Currently a Ph.D. candidate at the University of Minnesota in Plant and Microbial Biology. I specialize in bioinformatics approaches to genome-level studies and evolutionary problems.
Before returning to school, I was an independent IT contractor. PHP, Perl, MySQL, UNIX, PostgreSQL, and similar are the tools I often used. While I worked on a variety of projects, many contracts focused on interactive database-driven websites.
Science
I study the plant-microbe interaction partners of Medicago truncatula and Ensifer meliloti (previously Sinorhizobium meliloti). I have worked with the Medicago HapMap project for the past several years. Biologically My interests include how genomes evolve and how this affects phenotypic traits. Complex, quantitative, multi-locus traits especially interest me. My current “big” question is how we process and analyze pan-genomes in the context of tools and strategies we have developed working with single genomes. How do we adapt our tools to use this? Moreover, then how do we take this to biological relevancy.
I enjoy working with bioinformatics tools and methods, although I often find myself writing code to perform the analyses I need. Biotools is a bio* library for Clojure that I have developed, although it is not complete I have used it in several analyses. My most accomplished work is an -omics database generator, which integrates multi-omics data for one or more species and accessions (strains) into a single coherent database and generates an easy to use user-interface. I hope this bioinformatics tool can be of great help to the community, as I find myself using it nearly every day during genomic analysis.
Bioinformatics
Computationally I am interested in parallelization, big data, data integration, machine learning algorithms, and software usability. I prefer to work in Clojure when possible, but am fluent in Perl, R, Python, BASH scripting, JavaScript, HTML, Java. I have over 20 years of UNIX experience, starting with an early copy of FreeBSD, and later working with Linux. My current big interest is how we apply bioinformatics and machine learning to biological problems.
Personal Life
Outside of work I enjoy playing softball and run a fun, somewhat competitive team, the Twin Cities Narwhals. I also enjoy some outdoor activities, especially stand-up paddle boarding at area lakes.
This blog is representative of my views and thoughts alone and is not representative of my employers past present or future.