SiClE paper accepted to PeerJ

The paper describing a software package I created with Jennifer H. Wisecaver (now at Vanderbilt University) while we were both PhD students at the University of Arizona has been accepted for publication in the journal PeerJ. Even as a preprint on arXiv it was cited multiple times (included by papers in Nature Communications and PNAS).

The application SiClE (for Sister Clade Extractor) was created to perform high-throughput phylogenetic analysis. Given a tree and a search term it first determines if the search term is monophyletic in the tree then identifies the two sister clades. It has been used successfully as an initial filtering step to investigate horizontal gene transfer at the high-throughput scale. The program is open source and freely available under a Creative Commons License at http://eebweb.arizona.edu/sicle/.

Read the paper at https://peerj.com/articles/2359/.

Adaptive Local Realignment talk at ISMB 2016 time announced

I will be giving a talk titled  “Boosting alignment accuracy through adaptive local realignment” at ISMB 2016 in session TP021 on Sunday, 10 July at 2:00 PM in the Northern Hemisphere E1/E2 room. This will be a late breaking research talk so there is no associated publication yet, but information about using adaptive realignment can be found on the Facet website at http://facet.cs.arizona.edu/realignment.html. I will also be presenting a poster on the same work, during the Monday poster session you can find me at poster number N22. A preprint is also on bioRxiv DOI 10.1101/063131.

Welcome to the updated website

I recently converted my website to WordPress. Even though I used to work in web development myself, I no longer have the time or interest in maintaining a custom built website. I am hoping that by having a content management system updates when new publications and events happen will be more easily managed.