Associate Professor
Joined School 2001
SB (MIT),
MS (Cornell),
PhD (Cornell)
| browndg@uwaterloo.ca | |
| Web | http://www.bioinformatics.uwaterloo.ca/~browndg |
| Voice | 519-888-4567 x36278 |
| Fax | 519-885-1208 |
|
| Daniel G Brown
Associate Professor Joined School 2001 SB (MIT),
|
Professor Brown's primary research area is the understanding of sequential data, joining ideas from evolutionary theory with probabilistic modeling and discrete mathematical ideas.
His established expertise is in biological sequence analysis, where he has worked on a host of areas, ranging from homology search to algorithms for hidden Markov models to haplotype inference.
One focus in recent years has been on robust algorithms for hidden Markov model decoding: this work stems from the observation that the traditional algorithms for this problem don't work especially well in practice, and yet are widely used. Brown's algorithms with his students find optimal explanations of sequences that optimize properties of importance in application domains, rather than the objective of the classical Viterbi algorithm in this area.
Brown is also interested in why algorithms in bioinformatics tend to work faster in practice than might be predicted in theory, and has solved this question for problems in motif finding, homology search, haplotype inference and kinship detection.
Prof. Brown has recently added an interest in understanding sequential music information. Early work in this area with MMath student Hussein Hirjee has included studying the rhyme patterns of hiphop and resolving misheard lyrics queries.
Early Researcher Award (2007-2012)
Professor Brown's primary external research work since coming to Waterloo has been the year he spent at the Whitehead Institute / MIT Centre for Genome Research, in Cambridge, Massachusetts. During his time at the Whitehead, he worked on the analysis of the human and mouse genome sequences, and learned about the practice of large-scale sequencing and genome study work.
In 2006, he spent six months on sabbatical at the University of California, Davis, working on computational modeling of evolution; in 2009-2010, Brown spent time working with colleagues in Chicago and Europe on problems in computational population genetics and hidden Markov model decoding.
H. Hirjee, D.G. Brown. Solving misheard lyric search queries using a probabilistic model of speech sounds. Proceedings of the 2010 International Society for Music Information Retrieval Conference, pp 147-152. Best Student Paper Award.
D.G. Brown, J. Truszkowski. New decoding algorithms for Hidden Markov Models using distance measures on state paths. BMC Bioinformatics 11(Suppl 1): S40, 2010. Special issue for proceedings of 2010 Asia-Pacific Bioinformatics Conference.
B. Brejova, D.G. Brown, T. Vinar. The most probable annotation problem in HMMs and its application to bioinformatics. Journal of Computing and System Sciences 73 (7): 1060-1077, 2007.
B. Brejova, D. Brown, and T. Vinar. Vector seeds: an extension to spaced seeds. Journal of Computing and System Sciences 70:364-380, 2005.
International Human Genome Sequencing Consortium (including D. Brown), Initial sequencing and analysis of the human genome. Nature 409:860-921, 2001.
David R. Cheriton School of Computer Science
University of Waterloo
Waterloo, Ontario, Canada N2L 3G1
Tel: 519-888-4567 x33293
Fax: 519-885-1208
Contact | Feedback: cs-webmaster@cs.uwaterloo.ca | David R. Cheriton School of Computer Science | Faculty of Mathematics
Last modified: Monday, 20-Dec-2010 14:29:42 EST
