Wednesday, May 11, 2016

Computer engineer recognized for his work in computational biology

A professor of electrical and computer engineering at the University of California, San Diego, has received an honorable mention in the 2015 Doctoral Dissertation Award competition presented by the Association for Computing and Machinery.

Siavash Mirarab joined the Department of Electrical and Computer Engineering at UC San Diego in 2015 after earning a Ph.D. from the University of Texas at Austin. His dissertation, “Novel Scalable Approaches for Multiple Sequence Alignment and Phylogenomic Reconstruction,” addresses the growing need to analyze large-scale biological sequence data efficiently and accurately.

To address this challenge, Mirarab 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.
Mirarab’s research interests focus on accurate and scalable analysis of large-scale biological datasets. 

His work particularly focuses on evolutionary biology and computational methods that use genomic data to reconstruct the evolutionary past. He is interested in algorithmic developments that enable us to analyze very large datasets with high accuracy and with reasonable computational demands. These algorithms find application in various areas of computational biology, including multiple sequence alignment, metagenomics, and phylogenetic reconstruction from whole genomes.

Before receiving a Ph.D. at UT Austin, he earned a master’s degree in Electrical and Computer Engineering from University of Waterloo, Ontario, Canada, in 2008. He received his bacherlor’s degree in Electrical and Computer Engineering from the Tehran University, Iran, in 2000. In between his studies, he has worked for various companies, including IBM and Cisco.  His Ph.D. research has been supported by a Howard Hughes Medical Institute international graduate student fellowship and by Canadian NSERG PGSD awards.

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