This site is intended to be a simple warehouse for information about me, projects of mine, and contact information.
N.B. This site is in the middle of a redesign. Most of the projects hosted here were written in hand-coded HTML/CSS in 2011, so they look very different from the main page (now made-over with the help of Twitter Bootstrap).
I am a bioinformatics Ph.D. candidate at Penn State University, working with Anton Nekrutenko. My background is in biology, with a B.S. from Georgetown in the subject. But this website is the product of my computer science education at the bioinformatics master's program at Johns Hopkins University.
My GitHub profile is where you'll find all my public projects not hosted here. The repositories range from little, unpolished personal scripts to peer-reviewed genomics tools.
Current as of November 2014.
A tool I wrote in my research at Penn State. Du Novo is a tool for processing duplex sequencing data without a reference sequence, written in Python and C. It was published in Genome Biology: Stoler et al. 2016. You can find it in the Galaxy Toolshed here.
A tool I wrote to automatically "clean up" de novo assemblies, using information from the reference sequence. I wrote this when I was creating many small assemblies at Penn State, and I noticed many artifactual or overlapping contigs. It removes and merges them, respectively, and fixes other issues. I presented this work with a poster at Genome Informatics 2014 in Cambridge, UK.
Another research tool from Penn State. The Variant Annotator is part of a pipeline for discovering heteroplasmies in mitochondrial DNA. It filters sequence data, uncovering low frequency variants. Its Galaxy Toolshed repository is here. It is described in papers in BioTechniques and Genome Biology.
I contributed an analysis of mitochondrial indels to a study our lab published in PNAS in 2014. We sequenced the mitochondrial genomes of 39 families to examine the dynamics of mitochondrial inheritance. I developed a method to identify indels, using de novo assembly to customize alignment targets and reduce artifacts.
The Extraction of Native Giardia lamblia Actin Through Differential Detergent Treatment - May 2008
A personal productivity web application which allows extremely quick and simple note-taking on user-created pages. Uses Perl CGI scripting, MySQL, HTML5, and some Nginx magic. (Feel free to use it if you find it convenient. I sure do.)
A project to produce a personalized graphic based on an individual's genome sequence. Written in Python, using the Python Imaging Library. Also in the Galaxy Toolshed (here).
Several little tools and scripts I wrote for my own use. This link is for my convenience. I listed them on a Notepad page so they're easy to update frequently.