I will be presenting our work on generating universal sets for large k-mers, “Practical universal k-mer sets for minimizer schemes” with Fiyin Gbosibo, Carl Kingsford, and Guillaume Marçais, as a poster at ISMB/ECCB 2019 in Basel in July. The preprint is now available (see Publications).
Our paper “More accurate transcript assembly via parameter advising“, co-authored with Kwanho Kim and Carl Kingsford, was accepted for inclusion at The 2019 ICML Workshop on Computational Biology on June 14th in Long Beach, CA. As a result I will also be attending the 2019 International Conference on Machine Learning (ICML). Links to the paper are listed (see Publications).
Kwanho Kim, who I have been working with since 2017, graduated today with his Masters of Science in Computational Biology. He successfully defended his thesis titled “Analyzing the influence of assessment metrics on automated transcript assembly parameter selection” on April 30 and will be starting a position at The Broad Institute this summer. Congratulations Kwanho!
I am excited to announce that I will be starting a position as an Assistant Professor in the Computer Science Department at the University of Texas at El Paso in the Fall of 2019! Find out more at my group’s website.
I am in search of students to work on topics related to automated parameter selection. Contact me if you (or someone you know) is interested!
Related to the work we presented at ISMB last year, our new work on making a new hashing scheme that improves on Jaccard and Hamming distances for searching large sequences was recently accepted to ISMB/ECCB 2019 in Basel, Switzerland. This is work with Guillaume Marçais, Carl Kingsford, and Prashant Pandey. A preprint of the manuscript is on bioRxiv (see Publications).