Saturday, November 15, 2008

Canada MSc and PhD Studentships, Evolutionary and Functional Genomics

MSc and PhD Studentships, Evolutionary and Functional Genomics
University of Ottawa, Canada

Multiple PhD and MSc student positions are available in Evolutionary and Functional Genomics at XiaLab 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.

Deadline: as soon as filled

The research areas covered include, but not limited to:

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
Molecular evolution and phylogenetics (see relevant publications at You may participate in the devleopment of DAMBE software:

for building guide tree for mulptle alignment: I am currently replacing the pair-wise global alignment by a FASTA-like algorithm which appears to work faster and obtain better guide trees.
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.
strand-biased substitution patterns and their impact on phylognetic reconstruction.
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
Comparative genomics (see relevant publications at
Selection at the initiation, elongation and termination of transcription and translation (see relevant publications at

The positions are available immediately. The application procedures can be found by following the link at (or contact me directly if you found anything unclear).

Xuhua Xia
University of Ottawa