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Items: 47

1.

An Introduced Crop Plant Is Driving Diversification of the Virulent Bacterial Pathogen Erwinia tracheiphila.

Shapiro LR, Paulson JN, Arnold BJ, Scully ED, Zhaxybayeva O, Pierce NE, Rocha J, Klepac-Ceraj V, Holton K, Kolter R.

MBio. 2018 Oct 2;9(5). pii: e01307-18. doi: 10.1128/mBio.01307-18.

2.

Insights into origin and evolution of α-proteobacterial gene transfer agents.

Shakya M, Soucy SM, Zhaxybayeva O.

Virus Evol. 2017 Dec 7;3(2):vex036. doi: 10.1093/ve/vex036. eCollection 2017 Jul.

3.

Genomic insights into temperature-dependent transcriptional responses of Kosmotoga olearia, a deep-biosphere bacterium that can grow from 20 to 79 °C.

Pollo SMJ, Adebusuyi AA, Straub TJ, Foght JM, Zhaxybayeva O, Nesbø CL.

Extremophiles. 2017 Nov;21(6):963-979. doi: 10.1007/s00792-017-0956-9. Epub 2017 Sep 11.

4.

A null model for microbial diversification.

Straub TJ, Zhaxybayeva O.

Proc Natl Acad Sci U S A. 2017 Jul 3;114(27):E5414-E5423. doi: 10.1073/pnas.1619993114. Epub 2017 Jun 19.

5.

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. Epub 2016 Jun 24.

6.

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.

7.

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. Epub 2015 Jun 25.

8.

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.

9.

'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. Epub 2015 Mar 2.

PMID:
25630351
10.

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. Epub 2014 Dec 12.

11.

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. eCollection 2014.

12.

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. Epub 2013 Jul 10. No abstract available.

13.

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. Epub 2013 Mar 16.

PMID:
23504483
14.

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. Epub 2013 Jan 29.

PMID:
23358730
15.

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. Epub 2012 Jul 12.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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. Epub 2009 Mar 23.

21.

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.

PMID:
19271186
22.

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. Epub 2009 Jan 5.

23.

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.

24.

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.

25.

Actinorhodopsins: proteorhodopsin-like gene sequences found predominantly in non-marine environments.

Sharma AK, Zhaxybayeva O, Papke RT, Doolittle WF.

Environ Microbiol. 2008 Apr;10(4):1039-56. doi: 10.1111/j.1462-2920.2007.01525.x. Epub 2008 Jan 24.

PMID:
18218036
26.

Integron-associated gene cassettes in Halifax Harbour: assessment of a mobile gene pool in marine sediments.

Koenig JE, Boucher Y, Charlebois RL, Nesbø C, Zhaxybayeva O, Bapteste E, Spencer M, Joss MJ, Stokes HW, Doolittle WF.

Environ Microbiol. 2008 Apr;10(4):1024-38. doi: 10.1111/j.1462-2920.2007.01524.x. Epub 2008 Jan 7.

PMID:
18190517
27.

Genomic plasticity in prokaryotes: the case of the square haloarchaeon.

Cuadros-Orellana S, Martin-Cuadrado AB, Legault B, D'Auria G, Zhaxybayeva O, Papke RT, Rodriguez-Valera F.

ISME J. 2007 Jul;1(3):235-45. Epub 2007 May 31.

PMID:
18043634
28.

Searching for species in haloarchaea.

Papke RT, Zhaxybayeva O, Feil EJ, Sommerfeld K, Muise D, Doolittle WF.

Proc Natl Acad Sci U S A. 2007 Aug 28;104(35):14092-7. Epub 2007 Aug 21.

29.

Evolution: reducible complexity -- the case for bacterial flagella.

Doolittle WF, Zhaxybayeva O.

Curr Biol. 2007 Jul 3;17(13):R510-2.

30.

A hyperconserved protein in Prochlorococcus and marine Synechococcus.

Zhaxybayeva O, Gogarten JP, Doolittle WF.

