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Functional and Evolutionary Characterization of a Gene Transfer Agent's Multilocus "Genome".

Hynes AP, Shakya M, Mercer RG, Grüll MP, Bown L, Davidson F, Steffen E, Matchem H, Peach ME, Berger T, Grebe K, Zhaxybayeva O, Lang AS.

Mol Biol Evol. 2016 Oct;33(10):2530-43. doi: 10.1093/molbev/msw125.


Horizontal Gene Acquisitions, Mobile Element Proliferation, and Genome Decay in the Host-Restricted Plant Pathogen Erwinia Tracheiphila.

Shapiro LR, Scully ED, Straub TJ, Park J, Stephenson AG, Beattie GA, Gleason ML, Kolter R, Coelho MC, De Moraes CM, Mescher MC, Zhaxybayeva O.

Genome Biol Evol. 2016 Mar 18;8(3):649-64. doi: 10.1093/gbe/evw016.


Insights into thermoadaptation and the evolution of mesophily from the bacterial phylum Thermotogae.

Pollo SM, Zhaxybayeva O, Nesbø CL.

Can J Microbiol. 2015 Sep;61(9):655-70. doi: 10.1139/cjm-2015-0073.


Draft Genome Sequence of Erwinia tracheiphila, an Economically Important Bacterial Pathogen of Cucurbits.

Shapiro LR, Scully ED, Roberts D, Straub TJ, Geib SM, Park J, Stephenson AG, Salaau Rojas E, Liu Q, Beattie G, Gleason M, De Moraes CM, Mescher MC, Fleischer SG, Kolter R, Pierce N, Zhaxybayeva O.

Genome Announc. 2015 Jun 4;3(3). pii: e00482-15. doi: 10.1128/genomeA.00482-15.


'Ménage à trois': a selfish genetic element uses a virus to propagate within Thermotogales.

Lossouarn J, Nesbø CL, Mercier C, Zhaxybayeva O, Johnson MS, Charchuck R, Farasin J, Bienvenu N, Baudoux AC, Michoud G, Jebbar M, Geslin C.

Environ Microbiol. 2015 Sep;17(9):3278-88. doi: 10.1111/1462-2920.12783.


Evidence for extensive gene flow and Thermotoga subpopulations in subsurface and marine environments.

Nesbø CL, S Swithers K, Dahle H, Haverkamp TH, Birkeland NK, Sokolova T, Kublanov I, Zhaxybayeva O.

ISME J. 2015 Jul;9(7):1532-42. doi: 10.1038/ismej.2014.238.


Quantitative and functional characterization of the hyper-conserved protein of Prochlorococcus and marine Synechococcus.

Whidden CE, DeZeeuw KG, Zorz JK, Joy AP, Barnett DA, Johnson MS, Zhaxybayeva O, Cockshutt AM.

PLoS One. 2014 Oct 31;9(10):e109327. doi: 10.1371/journal.pone.0109327.


Anciently duplicated genes reduce uncertainty in molecular clock estimates.

Zhaxybayeva O.

Proc Natl Acad Sci U S A. 2013 Jul 23;110(30):12168-9. doi: 10.1073/pnas.1310930110. No abstract available.


Photosystem II protein clearance and FtsH function in the diatom Thalassiosira pseudonana.

Campbell DA, Hossain Z, Cockshutt AM, Zhaxybayeva O, Wu H, Li G.

Photosynth Res. 2013 May;115(1):43-54. doi: 10.1007/s11120-013-9809-2.


Cell sorting analysis of geographically separated hypersaline environments.

Zhaxybayeva O, Stepanauskas R, Mohan NR, Papke RT.

Extremophiles. 2013 Mar;17(2):265-75. doi: 10.1007/s00792-013-0514-z.


Genome sequence of the mesophilic Thermotogales bacterium Mesotoga prima MesG1.Ag.4.2 reveals the largest Thermotogales genome to date.

Zhaxybayeva O, Swithers KS, Foght J, Green AG, Bruce D, Detter C, Han S, Teshima H, Han J, Woyke T, Pitluck S, Nolan M, Ivanova N, Pati A, Land ML, Dlutek M, Doolittle WF, Noll KM, Nesbø CL.

Genome Biol Evol. 2012;4(8):700-8. doi: 10.1093/gbe/evs059.


Gene transfer agents: phage-like elements of genetic exchange.

Lang AS, Zhaxybayeva O, Beatty JT.

Nat Rev Microbiol. 2012 Jun 11;10(7):472-82. doi: 10.1038/nrmicro2802. Review.


Quartet decomposition server: a platform for analyzing phylogenetic trees.

Mao F, Williams D, Zhaxybayeva O, Poptsova M, Lapierre P, Gogarten JP, Xu Y.

BMC Bioinformatics. 2012 Jun 7;13:123.


Lateral gene transfer.

Zhaxybayeva O, Doolittle WF.

Curr Biol. 2011 Apr 12;21(7):R242-6. doi: 10.1016/j.cub.2011.01.045. No abstract available.


On the origin of prokaryotic species.

Doolittle WF, Zhaxybayeva O.

Genome Res. 2009 May;19(5):744-56. doi: 10.1101/gr.086645.108. Review.


On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales.

Zhaxybayeva O, Swithers KS, Lapierre P, Fournier GP, Bickhart DM, DeBoy RT, Nelson KE, Nesbø CL, Doolittle WF, Gogarten JP, Noll KM.

Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5865-70. doi: 10.1073/pnas.0901260106.


Detection and quantitative assessment of horizontal gene transfer.

Zhaxybayeva O.

Methods Mol Biol. 2009;532:195-213. doi: 10.1007/978-1-60327-853-9_11.


The genome of Thermosipho africanus TCF52B: lateral genetic connections to the Firmicutes and Archaea.

Nesbø CL, Bapteste E, Curtis B, Dahle H, Lopez P, Macleod D, Dlutek M, Bowman S, Zhaxybayeva O, Birkeland NK, Doolittle WF.

J Bacteriol. 2009 Mar;191(6):1974-8. doi: 10.1128/JB.01448-08.


Intertwined evolutionary histories of marine Synechococcus and Prochlorococcus marinus.

Zhaxybayeva O, Doolittle WF, Papke RT, Gogarten JP.

Genome Biol Evol. 2009 Sep 2;1:325-39. doi: 10.1093/gbe/evp032.


Unsupervised learning in detection of gene transfer.

Hamel L, Nahar N, Poptsova MS, Zhaxybayeva O, Gogarten JP.

J Biomed Biotechnol. 2008;2008:472719. doi: 10.1155/2008/472719.

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