"The work one does is another way of keeping a diary"
(Pablo Picasso)

Publications

IN PEER-REVIEWED JOURNALS

  1. Hynes AP, Shakya M, Mercer RG, Grull MP, Bown L, Davidson F, Steffen E, Matchem H, Peach ME, Berger T, Grebe K, Zhaxybayeva O, Lang AS. Functional and Evolutionary Characterization of a Gene Transfer Agent's Multilocus "Genome". Mol Biol Evol. 2016 Jun 24. E-pub ahead of print. [Open Access Article]

  2. Lori R. Shapiro, Erin D. Scully, Timothy J. Straub, Jihye Park, Andrew G. Stephenson, Gwyn Beattie, Mark Gleason, Roberto Kolter, Miguel C. Coelho, Consuelo M. DeMoraes, Mark C. Mescher, and Olga Zhaxybayeva: "Horizontal Gene Acquisitions, Mobile Element Proliferation, and Genome Decay in the Host-Restricted Plant Pathogen Erwinia tracheiphila", Genome Biol Evol. 2016, 8:649-664. [Open Access Article]

  3. Pollo SM, Zhaxybayeva O, Nesbo CL: "Insights into thermoadaptation and the evolution of mesophily from the bacterial phylum Thermotogae." Can J Microbiol. 2015, 61:655-70. [PubMed]

  4. Lori Shapiro, Erin Scully, Dana Roberts, Timothy Straub, Scott Geib, Jihye Park, Andrew Stephenson, Erika Salaau Rojas, Qian Liu, Gwyn Beattie, Mark Gleason, Consuelo De Moraes, Mark Mescher, Shelby Fleischer, Roberto Kolter, Naomi Pierce, and Olga Zhaxybayeva: "Draft genome sequence of Erwinia tracheiphila, an economically important bacterial pathogen of cucurbits". Genome Announcements 2015, 3: e00482-15. doi: 10.1128/genomeA.00482-15

  5. Lossouarn J, Nesbo CL, Mercier C, Zhaxybayeva O, Johnson MS, Charchuck R, Farasin J, Bienvenu N, Baudoux AC, Michoud G, Jebbar M, Geslin C. "Menage a trois": a selfish genetic element uses a virus to propagate within Thermotogales. Environ Microbiol. 2015, 17:3278-88. doi: 10.1111/1462-2920.12783.[PubMed]

  6. Nesbo CL, S Swithers K, Dahle H, Haverkamp TH, Birkeland NK, Sokolova T, Kublanov I, Zhaxybayeva O.: "Evidence for extensive gene flow and Thermotoga subpopulations in subsurface and marine environments." ISME J. 2015, 9:1532-42. doi: 10.1038/ismej.2014.238. [PubMed]

  7. Caroline E. Whidden, Katrina G. DeZeeuw, Jackie K. Zorz, Andrew P. Joy, David A. Barnett, Milo S. Johnson'13, Olga Zhaxybayeva, and Amanda M. Cockshutt: "Quantitative and Functional Characterization of the Hyper-Conserved Protein of Prochlorococcus and marine Synechococcus", PLoS ONE, 2014, 9: e109327.

  8. Olga Zhaxybayeva: "Anciently duplicated genes reduce uncertainty in molecular clock estimates", Proc Natl Acad Sci USA, 2013, 110:12168-9, E-pub July 10.

  9. Douglas A. Campbell, Zakir Hossain, Amanda M. Cockshutt, Olga Zhaxybayeva, Hongyan Wu, and Gang Li "Photosystem II protein clearance and FtsH function in the diatom Thalassiosira pseudonana", Photosynthesis Research, 2013, 115:43-54. [PubMed]

  10. Olga Zhaxybayeva, Ramunas Stepanauskas, Nikhil R. Mohan, and R. Thane Papke: "Cell sorting analysis of geographically separated hypersaline environments", Extremophiles, 2013, 17:265-75. [PubMed]

  11. Olga Zhaxybayeva: "The Mystery of Eukaryotic Cell Origin". Book review of "Secret Chambers: The Inside Story of Cells and Complex Life" by Martin Brasier (Oxford University Press). BioScience, 2012, 62: 997-998.

  12. Olga Zhaxybayeva, Kristen S. Swithers, Julia Foght, Anna Green, Brittany Held, David Bruce, Chris Detter, Shunsheng Han, Hazuki Teshima, James Han, Tanja Woyke, Sam Pitluck, Len Pennacchio, Matt Nolan, Natalia Ivanova, Amrita Pati, Miriam L. Land, Marlena Dlutek, W. Ford Doolittle, Kenneth M. Noll and Camilla L. Nesbo: "Genome sequence of the mesophilic Thermotogales bacterium Mesotoga prima MesG1.Ag.4.2 reveals largest Thermotogales genome to-date", Genome Biology and Evolution, 2012, 4: 700-708. doi: 10.1093/gbe/evs059.

