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Discussion - Spring 2002

Wednesday, February 6th

K. Sjölander. (1998). Phylogenetic inference in protein superfamilies: Analysis of SH2 domains. Download from UCSC.

Sjölander et al. (1996). Dirichlet mixtures: a method for improving detecting of weak but significant protein sequence homology. UCSC Technical Report, UCSC-CRL-96-09. Download from UCSC.

Monday, February 11th

M. O. Dayhoff, R. M. Schwartz, and B. C. Orcutt. (1978). A model of evolutionary change in proteins. In Dayhoff, M. O., ed., Atlas of Protein Sequence and Structure , vol. 5, sup. 3. National Biomedical Research Foundation, Washington D.C., p. 345--352.

Monday, February 18th

No class -- Presidents' Day.

Monday, February 25th

K. Kerr, M. Martin, and G. Churchill. (2000). Analysis of variance for gene expression microarray data. Journal of Computational Biology 7(6): 819-837 (www access from UC computers).

S. Dudoit, Y.H. Yang, M. Callow, and T. P. Speed. (2002). Statistical methods for identifying differentailly expressed genes in replicated DNA microarray experiments. Statistica Sinica 12(1): 111-139. (tech. report #578).

R. Wolfinger, G. Gibson, E. Wolfinger, L. Bennett, H. Hamdadeh, P. Bushel, C. Afshari, and R. Paules. (2001). Assessing gene significance from cDNA microarray expression via mixed models. Journal of Computational Biology 8(6): 625-637 (www access from UC computers).

Marianne Huebner's slides (pdf)

Monday, March 4th

Normalization for cDNA microarray experiments.
Slides (pdf) from Lecture 1, part II of Bioconductor short course.

Monday, March 11th

Discussion cancelled
The new RNA world: computational genomic screens for noncoding RNAs
Sean Eddy, Department of Genetics, Washington University, School of Medicine
QB3 Computational Biology Seminar Series
4pm, 101 Morgan Hall

Monday, March 18th

Classification in microarray experiments
Slides (pdf) from Lecture 5 of Bioconductor short course.

S. Dudoit, J. Fridlyand, and T. P. Speed. (2002). Comparison of discrimination methods for the classification of tumors using gene expression data. Journal of the American Statistical Association 97 (457): 77-87.

T. Hastie, R. Tibshirani, and J. H. Friedman. (2001). The Elements of Statistical Learning : Data Mining, Inference, and Prediction. Springer Verlag.

K. V. Mardia, J. T. Kent, and J. M. Bibby. (1979). Multivariate Analysis . Academic Press, Inc., San Diego.

B. D. Ripley. (1996). Pattern recognition and neural networks. Cambridge University Press, Cambridge, New York.

Technical reports from Leo Breiman's website.

Monday, March 25th

No class -- Spring break.

Monday, April 1st

Classification in microarray experiments, continued

Monday, April 8th

Classification in microarray experiments, continued

Monday, April 15st

Classification in microarray experiments, continued

Monday, April 22nd

No class

Monday, April 29th

Classification in microarray experiments, continued

Monday, May 6th

Overview of the Bioconductor project and marray packages

Bioconductor
Slides for the lecture pdf
Sweave: in R tools package, Manual and examples
R scripts: marrayClasses.demo.R, marrayInput.demo.R, marrayNorm.demo.R