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Evolution of Host-Pathogen Protein Interactions
I'm exploring computational methods that might help reveal how molecular interactions in host-pathogen systems shape the evolution of mammalian genomes. I am particularly interested in how viruses evolve with their hosts and have varying levels of pathogenicity.
I implemented a metagenomic data analysis to identify the adaptive genetic immune system of bacteria and archaea (CRISPRs) by combining various CRISPR finding tools (PILERCR, CRT) with profile HMMs for detecting homologous sequences (HMMER3).
The ocean virosphere is a library of genetic diversity. Yet, how local environments influence the diversity of viral resistance is not well understood. Metagenomic sequencing—directly measuring the genetic composition of environmental samples—allows us to explore the global diversity of anti-viral elements including that of unculturable and novel taxa.