177-14. Epub 2014 Jun 27.


Evolutionary genomics of Borrelia burgdorferi sensu lato: findings, hypotheses, and the rise of hybrids.

Qiu WG, Martin CL.

Infect Genet Evol. 2014 Oct;27:576-93. doi: 10.1016/j.meegid.2014.03.025. Epub 2014 Apr 3. Review.


Genetic divergence of bradyrhizobium strains nodulating soybeans as revealed by multilocus sequence analysis of genes inside and outside the symbiosis island.

Zhang XX, Guo HJ, Wang R, Sui XH, Zhang YM, Wang ET, Tian CF, Chen WX.

Appl Environ Microbiol. 2014 May;80(10):3181-90. doi: 10.1128/AEM.00044-14. Epub 2014 Mar 14.


Large-scale intersubspecific recombination in the plant-pathogenic bacterium Xylella fastidiosa is associated with the host shift to mulberry.

Nunney L, Schuenzel EL, Scally M, Bromley RE, Stouthamer R.

Appl Environ Microbiol. 2014 May;80(10):3025-33. doi: 10.1128/AEM.04112-13. Epub 2014 Mar 7.

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