Researchers

Michael Brudno, PhD
Assistant Professor & Canada Research Chair in Computational Biology
University of Toronto
Email: brudno@cs.toronto.edu
Phone: 416-978-2589

Dr. Brudno is the Canadian Chair in Computational Biology and his main research direction is the development of computational methods for the analysis of biological datasets, especially genomic DNA. Currently one of the main foci is the development of algorithms for assembly, mapping, and analysis of short read data. Other work includes genome alignment as well as detection and analysis of genome variation within a species. Brudno got his PhD from the ComputerScience Departmentof Stanford University developing several approaches for comparison of genomic sequences, including the LAGAN Alignment Toolkit, "glocal" alignment algorithms for sequences with rearrangements, and whole genome alignments. His postdoctoral work at the Computer Science Division, UC Berkeley, primarily addressed the problem of whole genome assembly from shotgun read data. After his post doctoral fellowship, Brudno was a Visiting Scientist at CSAIL (MIT)before starting as an Assistant Professor at the University of Toronto in January 2006.  He developed one of the first methods for multiple global alignment of long genomic sequences: the LAGAN alignment software (Brudno, Do et al 2003). Due to its novelty, LAGAN has become a highly cited paper, and the web version of the tool has been used more than 10,000 times by more than 800 users. An interface to LAGAN has been included in several highly used bioinformatics packages, such as BioPerl, Sockeye, and VISTA. He has collaborated with many biologists in the analysis of the output of LAGAN, perhaps most significantly working with the Rat Genome Sequencing Consortium to build some of the first mammalian whole genome multiple alignments (Brudno, Poliakov et al 2004). These alignments led to novel biological findings about the evolutionary rates between the species and to characterization of evolutionary constraint in mammalian genomes (Cooper, Brudno et al 2004, RGSPC 2004).  More recently, Brudno also worked on assembling the Ciona savignyi genome.  Because C. savignyi is highly polymorphic (5% SNP rate), assembling it with the available tools was impossible, as all methods for genome assembly attempt to mix the two haplotypes of an individual into a single sequence. He therefore developed a novel approach for assembling the haplotypes separately. The assembled genome led to a paper demonstrating that the high polymorphism in the Ciona population is due to its large effective population size (Small, Brudno et al 2007), providing empirical support for a basic tenant of Kimura‚Äôs population genetic theory (Donmez et al 2009).

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