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RESEARCH
INTERESTS
of
Olga Zhaxybayeva
Development
of tools to visualize the mosaic content of genomes
Quartet-based
genome analyses: adaptation of ML mapping.
We introduced a novel method to analyze systematically all gene
families in four genomes and represent results in one visually
informative diagram that utilizes barycentric coordinates:
- 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]
Example
of a Maximum Likelihood Map
- Olga
Zhaxybayeva and J. Peter Gogarten. An Improved Probability Mapping
Approach to Assess Genome Mosaicism, BMC
Genomics 2003 4:
37 [Free
Online Version]
Example
of an embedded quartet
Dekapentagonal
Maps.
Analogously to ML mapping of four genomes, we utilize dekapentagons
(i.e., polygons with 15 vertices) to analyses of five genomes (there
are 15 possible unrooted trees for five taxa). The method for optimal
arrangement of tree topologies on verices of dekapentagon is
implemented in an open-source program PentaPlot.
Example
of a dekapentagonal map
Bipartition
Plotting.
We developed bipartition plotting in order to break the limitation of
analyzing only a few genomes at a time, but at the same time avoiding
exhaustive examination of a large number of phylogenetic trees. The
results can be summarized in form of histogram-like plots (bipartition
plots or Lento plots).
- Zhaxybayeva,
O., Lapierre, P. and Gogarten J.P.: "Genome Mosaicism and Organismal
Lineages", Trends in Genetics,
2004, 20(5):
254-260. [DOI
link]
Example
of a bipartition plot
Quartet Decomposition Analysis.
Quartet decomposition method is developed to avoid drawbacks of
bipartition support value decay for larger datasets. The method
utilizes embedded quartets (see above), and summarizes gene family
histories in spectrograms (analogous to Lento plots, see above).
- 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.
[Free
Full Text] [Supplementary
Data]
Application
of quartet and bipartition methods: case studies
The above-described methods were sucessfully used to answer a wide
range of evolutionary questions.
a) The role of horizontal gene transfer in evolution of photosynthetic
bacteria:
- 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. [Free
in PMC]
- 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]
b) examination of recombination in 16S rRNA genes of Aeromonas
spp.:
- 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.
[Free
in PMC]
c) quantification of horizontal gene transfer in cyanobacteria:
- 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.
[Free
Full Text] [Supplementary
Data]
d) analyses of gene histories in haloarchaea, a group of organisms that
live in hypersaline environments:
- R. Thane
Papke, Olga Zhaxybayeva, Edward Feil, Katrin Sommerfeld, Denise Muise,
W. Ford Doolittle: "Searching for species in haloarchaea", PNAS
104:
14092-14097. [Free
in PMC]
e) analyses of Thermotogales genomes:
-
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]
Study
of Evolutionary Proceeses and Patterns through Phylogenetic Tree Shapes
Through simple birth-death coalescence models, we explored some
topological features of phylogenetic trees:
- 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]
Metagenomics
as a new way to study evolutionary processes
Using bioinformatics analyses, we discovered a novel protein family:
-
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]
My current research in this area is focused on:
- Modeling
communities' evolution
- Detection of
horizontal gene transfer in metagenomes
- Metagenome
visualization techniques
See my CV
for the full list of publications.
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