During the IGERT problems course in 2012 our project was to analyze and annotate a newly discovered and sequenced snake fungal pathogen, Ophidiomyces ophiodiicola. At the time we just called it the “snake fungus”. Recently, thanks to the the hard work of Manna Ohkura and her PhD advisor Marc Orbach, we published our results in ASM’s Genome Announcements. The full list of co-authors and a link to the open access paper can be found on the Publications page.
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.
My paper titled “Boosting alignment accuracy by adaptive local realignment” (with John Kececioglu) was accepted to the 21st International Conference on Research in Computational Molecular Biology (RECOMB) 2017 in Hong Kong in May. The paper is available here.
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/.
My paper titled “Predicting core columns of protein alignments improves parameter advising” was accepted to WABI 2016, and I will presenting it at the meeting in Aarhus, Denmark in August. The slides from my talk from WABI 2016 can be viewed online here.