kayee@u.washington.edu
206-732-6141 (office)
http://staff.washington.edu/kayee/
Postal Address
Center for Expression Arrays
Department of
Microbiology
Box 358070
University of Washington
Seattle, WA 98109
My primary interest lies in analyzing massive data sets. In general, I am interested in developing practical algorithms and evaluating existing computational or statistical approaches in data analysis. My current project is development of algorithms for microarray data that take advantage of variability estimates or technical replicates.
Ph.D. in Computer Science from University of Washington, Seattle, WA (2001). Thesis: Cluster analysis of gene expression data. Advisor: Walter L. Ruzzo
M.S. in Computer Science from University of Washington, Seattle, WA (1998). Qualifying exam topic: Algorithms for choosing informative differential gene expression experiments. Advisor: Richard M. Karp
M.Math. (1996) and B.Math. (1995) in Computer Science from University of Waterloo, Ontario, Canada (1996). Advisor: J. Ian Munro
Research Scientist, Center for Expression Arrays, University of Washington (2002 - present).
Research Assistant, University of Washington (1998 - 2001). Ongoing research in bioinformatics. Designed and implemented algorithms to analyze gene expression data, including various clustering algorithms, and evaluation methods for assessing clustering results. Applied statistical tools (like Splus and Maple) in data analysis.
Teaching Assistant, University of Washington (1996 - 1997). Duties included teaching sessions, helping students and grading homework, in introductory computer science classes and advanced algorithm classes.
Summer Student, Royal Bank of Canada, Toronto, Ontario, Canada (1997 summer). Designed and implemented applications under the windows environment.
Summer Student, National Research Council of Canada, Ottawa, Ontario, Canada (1995 summer). Designed and implemented an application program in C to pre-process an input Postscript file under the Macintosh programming environment.
M. Medvedovic, K. Y. Yeung and R. E. Bumgarner. Bayesian mixture model based clustering of replicated microarray data. To appear in Bioinformatics. Supplementary web site
K. Y. Yeung and R. E. Bumgarner. Multi-class classification of microarray data with repeated measurements: application to cancer. Genome Biology 2003 4: R83. Supplementary web site
K. Y. Yeung, M. Medvedovic and R. E. Bumgarner. Clustering gene expression data with repeated measurements. Genome Biology 4 (5):R34, 2003. Supplementary web site
K. Y. Yeung. Clustering or automatic class discovery: non-hierarchical, non-SOM. in "A practical approach to microarray data analysis". Kluwer Academic Publisher, Chapter 16, 2003.
M. T. Barrett, K. Y. Yeung, W. L. Ruzzo, L. Hsu, P. L. Blount, R. Sullivan, H. Zarbl, J. Delrow, P. S. Rabinovitch, and B. J. Reid. Transcriptional analyses of Barrett's metaplasia and normal upper gastrointestinal mucosae. Neoplasia 4:121-128, 2002.
K. Y. Yeung, C. Fraley, A. Murua, A. E. Raftery, and W. L. Ruzzo. Model-based clustering and data transformations for gene expression data. Bioinformatics 17:977--987, 2001. In conjunction with the 3rd Georgia Tech-Emory International Conference on Bioinformatics. Supplementary web site
K. Y. Yeung, and W. L. Ruzzo. Principal component analysis for clustering gene expression data. Bioinformatics 17:763--774, 2001. Supplementary web site
K. Y. Yeung, D. R. Haynor, and W. L. Ruzzo. Validating clustering for gene expression data. Bioinformatics 17:309--318, 2001. Supplementary web site
K. Y. Yeung, M. T. Barrett, J. Delrow, P. L. Blount, L. Hsu, W. L. Ruzzo, B. J. Reid, and P. S. Rabinovitch. Expression analysis of Barrett's epithelium and normal gastrointestinal tissues. Technical Report UW-CSE-2000-11-01, Department of Computer Science and Engineering, University of Washington, Seattle, WA, Nov 2000. Pdf version
R. M. Karp, R. Stoughton, K. Y. Yeung. Algorithms for choosing informative differential gene expression experiments. In Proceedings of the Third Annual International Conference on Computational Molecular Biology (Recomb), p 208-217, Lyon, France, 1999.
Invited talk at the 33rd Symposium on the Interface of Computing Science and Statistics, Orange County, California, June 2001. Title of talk: Model-based clustering and data transformations for gene expression data.
Fast Moving Fronts -- most cited paper in Computer Science: Model-based clustering and data transformations for gene expression data, ISI Essential Science Indicators (Jan 2004)
Fast breaking paper -- most cited paper in Computer Science: Validating clustering for gene expression data, ISI Essential Science Indicators (Dec 2002)
Rosetta Fellowship, University of Washington, WA (1998)
Alan George Student Leadership Award, University of Waterloo, Ontario, Canada (1996)
NSERC Scholarship, National Science and Engineering Research Council, Canada (1995)
Provost Scholarship, University of Waterloo, Ontario, Canada (1995)
ITRC Scholarship, University of Waterloo, Ontario, Canada (1995)
Honorable Mention in the Outstanding Female Undergraduate Student Competition, Computing Research Association (1995)
Lecturer at the Microarray Workshop, Center of Expression Arrays, University of Washington (once a quarter, 2002-present)
Guest lecture, STAT 593C "Model-based clustering", Department of Statistics, University of Washington (May 2003).
Guest lecture, PATHOLOGY 501 "Pathology Proseminars", Department of Pathology, University of Washington (Oct 2002).
Extensive programming experience in C, C++, Java, and Perl.
Proficient in mathematical and statistical software packages, including Matlab, Maple, Splus and R.
Experience in both academic and commercial microarray analysis software packages, including Resolver, SpotFire and BioConductor.
Familiar with various operating systems, including Linux, Unix, Mac OS X and Windows; and standard software applications.