Semester Schedule:

Aug 23: lecture 1: overview to Gene expression and microarray technology

Aug 28 (HW1 due) lecture 2: Introduction to R. Basics of Computational Biology

Aug 30 (HW2 due) lecture 3: R continued. Distance definition and choices.

Sept 4 (Labor day, no class)

Sept 6 (HW3 due) lecture 4: Distance from two distributions, R packages and Bioconductor

Sept 11 (HW4 due) lecture 5: hierarchical clustering
(p: Yichun Chen, Peggy Qiu, Cecile Cousot

Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring. Golub et al. Science 1999.)

Sept 13 lecture 6: k-means clustering

Sept 18 (HW5, 6 due) lecture 7: further discussions on clustering

Sept 20 (HW 7 due) lecture 8: Principle Component Analysis

Sept 25

A network-based analysis of systemic inflammation in humans. Calvano et al. Nature 2005)

lecture 9: PCA continued

Sept 27 lecture 10: Self Organization Map

Oct 2 lecture 11: DNA regulatory motif analysis

Oct 4 No class!

Oct 9 (p: Tze Howe Charn, Zachary Hafez, Maria Pineda
Comparative genomics: Genome wide analysis in metazoan eukaryotes. Ureta-Vidal et al, Nature Genetics 2003) Slides

Oct 11

(p: Rong Kong, Rohith Reddy, Nell Keith)
A genome-wide study of gene activity reveals developmental signaling pathways in the preimplantation mouse embryo. Wang et al, Dev Cell 2004.
Gene expression in the preimplantation embryo: in-vitro developmental changes. Reproductive BioMedicine 2005  Slides

Oct 16 Lecture 12: Gibbs Sampling and DNA motif finding

Oct 19 Homework (due Dec 4)

Oct 23 (Project proposal due; Review Due) Lecture 13: Biological database

Oct 25 Lecture 14: Hypothesis testing and multiple hypothesis testing

Oct 30 No class!

Nov 1

(p: Mike, Rebecca, Jackie
Reconstruction of cellular signalling networks and analysis of their properties. Subramaniam et al, Nature Reviews Molecular Cell Biology 2005. )

Nov 6 Lecture 15: Network Biology: understanding the cell's functional organization

Nov 8 (p: Rick, Dan, Chas
Principles of microRNA regulation of a human cellular signaling network. Cui et al, Molecular Systems Biology, 2006) Slides

Nov 13 Lecture 15 continued: Network Biology.

Nov 15 Lecture 16: Dynamically organized yeast protein interaction network. Reference: Jing-Dong Han et al, Nature 2004

Nov 20 (Thanksgiving, no class)

Nov 22 (Thanksgiving, no class)

Nov 27 Lecture 17: Gene Ontology
Nov 29

Dec 4 Yichun Chen

Dec 6 Maria Pineda

Dec 11 (No class, project paper due, deposit to DCL 3215 or by email)