Software and Algorithm development for genomic/proteomic analysis

Gene expression comparison Comparison of average intron lengths and total exon lengths in genes with high and low expression (genes from H. sapiens).

Gene expression Mixed-effect model representation of gene expression over time.

expression curves Estimated mean expression curves and 95% confidence bands for four of 17 clusters discovered by SSC in the D.melanogaster time course microarray data.

Intron loss/gain Duplicate genes exhibit accelerated rates of intron gain/loss in comparison with orthologous genes at almost all levels of synonymous divergence (dS).
Biology has gone from being a data-poor science to a data-rich one and thus presents an exciting challenge not only for biologists but also statisticians, computer scientists and other quantitative workers. The ever-growing wealth of bioloical data (genomic, proteomic, etc) generated by technologies enabled by genome sequencing projects is quickly out-pacing our ability to meaningfully synthesize it.

Thus the development of tools for "post-genomic analysis" - the interpretation and synthesis of thousands of data points from a chemical, clinical, evolutionary, or other perspective - is an important aspect of our research program. We have developed and published software tools for comparative genomic sequence analysis (Shared Motif Method), functional genomic analysis (GeneMerge) and gene clustering for time-course microarray data (SSClust). Please see Software more information on these applications.

High-throughput phenotyping & fast-mapping of QTL using tiling microarrays

Transcript abundance Expression level of the genes of the phototransduction pathway in D. melanogaster and D. simulans are largely conserved between the two sibling species.

coming soon...

Development of theory and tests of homology and character stasis

coming soon...

Species delimitation in the fossil record using extant intra- and inter-species variation

intra- and inter-species variation

scatterplot Scatterplot of dN versus dS for pairwise mammalian orthologs.
coming soon...