Core Columns Paper Accepted to AMB

The journal version of my WABI paper has been accepted for publication in the Algorithms for Molecular Biology journal and will appear there soon. This extended version includes many of the algorithmic details that were left out of the original paper WABI publication as well as an expanded results section.  A pre-publication version of the submission is available on my Publications page.

Elected to the ISCB Board of Directors

The votes are in, and I have been elected the ISCB Student Council Representative to the ISCB Board of Directors. This role is to be the liaison between the executive team of the student council and the board directors of the ISCB (our parent organization). I will officially take the post in January but I am already looking forward to further strengthening the cooperation between ISCB and the student council. Thank you all who voted!

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

Read the paper at

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 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.