kayee@u.washington.edu
206-732-6156 (office)
http://faculty.washington.edu/kayee/
Postal Address
Department of
Microbiology
Box 358070
University of Washington
Seattle, WA 98195
A highly motivated, energetic, frequently published and referenced multi-disciplinary researcher with experience in computer science, statistics and biomedical sciences. Interested in development of improved pattern recognition algorithms and publicly available software for the analysis of functional genomics data.
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. Advisor: J. Ian Munro
Research Assistant Professor, Department of Microbiology, University of Washington (June 2004 - present). Develop improved pattern recognition algorithms for functional genomics data. Collaborated with multi-disciplinary scientists. The goal is to expand research expertise to beyond microarray data. Since graduation, research efforts resulted in a total of 11 publications, among which four are first-authored peer-reviewed articles.
Research Scientist/Senior Fellow, Department of Microbiology, University of Washington (Jan 2002 - May 2004). Research in bioinformatics. Interacted with inter-disciplinary scientists to design and implement clustering and classification algorithms for gene expression analysis. Analyzed gene expression datasets using both commercial (eg. Rosetta Resolver, SpotFire) and open source (eg. bioconductor) software packages.
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. Research efforts result in five peer-reviewed published papers, two of which were identified by the Institute of Scientific Information to be highly cited papers in Computer Science.
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.
R. Gottardo, A. E. Raftery, K. Y. Yeung and R. E. Bumgarner. Bayesian robust inference for differential gene expression in cDNA microarrays with multiple samples. To appear in Biometrics. Preprint. An early verion is available as Technical Report 455, Department of Statistics, University of Washington, Seattle, WA, July 2004.
R. Gottardo, A. E. Raftery, K. Y. Yeung and R. E. Bumgarner. Quality Control and Robust Estimation for cDNA Microarrays with Replicates. To appear in the Journal of the American Statistical Association (JASA). Preprint. An earlier version is available as Technical Report 438, Department of Statistics, University of Washington, Seattle, WA, Dec 2003.
Q. Li , C. Fraley , R. E. Bumgarner, K. Y. Yeung and A. E. Raftery. Donuts, scratches and blanks: Robust model-based segmentation of microarray images. Bioinformatics 2005 21: 2875 - 2882.
K. Y. Yeung, R. E. Bumgarner and A. E. Raftery. Bayesian model averaging: development of an improved multi-class, gene selection and classification tool for microarray data. Bioinformatics 2005 21: 2394-2402. Supplementary web site
G. J. Vanasse, R. K. Winn, S. Rodov, A. W. Zieske, J. T. Li, J. C. Tupper, M. A. Peters, K. Y. Yeung, and J. M. Harlan. Bcl-2 overexpression leads to increases in suppressor of cytokine signaling-3 expression in B cells and de novo follicular lymphoma. Molecular Cancer Research 2004, 2: 620-631.
K. Y. Yeung and R. E. Bumgarner. Pattern recognition in expression data. Recent Developments in Nucleic Acids Research 2004, 1: 333-354.
K. Y. Yeung, M. Medvedovic and R. E. Bumgarner. From co-expression to co-regulation: how many microarray experiments do we need? Genome Biology 5:R48, 2004. Supplementary web site
M. Medvedovic, K. Y. Yeung and R. E. Bumgarner. Bayesian mixture model based clustering of replicated microarray data. Bioinformatics 20:1222--1232, 2004. 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.
First Edition of the Advanced School in Biomedicine and Bioinformatics, Lipari, Italy. June 2004. Title of talk: Model-based clustering and validation techniques for gene expression data.
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.
NIH Mentored Quantitative Research Career Development Award (K25), May 2004 - April 2009. This award will provide 5 years of funding to support Dr. Yeung's research.
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, 2002-2004)
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).
Bioinformatics research
Technical skills
NIH grant writing and application
Reviewer for journals including Bioinformatics, BMC Bioinformatics, Nucleic Acids Research, Genome Biology, Applied Genomics and Proteomics, Biometrics, Journal of Bioinformatics and Computational Biology, Theoretical Biology and Medical Modelling, Genomics, Pharmacogenomics.
Presentation and teaching skills