Research Interests
My research interests center on the etiologies of human genome response to external and internal insults. Specifically, I am interested in producing
general predictive methods and direct assays for identifying disease-predisposing quantitative trait loci and disambiguating functional allelic combinations from
those that give rise to pathway disruptions.
Although recent advances in genome sequencing technology make it possible, full genomic screening for complex trait disorders remains currently impractical do to
incomplete annotation of human genes, incomplete understanding of regulatory and protein interaction networks, and a dearth of methods for accurately predicting
functional impact of allelic polymorphisms. My most recent research projects have enabled my long-term aims by employing phylogenomic methods to improve the annotation
of the human genome, identify regulatory networks, and resolve protein interaction networks.
Past Research:
Human Genome Analysis
Using the PhyloFacts platform, all human genes are being clustered into Universal Protein families,
not only to improve annotation of all members, but also to reveal the rich history of host-pathogen trans-species gene transfer evident at many immune-response loci.
Microbial/Metagenomic Analysis
In order to better comprehend host-pathogen responses, bioprospect novel biocatalysts and improve standing models of protein function, a large scale analysis of
microbial genomes proceeds in parallel to the human genome effort.
Enzyme Analysis
An analysis of enzymes and their propensity for variation of function, and the sequence features responsible
for those changes, is being investigated to improve understanding of what makes an enzyme work, which changes might break it, and what changes might deliberately alter its biochemical properties.
Remote Alignment Development
The development of novel remote alignment efforts, using either two-track Hidden Markov Models supplemented by secondary structure, phylogeny or free graph directed remote homology search.
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