Daniel G. Brown

Ph.D. (Computer Science), Cornell, 2000
S.B. (Mathematics with Computer Science), MIT, 1995

(Me, with chickenpox spots, February 2007. Not pleasant.)
(Many more cute photos of Rover)
(A formal photo of me from early 2005)
(An old photo of me from the late '90s, when I lived in Ithaca. I don't look like this anymore...)

David R. Cheriton School of Computer Science
University of Waterloo
200 University Ave., W.
Waterloo, ON N2L 3G1
Canada
voice: 519-888-4567 x36278
fax: 519-885-1208
email: browndg@uwaterloo.ca

I am a member of the Bioinformatics group in the school of CS at the University of Waterloo. We support a substantial amount of research and graduate study, especially considering our small size.

You may find my CV in many versions here. [.pdf, .doc, .html]

Teaching

These are the courses I have taught since 2002:

• Computational techniques in biological sequence analysis (CS 482/682): Fall 2003, 2004, 2005, 2006, 2007, Winter 2005 (and, as CS 882, in Winter 2003), a course I developed and co-ordinate
• Designing Functional Programs (CS 135): Fall 2006 and 2007
• Introduction to Computer Science 2 (CS 116): Winter 2009 (two sections), a course I developed and co-ordinate
• Theory of computation (CS 360): Fall 2005 and Summer 2003 (two sections)
• Advanced topics in bioinformatics: large-scale sequence analysis (CS 882): Winter 2005 and Spring 2002
• Algorithms (CS 341): Winter 2002

Recent highlights

• I'm getting interested in music information retrieval. MMath student Hussein Hirjee and I are studying the sound patterns of lyrics, and also trying to study other properties of hip-hop, which I don't actually listen to. Our first paper in this area is at ISMIR 2009.
• Decoding probabilistic models. Jakub Truszkowski and Daniil Golod and I are looking at extensions to the Viterbi algorithm for HMMs. Two papers to appear at APBC 2010 are in this area: one considers "robust" decoding of HMMs where we allow some play in the margins of intervals of a specific label, while the other concerns summarizing the k best paths through a model instead of just the Viterbi path.
• Pairwise alignment. My PhD student Alex Hudek and I have been trying to develop better alignment techniques based on both using the forward algorithm for HMMs instead of Viterbi, and also on better understanding of levels of homology of sequences that evolve at different rates.
• Probabilistic analysis of motif-finding algorithms: with my former students Ian Harrower, Christina Boucher, Tomas Vinar and Brona Brejova, I have been studying combinatorics of motif finding, for motifs one would actually want to discover. Christina has been studying heuristics for motif finding problems, and with my other students, I investigated why motif finding is easier than previous theorems suggested. A paper on this topic appeared in CPM 2006; a previous one that showed that worst-case runtimes for a simple PTAS for motif finding are worse than feared was in CPM 2005.
• Mathematical understanding of haplotype inference: with PhD student Ian Harrower, I have been studying the mathematical structure of haplotype phasing. Our early theorems in this area was in CSB 2006; some earlier work on optimization models is in WABI 2004 and in a 2006 TCBB paper.
• Probabilistic analysis of alignment: several of my collaborators and I have extended the early work of Ma, Tromp and Li on seeding of alignments, extending this work to alignments of coding sequences, of protein sequences, to using multiple seeds, to a generalization called vector seeds, and more. This is likely still the most-cited work that I have done in the past several years.

You can find most of my papers since 2001 on our lab's webpage.

Software

These are a few programs I developed from 1999 to 2002:

• MapPop, software that implements the genetic mapping work in my thesis and in several of the papers above, is now available, at genome.cornell.edu/software/MapPop.
• SnpSelect, software that implements an algorithm for the SNP pooling problem described above, is available by request.

My PhD thesis

• D.G. Brown. Algorithmic methods in genetic mapping, 2000. .ps version (1.2 MB).

My thesis is dedicated to the memory of Gian-Carlo Rota; to my great joy, I found a list of quotes from Prof. Rota while going through some old files recently. Enjoy.

Non-work-related things

And finally, I am not the bestselling author Dan Brown, nor are we related. I don't like his writing. Oddly, we both know Eric Savage. Eric was a grad student with me (dan brown the computer scientist) at Cornell. He currently teaches at Phillips Exeter, where Dan Brown (the author) worked as well until his writing paid enough for him to quit. Please don't send me fan mail or threats.