Using BioJava from R

Posted on
I’m a fan of literate programming. When I’m writing a paper, I typically use LaTeX to draft the paper, Java to generate the data, and R to create figures and do basic analysis. With Sweave (or the... Read More

ISMB 2012

Posted on
[caption id="attachment_336" align="alignright" width="225" caption="My badge for ISMB, showing admission to 3DSIG and BOSC, as well as ISMB membership and Open Access pride."]Read More

Topic Page update

Posted on
Two weeks ago our Wikipedia article on Circular permutation in proteins was featured in on Wikipedia’s mainpage as a “Did you know…” article: We were quickly replaced by the Ri... Read More


For our weekly journal club I talked about a new method for de novo protein folding called EVfold. [Slides] Details can be read in the paper (plus 15 page supporting text) Marks, D. S., Colwell, L. J.... Read More


I had a great time over Halloween at PDB40 at Cold Springs Harbor Laboratory, celebrating 40 years of protein structure. I especially like the talks from older structural biologist about the history o... Read More


Posted on
I had a great time attending 3DSIG and ISMB/ECCB in Vienna. The quality of the talks was very high and it was fun to meet so many other computational biologists. It is nice to finally put faces and pe... Read More

IL-1 Principle Motions

Posted on
For my rotation with Pat Jennings and José Onuchic I’ve been analyzing simulations of the IL-1 complex. I made up this page to display some of the movies I made of principle motions in IL-1R bo... Read More