Advancement: Rapid evolution: tools for pathogen phylogenomics and a population study of introner elements

Alexander Kramer
Biomolecular Engineering & Bioinformatics PhD Student
Engineering 2, Rm 180 (Simularium)
Russell Corbett-Detig

Join us in-person: Engineering 2, Rm 180 (Simularium)

Description: Over ten million complete SARS-CoV-2 genomes have been deposited in online databases. This dataset has fostered the development of new tools and methods for handling genomic data at pandemic scale. For example, phylogenetic trees can now be effectively constructed from millions of genomes. My proposed research addresses several remaining needs for phylogenetics on large datasets, especially of pathogen genomes. Privacy is a major consideration for genomic data related to human pathogens. I will develop a web browser tool for private phylogenetic analysis of pathogen genomes without transmitting data over the Internet. To address visualization needs, I will develop a phylogeny-linked genome browser, scalable to millions of sequences, that displays mutations in genomes alongside their position in a tree. I will also contribute to the development of a new method of inferring large phylogenies from divergent genomes by placing genomes on existing trees.

Besides this timely work on SARS-CoV-2 and other pathogens, my research will also investigate a timeless question: where do new introns come from? One possibility is that specialized transposons, called introners, create introns on genome-wide scales. By sequencing isolates from a population of algae that has thousands of polymorphic introns which appear to be introners, I will study the proximate and ultimate factors that drive the evolution of new introns.