  13. Andrew S. Lang, Olga Zhaxybayeva, and J. Thomas Beatty: "Gene Transfer Agents: phage-like elements of genetic exchange", Nature Reviews in Micriobiology, 2012, 10: 472-482.

  14. Feglou Mao, David Williams, Olga Zhaxybayeva, Maria Poptsova, J. Peter Gogarten and Ying Xu: "Quartet Decomposition Server: A Platform for Analyzing Phylogenetic Trees", BMC Bioinformatics, 2012, 13:123.

  15. Olga Zhaxybayeva and W. Ford Doolittle: "Lateral Gene Transfer. A Primer", Current Biology, 2011, 21: R242-6. [PubMed]

  16. W. Ford Doolittle and Olga Zhaxybayeva: "Metagenomics and the units of biological organization", BioScience, 2010, 60: 102-112.

  17. Olga Zhaxybayeva, W. Ford Doolittle, R. Thane Papke and J. Peter Gogarten: "Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus", Genome Biology and Evolution, 2009, 1: 325–339. [Open Access]

  18. W. Ford Doolittle and Olga Zhaxybayeva: "On the origin of prokaryotic species", Genome Research 2009, 19:744-56. [PubMed]

  19. Olga Zhaxybayeva, Kristen Swithers, Pascal Lapierre, Greg Fournier, Derek Bickhard, Robert T. DeBoy, Karen E. Nelson, Camilla L. Nesbo, W. Ford Doolittle, J. Peter Gogarten and Kenneth M. Noll: "On the Chimeric Nature, Thermophilic Origin and Phylogenetic Placement of the Thermotogales", Proc Natl Acad Sci USA 2009, 106:5865-70. [PubMed]

  20. Camilla L. Nesbo, Eric Bapteste, Bruce Curtis, Hakon Dahle, Philippe Lopez, Dave Macleod, Marlena Dlutek, Sharen Bowman, Angie Lewis, Olga Zhaxybayeva, Nils-KÃ¥re Birkeland and W. Ford Doolittle: "The genome of Thermosipho africanus TCF52B: lateral genetic connections to the Firmicutes and Archaea", J.Bact. 2009, 191:1974-8. [PubMed]

  21. Lutz Hamel, Neha Nahar, Maria S. Poptsova, Olga Zhaxybayeva and J. Peter Gogarten: "Unsupervised Learning in Detection of Gene Transfer", Journal of Biomedicine and Biotechnology, 2008, 2008: 472719. [Open Access]

  22. Adrian K. Sharma, Olga Zhaxybayeva, R. Thane Papke and W.Ford Doolittle: "Actinorhodopsins: proteorhodopsin-like gene sequences found predominantly in non-marine environments", Environmental Microbiology, 2008, 10: 1039-1056. [PubMed]

  23. Jeremy Koenig, Yan Boucher, Robert Charlebois, Camilla Nesbo, Olga Zhaxybayeva, Eric Bapteste, Matthew Spencer, H. W. Stokes and W. Ford Doolittle: "Integron-associated gene cassettes in Halifax Harbour: assessment of a mobile gene pool in marine sediments", Environmental Microbiology, 2008, 10: 1024-1038. [PubMed]

  24. J Peter Gogarten, Gregory Fournier and Olga Zhaxybayeva: "Gene transfer and the reconstruction of life's early history from the molecular record", Space Science Reviews, 2008, 135: 115-131.

  25. Lutz Hamel, Neha Nahar, Maria S. Poptsova, J. Peter Gogarten and Olga Zhaxybayeva "Unsupervised Learning in Spectral Genome Analysis", Proceeding of the IEEE Conference Frontiers in the Convergence of Bioscience and Information Technologies (FBIT 2007), October 2007, pp317 - 321, IEEE Press, ISBN 0-7695-2999-2. [Reprint]

  26. R. Thane Papke, Olga Zhaxybayeva, Edward Feil, Katrin Sommerfeld, Denise Muise, W. Ford Doolittle: "Searching for species in haloarchaea", PNAS 2007 104: 14092-14097.

