ECE Prof. Siavash Mirarab (left) is also a member of the joint Bioinformatics program with CSE and other UC San Diego departments (along with CSE faculty, including Vineet Bafna, Nuno Bandeira and Pavel Pevzner), so it's worth noting that he was a runner-up for the ACM Doctoral Dissertation Award. The award and two Honorable Mention awards were just announced and will be handed out at a banquet June 11 in San Francisco. Prof. Mirarab received an Honorable Mention for his dissertation on "Novel scalable approaches for multiple sequence alignment and phylogenomic reconstruction." He was nominated for the top award by his alma mater, the University of Texas at Austin, where he finished his doctorate before joining the ECE faculty in September 2015.
Mirarab’s dissertation addressed the growing need to analyze large-scale biological sequence data efficiently and accurately. To address this challenge, he introduces several methods: PASTA, a scalable and accurate algorithm that can align data sets up to one million sequences; statistical binning, a novel technique for reducing noise in estimation of evolutionary trees for individual parts of the genome; and ASTRAL, a new summary method that can run on 1,000 species in one day and has outstanding accuracy. These methods were essential in analyzing very large genomic datasets of birds and plants.