Welcome! I am the Project Lead for Data Carpentry and an assistant professor in BEACON at Michigan State University with an adjunct appointment at the Kellogg Biological Station.

My appreciation and enthusiasm for data and data training comes most recently from working in bioinformatics and microbial ecology.

My work in bioinformatics focuses on metagenomic analysis, with an emphasis on functional analysis post-assembly. My aim is to be able to both generate hypotheses from complex matrices of functional traits and to be able to address specific hypothesis-driven questions about the environment of interest. Toward this aim, I'm developing approaches and tools that make this both computationally tractable and accessible to biological researchers.

My specific research focus is on understanding how agricultural practices affect soil microbial communities and how those communities might affect changes in the production and consumption of greenhouse gases. I work primarily at the Kellogg Biological Station Long-Term Ecological Research station and the Great Lakes Bioenergy Research Center Extensive Sites, where I collect soil samples for targeted molecular and whole genome shotgun metagenomic analyses. I am also developing computational tools to manage and utilize this metagenomic data to address relevant questions in microbial community ecology. I developed a Replicate Filter to remove artificial replicates from 454 and Ion Torrent data.

As a part of the Sustainability group for the Great Lakes Bioenergy Center, I have been able to address questions about the effects of crop type and management on microbial communities and their methane consumption and nitrous oxide production to determine an aspect of the sustainability of that crop for the environment.

I also work with many researchers at MSU, primarily on metagenomics and genome assembly. I'm affiliated with the ERIN: Enterics Research Investigational Network group and the Institute for Cyber-Enabled Research (iCER).

As a component of enabling 'big data' research for biologists, I am committed to training researchers in computational techniques. I am instructor for Software Carpentry, an organization that teaches software development skills to researchers, and conduct workshops in Next-Generation Sequencing analysis through iCER and NGS workshops.


  Last updated: December 6, 2013
Title photo credit: William R. Hewlett, California Academy of Sciences