  27. Olga Zhaxybayeva, J Peter Gogarten and W. Ford Doolittle: "A hyperconserved protein in Prochlorococcus and marine Synechococcus", FEMS Microbiol Lett, 2007, 274: 30-34. [Pre-review MS]. The definitive version of the manuscript is available: [Reprint]

  28. W. Ford Doolittle and Olga Zhaxybayeva: "Evolution: reducible complexity - the case for bacterial flagella", Current Biology, 2007, 17: R510-R512.

  29. Sara Cuadros-Orellana, Ana-Belen Martin-Cuadrado, Boris Legault, Giuseppe D'Auria, Olga Zhaxybayeva, R. Thane Papke, Francisco Rodriguez-Valera: "Genomic Plasticity in Prokaryotes: the Case of the Square Haloarchaeon", ISME Journal, 2007, 1, 235-245.[Reprint]

  30. Olga Zhaxybayeva, Camilla L. Nesbo and W.Ford Doolittle: "Systematic overestimation of gene gain through false diagnosis of gene absence", Genome Biology, 2007, 8:402. [Open Access]

  31. "The Astrobiology Primer: An Outline of General Knowledge. Version 1, 2006". Editors: L.J. Mix, J.C. Armstrong, A.M. Mandell, A.C. Mosier, J. Raymond, S.N. Raymond, F.J. Stewart, K. von Braun, and O. Zhaxybayeva, Authors: L. Billings, V. Cameron, M. Claire, G.J. Dick, S.D. Domagal-Goldman, E.J. Javaux, O.J. Johnson, C. Laws, M.S. Race, J. Rask, J.D. Rummel, R.T. Schelble, and S. Vance, Astrobiology, 2006, 6: 735-813. [Open Access]

  32. Olga Zhaxybayeva, J. Peter Gogarten, Robert L. Charlebois, W. Ford Doolittle and R. Thane Papke: "Phylogenetic Analyses Of Cyanobacterial Genomes: Quantification Of Horizontal Gene Transfer Events", Genome Research, 2006, 16:1099-1108. [Supplementary Data]

  33. Camilla L. Nesbo, Marlena Dlutek, Olga Zhaxybayeva and W. Ford Doolittle: "Evidence for the existence of mesotogas - members of the Thermotogales adapted to low temperature environments", Applied and Environmental Microbiology, 2006, 72:5061-5068.

  34. Olga Zhaxybayeva, Pascal Lapierre and J. Peter Gogarten: "Ancient Gene Duplications and the Root(s) of the Tree of Life", Protoplasma, 2006, 227:53-64.

  35. Alessia Morandi, Olga Zhaxybayeva, J. Peter Gogarten and Joerg Graf: "Evolutionary and Diagnostic Implications of Intragenomic Heterogeneity in the 16S rRNA Gene in Aeromonas Strains", J. Bact., 2005, 187:6561-4.

  36. Lutz Hamel, Olga Zhaxybayeva and J. Peter Gogarten: "PentaPlot: A software tool for the illustration of genome mosaicism", BMC Bioinformatics, 2005, 6: 13.
    [Open Access Article] [Accompanying Software - PentaPlot]

  37. Olga Zhaxybayeva and J. Peter Gogarten. Review of "Cladistics: a practical primer on CD-ROM" by Peter Skelton and Andrew Smith. Origin of Life and Evolution of Biospheres, 2005, 35: 69-71

  38. Brianna L. Sollod, David Wilson, Olga Zhaxybayeva, J. Peter Gogarten, Roger Drinkwater, and Glenn F. King: "Were arachnids the first to use combinatorial peptide libraries?", Peptides, 2005, 26: 131-139.

  39. Zhaxybayeva, O., Lapierre, P. and Gogarten J.P.: "Genome Mosaicism and Organismal Lineages", Trends in Genetics, 2004, 20(5): 254-260. [DOI link]

  40. O. Zhaxybayeva and J. Peter Gogarten: Cladogenesis, Coalescence and the Evolution of the Three Domains of Life. Trends in Genetics 2004, 20(4): 182-187. [DOI link]

  41. Olga Zhaxybayeva, Lutz Hamel, Jason Raymond, and J. Peter Gogarten: Visualization of Phylogenetic content of Five Genomes with Dekapentagonal Maps. Genome Biology 2004, 5: R20
    [Open Access Article] [Accompanying Software - PentaPlot]

  42. Olga Zhaxybayeva and J. Peter Gogarten. Spliceosomal Introns: New Insights into Their Evolution. Current Biology 2003, 13: R764-766 [Abstract]

  43. Olga Zhaxybayeva and J. Peter Gogarten. An Improved Probability Mapping Approach to Assess Genome Mosaicism, BMC Genomics 2003 4: 37 [Free Online Version]

