Research Interests
Dynamic, complex systems of interacting components underlie many challenges humanity faces, including healthcare, financial market stability, social policy, and climate change. I have always been fascinated by such systems, and my professional life is dedicated to understanding complex systems to address problems of significance.
My research has focused on the evolutionary dynamics of a variety of biological systems, from microbes to cancer. My graduate work was focused on applying this deeper understanding to the discovery of novel antibiotics and microbial enzymes for biofuels production. After completing my doctorate, I have focused my attention on using knowledge of population dynamics to design non-invasive diagnostics to monitor the impact of treatment on cancer progression.
To enable this research, I have continually expanded my knowledge of the tools necessary to understand these systems. These include cutting edge genomics approaches, machine learning, and Julia package development.
Professional Experience
Moved with the Murtaza lab to UW-Madison to continue non-invasive diagnostics development.
In the Murtaza Lab I developed the computational pipeline and contributed to wet lab development of a highly sensitive method for detecting patient-specific tumor mutations from as little as 5ng of plasma derived DNA.
My thesis focused on the evolution of bacterial diversity and function across a range of phylogenetic scales. In particular, I investigated on the evolutionary dynamics of natural product biosynthesis clusters across the genus Streptomyces and within a single population of fungus growing ant-associated Pseudonocardia. My graduate work contributed to 12 publications.
My project was focused on exploring the impact of autophagy on Tau protein degradation in Alzheimer's Disease, using siRNA experiments in cell lines and mouse-derivied primary hypocampal neurons.
I investigated the genomic diversity of the most extreme bacterial genomes, the ultra-small genomes of cicadas and other plant sap feeding insects. My work contributed to three publications.
Selected Projects
I have worked on a diverse range of research projects applying evolutionary theory to problems of practical importance, in both leading and collaborative roles. These have included cancer biomarker detection, antibiotic discovery, and enzyme discovery for improved biofuels production. Projects in which I have played a leading role include: