Previous Projects

Ewing sarcoma, a pediatric tumor, is a unique cancer because it is almost always driven by a single, well-characterized mutagenic event: a chromosomal translocation leading to the fusion protein EWS-FLI1. To explore how this fusion protein interacts with the epigenome, I am examining genome-wide epigenetic profiles of Ewing sarcoma. This project is a collaboration with Eleni Tomazou and Heinrich Kovar at St. Anna's Children's Cancer Research Institute in Vienna.

The canonical epigenetic mark, DNA methylation, is known to be reliably maintained through cell division. However, the process is not 100% accurate, so "errors" can occur and accumulate, leading to epigenetic diversity. I am interested in the processes that allow epigenetic signals, such as DNA methylation, to be inherited during cell division. In particular, I am develping models of DNA methylation maintenance, and applying these models to DNA methylation data to assess how methylation fidelity differs among cell-types (such as cancer vs. non-cancer) or drug treatments. Failure to maintain DNA methylation patterns can lead to epigenetic heterogeneity in a population, creating diversity that provides the raw material for evolution, as growth pressures select for highly proliferative epigenetic states. This may ultimately be a fundamental process in cancer.

I worked with Terry Furey, Greg Crawford, and Boris Lenhard to understand human cell-type differences in regulatory DNA, using high-throughput DNase-seq experiments in over 100 human cell types.

Publications:
2013 Genome Research
2012 Genes
2012 Genome Biology
2012 Nature
2012 Nature
2012 Genome Research
2011 Genome Research

During my PhD, I worked with Terry Furey and Greg Crawford on comparing DNaseI Hypersensitivity among primates, and across human cell types. I work closely with Yoichiro Shibata, a guru molecular biologist, to analyze our DNase-seq and digital gene expression data. I have pioneered methods for comparing hypersensitivity across samples.

Publications:
2012 PLoS Genetics

For a project at Duke with Alex Hartemink and Steve Haase, I developed image processing tools to examine yeast cells in microsope images. My tool was able to identify flourescent tags on spindle-pole bodies and myosin rings and use them to classify budding yeast into cell-cycle stages.

I am the primary author of a web-based bioinformatics tools suite called MOSAS (an acronym for Manipulation, Organization, and Storage Of Sequences). In phylogenetics, many researchers struggle with storage and organization of sequences. My online toolbox provides a user-friendly interface to store, search, re-organize, download, and analyze sets of sequences. For example, the website allows one to construct and edit "datasets," for example containing all sequences of a particular gene. It also contains an annotation engine to facilitate annotating mitchondrial genomes. Unfortunately, the software is no longer available.

Publications:
2010 Mitochondrial DNA

In Michael Whiting's Lab, I learned basic wet-lab techniques and genome assembly, working on the NSF Tree of Life project. Specifically, I sequenced, assembled, and annotated mitochondrial genomes of different beetle species. I then used the sequences to construct phylogenies. I addressed problems with model violation (base compositional heterogeneity) and worked on bioinformatics tools to facilitate data analysis.

Publications:
2008 Molecular Biology and Evolution
2009 Systematic Biology
2009 Systematic Entomology

I worked with Keith Crandall and Andrew Stacey at BYU on a project simulating populations to chart drift of minor allele frequencies. I used a python module to simulate hypothetical admixture events under varying model assumptions. We explored the outcome of genetic drift and quantified the affect of population sizes, mutation rates, and time since admixture.

Publications:
2008 BMC Genetics

I worked for just over a year on programming a united-atom forcefield in C++ for Roche Palo Alto Computational Chemistry group (now relocated to Genentech, South San Francisco). The calculations included torsion potentials, angle bending potentials, bond stretching potentials, and pi charge calculations, among others. I re-implemented the forcefield, originally programmed in FORTRAN and C, into object-oriented C++.