FEMS Microbiol Lett. 2007 Sep;274(1):30-4. Epub 2007 Jun 15.

31.

Systematic overestimation of gene gain through false diagnosis of gene absence.

Zhaxybayeva O, Nesbø CL, Doolittle WF.

Genome Biol. 2007;8(2):402.

32.

Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events.

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

Genome Res. 2006 Sep;16(9):1099-108. Epub 2006 Aug 9.

33.

Evidence for existence of "mesotogas," members of the order Thermotogales adapted to low-temperature environments.

Nesbø CL, Dlutek M, Zhaxybayeva O, Doolittle WF.

Appl Environ Microbiol. 2006 Jul;72(7):5061-8.

34.

Ancient gene duplications and the root(s) of the tree of life.

Zhaxybayeva O, Lapierre P, Gogarten JP.

Protoplasma. 2005 Dec;227(1):53-64. Epub 2005 Dec 30.

PMID:
16389494
35.

Evolutionary and diagnostic implications of intragenomic heterogeneity in the 16S rRNA gene in Aeromonas strains.

Morandi A, Zhaxybayeva O, Gogarten JP, Graf J.

J Bacteriol. 2005 Sep;187(18):6561-4.

36.

PentaPlot: a software tool for the illustration of genome mosaicism.

Hamel L, Zhaxybayeva O, Gogarten JP.

BMC Bioinformatics. 2005 Jun 6;6:139.

37.

Were arachnids the first to use combinatorial peptide libraries?

Sollod BL, Wilson D, Zhaxybayeva O, Gogarten JP, Drinkwater R, King GF.

Peptides. 2005 Jan;26(1):131-9. Review.

PMID:
15626513
38.

Genome mosaicism and organismal lineages.

Zhaxybayeva O, Lapierre P, Gogarten JP.

Trends Genet. 2004 May;20(5):254-60. Review. No abstract available. Erratum in: Trends Genet. 2005 Jan;21(1):36.

PMID:
15109780
39.

Cladogenesis, coalescence and the evolution of the three domains of life.

Zhaxybayeva O, Gogarten JP.

Trends Genet. 2004 Apr;20(4):182-7. Erratum in: Trends Genet. 2004 Jul;20(7):291.

PMID:
15041172
40.

Visualization of the phylogenetic content of five genomes using dekapentagonal maps.

Zhaxybayeva O, Hamel L, Raymond J, Gogarten JP.

Genome Biol. 2004;5(3):R20. Epub 2004 Feb 16.

41.

Spliceosomal introns: new insights into their evolution.

Zhaxybayeva O, Gogarten JP.

Curr Biol. 2003 Sep 30;13(19):R764-6. Review.

42.

An improved probability mapping approach to assess genome mosaicism.

Zhaxybayeva O, Gogarten JP.

BMC Genomics. 2003 Sep 15;4(1):37.

43.

Evolution of photosynthetic prokaryotes: a maximum-likelihood mapping approach.

Raymond J, Zhaxybayeva O, Gogarten JP, Blankenship RE.

Philos Trans R Soc Lond B Biol Sci. 2003 Jan 29;358(1429):223-30.

44.

Whole-genome analysis of photosynthetic prokaryotes.

Raymond J, Zhaxybayeva O, Gogarten JP, Gerdes SY, Blankenship RE.

Science. 2002 Nov 22;298(5598):1616-20.

45.

Inteins: structure, function, and evolution.

Gogarten JP, Senejani AG, Zhaxybayeva O, Olendzenski L, Hilario E.

Annu Rev Microbiol. 2002;56:263-87. Epub 2002 Jan 30. Review.

PMID:
12142479
46.
47.

Horizontal transfer of archaeal genes into the deinococcaceae: detection by molecular and computer-based approaches.

Olendzenski L, Liu L, Zhaxybayeva O, Murphey R, Shin DG, Gogarten JP.

J Mol Evol. 2000 Dec;51(6):587-99.

PMID:
11116332

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