Schedule:

Sep 13 (Lecture 1): Dr. Ru-Fang Yeh, UCSF
Overview of statistical issues in bioinformatics. Introduction to microarray analysis.
slides

Sep 20 (Lecture 2): Dr. Yuanyuan Xiao, UCSF
Overview of design and data preprocessing for different microarray platforms: expression / microRNA / tiling / SNP arrays.
slides

Sep 27 (Lecture 3): Dr. Jane Fridlyand, Genentech
Copy number arrays and other topics in analysis of cancer genomics data.
slides

Oct 4 (Lecture 4): Dr. Henrik Bengtsson, UC Berkeley
Further SNP Chip preprocessing: Copy number analysis applications.
slides

Oct 11 (Lecture 5): Dr. Mark Segal, UCSF
Microarray expression data with linked survival phenotypes: DLBCL revisited.
slides

Oct 18 (Lecture 6): Dr. Lawrence Hon, Genentech
Factors affecting microRNA regulation.
slides

Oct 25 (Lecture 7): Dr. Ru-Fang Yeh, UCSF
Statistical approaches to the analysis of tiling arrays and ChIP-chip data.
slides

Nov 1 (Lecture 8): Dr. Katie Pollard, UC Davis
Detecting lineage-specific evolution of DNA: biased gene conversion.

Nov 8 (Lecture 9): Dr. Mark Segal, UCSF
Periodic sequence motifs: the nucleosome positioning code revisited.
slides

Nov 15 (Lecture 10): Dr. Mark Segal, UCSF
Validation in genomics: CpG Island methylation revisited.
slides

Grades:

     100% - classroom participation

Recommended Readings:

1. The Elements of Statistical Learning by T. Hastie, R. Tibshirani, J. H. Friedman. 2001. Springer.
2. Bioinformatics and Computational Biology Solutions using R and Bioconductor, edited by R. Gentleman et al. 2005. Springer.
3. Statistical Analysis of Gene Expression Microarray Data, edited by T.P. Speed. 2003. Chapman & Hall/CRC.
4. A Primer of Genome Science by G. Gibson & S.V. Muse. 2001. Sinauer Associates.