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I. Dna Topology: Dna Unknotting, Dna Unlinking and Chromosome Architecture

I am a mathematical biologist specialized in the applications of topology to the study of DNA. In my research I collaborate closely with experimental biologists to ensure that the problems approached and the solutions proposed remain biologically relevant. I use my background in pure mathematics to study DNA topology and DNA rearrangements using analytical (topology, knots, tangles and graphs) and computational (Monte Carlo simulations, computer visualization) methods. During my PhD, I used modern tools in knot theory and low-dimensional topology to study two site-specific recombination systems: Gin of bacteriophage Mu and Xer of Escherichia coli [4,10,13]. In August 2000 I became a postdoc in Rainer Sachs’ group and a Visiting Assistant Professor at UC Berkeley (Math Dept). In Professor Sachs’ group I used graph theory, statistical methods and Monte Carlo computer simulations to study genomic rearrangements found in radiation data [5-8,11,12,14]. I also extended the DNA topology work from my dissertation to a more general study of site-specific recombination and started a novel study of type II topoisomerases, which led to my mentoring several undergraduates in research. At the same time, jointly with J. Arsuaga I studied DNA packing in bacteriophage capsids [2,3,9,15]. Since 2000, I have mentored 16 UC Berkeley undergraduates on the study of DNA knots, site-specific recombinases and type II topoisomerases, and have co-authored research papers with some of them [4,17,18]. Jointly with J. Arsuaga and R. Sachs, I applied for an NSF grant in Spring 2002, which fully funded my last three years at Berkeley. In August 2005, I joined the math faculty at San Francisco State University (SFSU). Since 2005 I have tirelessly applied for both internal and external funding. In collaboration with my co-investigators I have brought over $1.7 million to the university in federal research grants, and I have received seed funding from a variety of sources. In 2011, I received an NSF CAREER Award, and in 2012 a Presidential Early Career Award for Scientists and Engineers (PECASE). The CAREER award provides funding to study the process of DNA unlinking by Xer recombination.