Date: Tue, 10 Dec 1996 21:22:25 GMT Server: NCSA/1.4.2 Content-type: text/html Last-modified: Sun, 17 Nov 1996 06:15:06 GMT Content-length: 6657 Untitled

Curriculum Vitae

Brendan Marshall Mumey

I am currently a Ph.D. candidate in the Department of Computer Science at the University of Washington. I entered in the fall of 1992 and expect to graduate by the fall of 1996. I am 28 years old. I have dual US and Canadian citizenship.

Contact Information

Department of Computer Science

University of Washington

Seattle, WA, 98195-2350

Voice: (206) 685-4087 (day) or (206) 322-2099 (evening)

Fax: (206) 543-2969

E-mail: brendan@cs.washington.edu

WWW: http://www.cs.washington.edu/homes/brendan/

Research

My general interests run to applying theoretical techniques to solve problems which have practical motivation. My current work is in computational biology. Specifically, I have worked on the problem of comparing DNA clones based on their "multiple complete digest" fingerprint. This fingerprint is gathered by digesting each clone with several different restriction enzymes and measuring (using gel electrophoresis) the lengths into which each clone is divided. Using a stochastic model of this process, I developed an estimator of the a posteriori probability that two clones overlap given their measured fingerprints. An overlap test based on this approach is provably powerful in the sense of achieving nearly the lowest rate of false negatives for a given rate of false positives. Using this overlap test, I have implemented a clone ordering algorithm which is crucial to finishing the map.

More recently, I have been working on a clustering problem which arises in the context of classifying prostate cancer cells. The raw data consists of quantized hybridization levels for several hundred cell lines against perhaps 25,000 cDNA oligos. The problem is to discover the important features which determine the general type and lethality of a particular cell line. This is joint with work with Dick Karp and Leroy Hood's lab in the molecular biotechnology department at the University of Washington.

I have also done some work in computational astrophysics; my contribution being a new parallel algorithm and implementation for detecting clusters in points sets. With Maria Klawe I developed new upper and lower bounds for computing the optimal alphabetic tree data structure.


Education

Ph.D. (expected fall 1996), Computer Science, University of Washington. Advisor: Dr. Larry Ruzzo.

M.Sc., Computer Science, University of British Columbia, August, 1992. Advisor: Dr. Maria Klawe. Thesis title: Some New Results on Constructing Optimal Alphabetic Binary Trees.

B.Sc. (Honors First Class), Mathematics, University of Alberta, May, 1990.

Academic Experience

University of Washington. Pre-doctoral fellowship in genomic sciences. Awarded September, 1995.

University of Washington. Teaching assistant for CSE321, an introductory discrete mathematics course. September-December, 1994. Received very good to excellent evaluations.

University of Washington. Research assistant. September, 1992 until present.

UCSD Supercomputer Center. Participant in the 1993 Metacenter Computational Science Institute in Parallel Computing. August, 1993.

University of British Columbia. NSERC Postgraduate fellow. September, 1990 to August, 1992.

Other Achievements

Several undergraduate prizes in Mathematics. Placed in the top 3% in 1990 Putnam undergraduate mathematics competition. Accepted to the doctoral program in computer science at MIT.

Publications

B. Mumey, A powerful clone overlap test. Submitted to the ISMB'96 conference.

M. Klawe and B. Mumey, Upper and Lower Bounds on Constructing

Optimal Alphabetic Trees. Proceedings of the 1993 ACM/SIAM Symposium on

Discrete Algorithms. January, 1993. The SIAM Journal on Discrete Math. November, 1995.

B. Mumey, Fast Cluster Detection in Point Sets. Presented at the 1994 DIMACS Challenge.

My papers are available on-line at: http://www.cs.washington.edu/homes/brendan/

References

Dr. Larry Ruzzo

Department of Computer Science

University of Washington

(206) 543-6298

ruzzo@cs.washington.edu

Dr. Richard Karp

Department of Computer Science

University of Washington

(206) 543-1695

karp@cs.washington.edu

Dr. Maria Klawe

Department of Computer Science

University of British Columbia

(604) 822-3064

klawe@cs.ubc.ca