Ka Yee Yeung: Research and Projects

Publications

• 2008
  • MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis. Vu T Chu, Raphael Gottardo, Adrian E Raftery, Roger E Bumgarner, Ka Yee Yeung. Genome Biology 2008, 9: R118. Supplementary web site.

• 2006
  • Bayesian Context-specific infinite mixture model for clustering of gene expression profiles accross diverse microarray datasets. Xiangdong Liu, Siva Sivaganesan, Ka Yee Yeung, Junhai Guo, Roger Bumgarner, Mario Medvedovic. Bioinformatics 2006, 22: 1737-1744.

  • Bayesian Robust Inference for Differential Gene Expression in cDNA Microarrays with Multiple Samples. Raphael Gottardo, Adrian Raftery, Ka Yee Yeung and Roger Bumgarner. Biometrics 2006, 62: 10-18. Earlier version: Technical Report 455 (July 2004) , Department of Statistics, University of Washington.

  • Robust estimation of cDNA microarray intensities with replicates. Raphael Gottardo, Adrian Raftery, Ka Yee Yeung and Roger Bumgarner. Journal of the American Statistical Association 2006, 101: 30-40. Earlier version: Technical Report 438 (Dec 2003), Department of Statistics, University of Washington. Supplementary web site.

• 2005
  • Donuts, scratches and blanks: Robust model-Based segmentation of microarray images. Qunhua Li , Chris Fraley , Roger Bumgarner, Ka Yee Yeung and Adrian Raftery. Technical Report 473 (Jan 2005), Department of Statistics, University of Washington. Bioinformatics 2005, 21: 2875 - 2882.

  • Bayesian Model Averaging: Development of an improved multi-class, gene selection and classification tool for microarray data. Ka Yee Yeung, Roger Bumgarner and Adrian Raftery. Technical Report 468 (Oct 2004), Department of Statistics, University of Washington. Bioinformatics 2005, 21: 2394-2402.

• 2004
  • Bcl-2 overexpression leads to increases in suppressor of cytokine signaling-3 expression in B cells and de novo follicular lymphoma. Gary J. Vanasse, Robert K. Winn, Sofya Rodov, Arthur W. Zieske, John T. Li, Joan C. Tupper, Mette A. Peters, Ka Y. Yeung, and John M. Harlan. Molecular Cancer Research 2004, 2: 620-631.

  • Review article: Pattern recognition in expression data. Ka Yee Yeung , and Roger Bumgarner. Recent Developments in Nucleic Acids Research 2004, 1: 333-354.

  • Bayesian Robust Inference for Differential Gene Expression in cDNA Microarrays with Multiple Samples. Raphael Gottardo, Adrian Raftery, Ka Yee Yeung and Roger Bumgarner. Technical Report 455 (July 2004), Department of Statistics, University of Washington. To appear in Biometrics.

  • From co-expression to co-regulation: how many microarray experiments do we need? Ka Yee Yeung, Mario Medvedovic and Roger Bumgarner. Genome Biology 2004, 5: R48.

  • Bayesian mixture model based clustering of replicated microarray data. Mario Medvedovic, Ka Yee Yeung and Roger Bumgarner. Bioinformatics 2004 20:1222-1232.

• 2003
  • Multi-class classification of microarray data with repeated measurements: application to cancer. Ka Yee Yeung, and Roger Bumgarner. Genome Biology 2003 4: R83. Correction: Genome Biology 2005, 6:405

  • Clustering gene expression data with repeated measurements. Ka Yee Yeung, Mario Medvedovic and Roger Bumgarner. Genome Biology 2003 4(5):R34.

  • Book chapter: Clustering or automatic class discovery: non-hierarchical, non-SOM. in "A practical approach to microarray data analysis", Kluwer Academic Publisher, 2003.

• 2002
  • Expression analysis of Barrett's epithelium and normal gastrointestinal tissues. This is joint work with Mike Barrett, Jeff Delrow, Li Hsu and Brian Reid at the Fred Hutchinson Cancer Research Center, Larry Ruzzo in Computer Science, and with Peter Rabinovitch in Pathology at University of Washington. Neoplasia 2002, 4(2):121-8. Technical Report UW-CSE-00-11-01 (November 2000) pdf.

• 2001
  • ISI "fast moving fronts" and "new hot paper" in Computer Science (Jan 2004): Model-based clustering and data transformations for gene expression data. Ka Yee Yeung, Chris Fraley, Alejandro Murua, Adrian Raftery and Larry Ruzzo. Bioinformatics 2001 17: 977-987.

  • Principal Component Analysis for clustering gene expression data. Ka Yee Yeung, and Larry Ruzzo. Bioinformatics 2001 17: 763-774.

  • ISI "fast-breaking paper" in Computer Science(Dec 2002) : Validating Clustering for Gene Expression Data. Ka Yee Yeung, David Haynor and Larry Ruzzo. Bioinformatics 2001 17: 309-318.

• 1999
  • Algorithms for Choosing Informative Differential Gene Expression Experiments. Richard M. Karp, Roland Stoughton, and Ka Yee Yeung. In the Third Annual International Conference on Computational Molecular Biology (Recomb'99).

Presentation and talks

• Model-based clustering and validation techniques for gene expression data (5 Mbytes pdf file) Slides for the 2 lectures I gave at the Lipari Bio-info Summer School , June 2004.
• Clustering 101 (PowerPoint file) This is a short introduction to clustering to CEA users. This is an attempt to explain what clustering is to biologists with little mathematical background.
• First introduction to cluster analysis of array data (PowerPoint file). This is a presentation for Pathology 501 at University of Washington on Oct 18, 2002.

Dissertations

• Ph.D. Dissertation: Computer Science Department at University of Washington. Cluster analysis of gene expression data (Dec 10, 2001 version). Advisor: Prof Larry Ruzzo. My thesis contains the most detailed and most recent writeup of my projects in graduate school (including the model-based clustering work in Chapter 5 , PCA work in Chapter 4 and FOM work in Chapter 3).
• Master's Thesis: Computer Science Department at University of Waterloo Thesis topic : Root finding problem. Advisor: Prof Ian Munro. Available as a technical report at University of Waterloo. postscript version.

Back to Ka Yee's home page.