   BMI 209 Home Announcements Syllabus Schedule & Handouts Links |
BMI 209 - Statistical Analysis of Microarray Data 9/21 Lecture 1: Introduction to genomics and microarray technology [DeRisi] 9/28 Lecture 2: Introduction to microarray bioinformatics [Yeh] - Sequence databases,
gene finding and probe
design, microarray standards (MIAME)
- Exploratory data
analysis for two-color
spotted
arrays and Affymetrix gene chip data; sources of variability,
experimental designs, and normalization issues.
Reading:
GK Smyth, YH Yang and
TP Speed. Statistical
Issues in cDNA Microarray Data Analysis. In: Functional
Genomics: Methods and Protocols, M. J. Brownstein and A. B. Khodursky
(eds.), Methods in
Molecular Biology Volume 224, Humana Press, Totowa, NJ, 2003, pages
111-136.
10/12 Lecture 4: Array analysis I: Identify DE genes in two-sample studies [Yeh] 10/19 Lecture 5: Array analysis II: Identify DE genes with complex models [Yang] - Introduction to linear
models and its
application in analyzing complex gene expression experiments with two
or more treatment comparisons.
[Slides] 10/26 Lecture 6: Array analysis III: Clustering [Fridlyand] 11/2 Lecture 7: Array analysis IV: Discrimination [Fridlyand] GH-S261 11/9 Lecture 8: Array Analysis V: Prediction [Segal] 11/16 Lecture 9: Array Analysis VI: Functional annotation [Yang & Yeh] - Making sense of
co-expression
using Gene Ontology and sequence information. Special Topic I: Introduction to array CGH data analysis [Fridlyand] [Slides] 11/23: Lecture 10: Special Topic II: eQTL [Sen]
Student presentations I: 1. Dale Webster & Christina Chaivorapol -- paper review: Tusher, VG, Tibshirani R, and Chu G. Significance analysis of microarrays applied to the ionizing radiation response. response. Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5116-21. 2. Nita Lee - case study: cervical dysplasia and cancer 11/30: Student presentations II.
3. Alex Adai & Jenny Shock - case study: mRNA decay in Plasmodium falciparum 4. Geoff Benton - case study on breast cancer cell types 5. Marco Sorani - re-analysis of data from Curr Opin Pharmacol. 2003 Jun;3(3):309-16. Expression profiling and pharmacogenomics of muscle and muscle disease. Hoffman EP, DuBois DC, Hoffman RI, Almon RR. 6. Gregg Whitworth - case study: yeast time course splicing microarray Textbook & General References No textbook is required. References will be provided and posted on the course website for individual lectures at least one week prior to the lecture. Recommended readings: 1. A Primer of Genome Science by G. Gibson & S.V. Muse. 2001. Sinauer Associates 2. Statistical Analysis of Gene Expression Microarray Data edited by T.P. Speed. 2003. Chapman & Hall/CRC. |