Research
Graduate
Current ResearchI am developing a high-throughput method to map all 2'-O-methylation sites in an entire transcriptome. Primarily I am working with archaeal genomes, particularly Pyrobaculum species.
RotationsSpring 2008 I rotated in Susan Strome's lab investigating the expression of MES-4, a chromatin regulator in Caenorhabditis elegans using almost exclusively wet lab techniques.
Winter 2008 I worked with David Haussler and the development of tools for the UCSC Cancer Genomics Browser.
Fall 2007 I investigated the electrostatic surface properties of DNA/RNA binding proteins with Dr. Dietlind Gerloff. Specifically, I studied families of protein domains that interact with DNA, and to which degree the electrostatic surface properties near the interaction sites are conserved. Particularly the protein surface in proximity of the phosphate backbone of the DNA has been reported by others to show a strong preference for positively charged amino acids, though the signal is not as prevalent as these reports suggest.
Undergraduate
Benham LabMy mentor for most of my undergraduate work was Craig Benham. His research group has developed statistical mechanical methods to computationally analyze the occurrence of structural transitions in stressed DNA molecules. Stress induced DNA duplex destabilization (SIDD), the destabilization of the DNA helix from the torsional stresses caused by the superhelicity of DNA, has been found to play roles in gene regulation. Right now I am trying to compare the SIDD profiles of orthologs from different organisms. Below is an example of a SIDD profile.
SIDD calculations quantify the topological effects on the energetics of the DNA molecule. The torsional stresses resulting from the superhelicity of DNA affect the stability of the molecule, causing the duplex to be more difficult or more easily opened at different positions. The G(x) is the free energy required to guarantee strand separation at a specific position. The lower the free energy, G(x), at a position the easier it is to open the strands.
CLIMBDuring my Senior year I was part of the NSF funded CLIMB program (Collaborative Learning at the Interface of Mathematics and Biology). It is an undergraduate research program where participants work together on projects while learning how to solve biological questions with mathematics and computational techniques. During Fall quarter, I collaborated with my peers in the program to solve problems in the areas of behavioral ecology, fisheries ecology, biofluids, cell biology, and neuroscience. During the next two quarters, my cohort and I developed our summer project on the population dynamics of vernal pool plant populations. We discussed papers, contacted other scientists studying vernal pools, and tried applying different ecological theories. During the summer we implemented the project by developing a mathematical model of the plant population and wrote a simulation to add stochastic weather effects.
VIGREI was part of the VIGRE Program during the summer of 2006. VIGRE (Vertical Integration of Research and Education in the Mathematical Sciences) is an NSF funded program that provides support for graduate and undergraduate research in the mathematical sciences.
UC LEADSI participated in the UC LEADS Program from June 2004- June 2006. UC LEADS (University of California Leadership Excellence through Advanced DegreeS) is a two year program funds underrepresented or financially disadvantaged undergraduates in research. Students have the opportunity to conduct research at another UC campus their second year in the program.
