Ph.D. Candidate: Mark Kowarsky
Research Advisor: Stephen Quake
Date: Tuesday, May 7, 2019
Location: Clark Center Auditorium, Clark Center South Wing - Basement Beneath Courtyard
Using sequencing to analyze exotic circulating nucleic acids in primates and the processes in the life of a sea squirt
High throughput sequencing allows the accurate quantification of millions to billions of biomolecules at a time. I have looked to answer questions across a range of biological fields by building analysis pipelines for this data, utilising high-performance computing infrastructure, and applying techniques from machine learning.
In the last decade, studies of circulating nucleic acids in humans have yielded noninvasive tests of fetal chromosome abnormalities and signatures of rejection events in transplant recipients. Here I describe how circulating nucleic acids also have microbial and viral signatures which allow us to detect pathogens in a hypothesis-free manner, to identify highly divergent and novel microbes in humans, to characterize the microbiome of non-human primates, and to unveil disease dynamics and changes in the immune system in individuals living with HIV.
Sea squirts, or tunicates, are the sister group of vertebrates and are separated by about 400 million years from us. The tunicate Botryllus schlosseri is a colonial organism with a natural allogeneic fusion reaction that produces chimeras, and therefore serves as a model system for transplantation. Here I used deep sequencing to present a molecular, genetic and cellular description of the process of resorption of unstable chimer