I'm a mathematical biologist who is interested in developing mathematically sound approaches to the analysis of high-throughput DNA sequencing data. I often employs probabilistic and optimization techniques to facilitate the analysis of such data. You can take a look at my publications for a more detailed look at the kind of research I do.
On the mathematical side, my research interests include:
On the biological side, my application areas include the analysis of *-omics data, specializing in metagenomics (the study of microbial communities through their sequenced DNA).
Due to being an applied mathematician in the area of mathematical biology, I maintain a number of collaborations with biological scientists. Here is a selection of the collaborations I am involved with:
The CAMI consortium is an international group of scientists, practitioners and mathematicians who concerned with the proper interpretation, comparison, and analysis of metagenomic data. We have held a competition to compare the myriad of metagenomic computational techniques and currently have the paper under review at Nature Methods (preprint here). I am an organizing member in charge of the portion of CAMI regarding taxonomic profiling (answering the question of which organisms are present in a given sample and at what frequency). A brief presentation given at a recent OSU metagenomics conference is available in powerpoint format here.
SSiMBio is a a broad collaboration taking place at Oregon State University across multiple departments, involving 11 researchers and 6 graduate students. Our aim is to develop a systems-biology framework around the intertidal sea anemone Anthopleura elegantissima. By integrating datasets across disciplines, we hope to develop a complete picture of the biological responses that are associated in the system and particularly around the symbiotic state of this organism.
The CGSI is a summer institute at UCLA which brings together faculty, students, and industry to focus on cutting-edge research on all things genomics. The institute (funded by the NIH) is held during the Summer and consists of a week long conference followed by a 3 week long program which provides a research residency in computational genomics. I am helping to organize this institute.