Graduate positions: Evolutionary and Functional Genomics

August 3, 2008
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Graduate positions: Evolutionary and Functional Genomics

Multiple PhD and MSc student positions are available in Evolutionary and
Functional Genomics at my laboratory in Department of Biology,
University of Ottawa, Canada. Minimum support is $18,500/year, but
students with grade point average above A will get substantially more.
The research areas covered include, but not limited to:

1. Short-term and long-term changes of gene expression and gene
regulation in response to envirornmental hormone-like chemicals. The
student will focus on developing statistical methods for microarray data
analysis, e.g., Xiong, H., Zhang D., Martyniuk, C.J., Trudeau, V.L. Xia,
X.. 2008. Using Generalized Procrustes Analysis (GPA) for normalization
of cDNA microarray data. BMC Bioinformatics, 9(2008) 25

2. Molecular evolution and phylogenetics (see relevant publications at
http://dambe.bio.uottawa.ca/publications.asp). You may participate in
the devleopment of DAMBE software:

(1) for building guide tree for mulptle alignment: I am currently
replace the pair-wise global alignment by a FASTA-like algorithm which
appears to work faster and obtain better guide trees.
(2) for estimating synonymous and nonsynonymous substitutions: the
conventional LPB (or PBL) method is not quite suitable for sliding
window analysis because of the stochastic fluctuation of observed
window-specific transitions and transversions. I am adding a
simultaneous estimation method for all windows with a fixed substitution
matrix for correcting multiple hits.
(3) strand-biased substitution patterns and their impact on
phylognetic reconstruction.

3. Evolutionary genomics of microbial pathogens, e.g., Xia, X. and G.
Palidwor. 2005. Genomic Adaptation to Acidic Environment: Evidence from
Helicobacter pylori. American Naturalist 166:776-784
4. Comparative genomics (see relevant publications at

http://dambe.bio.uottawa.ca/publications.asp)

5. Selection at the initiation, elongation and termination of
transcription and translation (see relevant publications at

http://dambe.bio.uottawa.ca/publications.asp)

The positions are available immediately. The application procedures can
be found by following the link at http://dambe.bio.uottawa.ca/grad.asp
(or contact me directly if you found anything unclear).

Xuhua Xia
University of Ottawa

http://dambe.bio.uottawa.ca

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