  44. Jason Raymond, Olga Zhaxybayeva, J. Peter Gogarten and Robert E. Blankenship. Evolution of photosynthetic prokaryotes: a maximum-likelihood mapping approach. Phil. Trans. R. Soc. Lond. B 2003, 358: 223-230. [Abstract]

  45. RAYMOND, J.#, ZHAXYBAYEVA, O.#, GOGARTEN, J.P., GERDES, S., BLANKENSHIP, R.E.: Whole Genome Analysis of Photosynthetic Prokaryotes. Science 2002, 298: 1616-1620.
    [Reprint] [Supplementary Data]

    #- these authors contributed equally to the published work

  46. J. Peter Gogarten, Alireza G. Senejani, Olga Zhaxybayeva, Lorraine Olendzenski, and Elena Hilario. Inteins: Structure, Function, and Evolution. Annu. Rev. Microbiol. 2002, 56: 263-287 [reprint]

  47. Olga Zhaxybayeva, J Peter Gogarten. Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses. BMC Genomics 2002, 3:4. [Free Online Version] [Supplementary Data]

  48. Olendzenski, L., Liu, L., Zhaxybayeva, O., Murphey, R., Shin, D.G., and Gogarten, J.P. 2000. Horizontal Transfer of Archaeal Genes into the Deinococcaceae: Detection by molecular and computer based approaches. Journal of Molecular Evolution, 51(6): 587-599. [PubMed]. Data is available here.

BOOK CHAPTERS

  1. Doolittle, W.F. and Zhaxybayeva, O. (2013): "What is Prokaryote?", pp. 21-37 in "The Prokaryotes: Prokaryotic Biology and Symbiotic Associations", 4th Ed. ( Eds: E. Rosenberg, E. F. DeLong, S. Lory, E. Stackebrandt, F. Thompson), Springer. [Online Access]

  2. Zhaxybayeva, O.: Detection and quantitative assessment of horizontal gene transfer (2009), chapter 11 in "Horizontal Gene Transfer: Genomes in Flux" (Eds. M. Gogarten, L. Olendzenski and JP Gogarten), Humana Press. [Online Access] [PubMed]

  3. Zhaxybayeva, O., Gogarten, J.P. and Olendzenski, L. (2008): Orthologs, Paralogs, and Xenologs in Human and Other Genomes (version 2.0), in "Encyclopedia of Life Sciences", John Wiley and Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0005298.pub2. [Online Access]

  4. Gogarten JP and Zhaxybayeva O. (2008): The role of gene transfer in microbial evolution. Chapter 6 in "Computational Methods for Understanding Bacterial and Archaeal Genomes" (eds. Y.Xu and J. P. Gogarten), World Scientific Publishing.

  5. Doolittle WF, Nesbo CL, Bapteste E and Zhaxybayeva O (2007): Lateral Gene Transfer. In "Evolutionary Genomics and Proteomics" (eds. M Pagel and A Pomiankowski), Sinauer Associates.

  6. J. Peter Gogarten, Olga Zhaxybayeva (2007). Horizontal gene transfer, gene histories and the root of the tree of life. Chapter 9 in "Planetary systems and the Origins of Life", RE Pudritz, PG Higgs and J Stone (eds.), Cambridge University Press.

  7. OLENDZENSKI, L. ZHAXYBAYEVA, O., and GOGARTEN JP. (2004) A Brief History on Views of Prokaryotic Evolution and Taxonomy. In "Microbial Genomes", CM Fraser, T Read and KE Nelson (eds), Humana Press, pp. 143-154 [Humana Press Catalog Entry]

  8. OLENDZENSKI, L., ZHAXYBAYEVA, O., and GOGARTEN, J.P. (2003): Orthologs, Paralogs and Xenologs in Human and other Genomes. In "Encyclopedia of the Human Genome", Nature Publishing Group [Online Version][Catalog Entry]

  9. Olendzenski, L., Zhaxybayeva, O., and Gogarten, J.P. 2002. Horizontal Gene Transfer: A new taxonomic principle? Chapter 34 in: Horizontal Gene Transfer 2nd ed., Syvanen, M. and Kado C.I. (eds.) Academic Press, London. [AP Catalog Entry]

  10. Olendzenski, L., Zhaxybayeva, O., and Gogarten, J.P. 2001. What's in a Tree?: Does Horizontal Gene Transfer Determine Microbial Taxonomy? In: Cellular Origin and Life in Extreme Habitats, Vol 4:Symbioses, Seckbach, J. (ed.) Kluwer Academic Publishers, Netherlands. p. 65-78. [Kluwer Catalog Entry]