Course Materials for BIO/CSE/STAT 597/8F
End-of-the-school-year party: Tue. April 30, Rm. 327 Thomas, 2:30-3:45.
What is BIO/CSE 597F?
Nucleic Acids Research 2002 Database Issue
Study guide for exam
Schedule for class presentations
Some of the materials will be presented as PostScript and PDF documents,
so you will need to handle at least one of these formats.
If your system doesn't already have one, you may want to fetch and install a
free PostScript/PDF viewer manufactured by Aladdin Inc, called
The Aladdin web page has instructions for attaching it to
Netscape or MS Internet-Explorer.
Another popular program for reading PDF files is
Adobe Acrobat Reader.
lecture 3 (without preliminary data)
supplementary material on SAGE (from NCBI)
more supplementary material on SAGE (from NCBI)
paper on SAGEmap
paper on SAGE data errors
SAGEmap Web site at NCBI
SAGE "home page" at Johns Hopkins
query yeast SAGE data at Stanford
introduction to spotted arrays
introduction to affy
normalization and missing values
smoothing and lowess
filtering and other transformations
homework 1 (due Feb. 6)
PCA and plotting
more dimension reduction
multi-dimensional scaling (Susan Holmes)
Homework 2: assignment,
Robert Tibshirani, Guenther Walther and Trevor Hastie.
"Estimating the number of clusters in a dataset via the Gap statistic".
A. Ben-Hur, A. Elisseeff, and I. Guyon.
"A Stability Based Method for Discovering Structure in Clustered Data".
K. Y. Yeung, C. Fraley, A. Murua, A. E. Raftery and W. L. Ruzzo.
"Model-based clustering and data transformations for gene expression data."
F. Bartolucci and F. Chiaromonte.
"Clustering of expression data from microarrays: a mixture-based approach."
Microarray Gene Expression Database Group
working with a response
Combining expression data and genomic sequence data:
Readings on binding-site clusters:
Berman et al. and
Krivan and Wasserman
Detecting binding-site clusters, a research problem:
Regulatory Sequence Analysis Tools :
details on k-mer matches and
details on spaced dyads
INCLUSive: INtegrated CLustering, Upstream Sequence retrieval and motif
lecture on DNA sequence patterns
Is a given sequence pattern associated with co-expression?
Gibbs Motif Sampler,
2D gel databases:
Database of Interacting Proteins:
Biomolecular Interaction Network Database:
Expression data and protein-protein interactions:
Subcellular location of yeast proteome:
Expression level and subcellular location: