Reading Assignments
01/24 - Additional readings for lectures 2-5
Prediction of Complete Gene Structures in Human Genomic DNA
Multiple-sequence functional annotation and the generalized hidden
Markov phylogeny
Combining Phylogenetic and Hidden Markov Models in Biosequence Analysis
Applications of Generalized Pair Hidden Markov Models to Alignment and
Gene Finding Problems
02/02 - Additional readings for lectures 6-8
Fitting a mixture model by expectation maximization to discover motifs in
biopolymers
Bayesian models for multiple local sequence alignment and gibbs
sampling strategy
02/14 - Additional readings for lectures 8-9
Array CGH
02/21 - Additional readings for lectures 10-11
Stephens, M., Smith, N., and Donnelly, P. (2001).
A new statistical method
for haplotype reconstruction from population data. American Journal of
Human Genetics, 68, 978--989.
T. Niu, Z.S. Qin, X. Xu, and J. Liu (2002)
Bayesian Haplotype Inference
for Multiple Linked Single Nucleotide Polymorphisms. Am. J. Hum. Genet
Stephens, M., and Donnelly, P. (2003).
A comparison of Bayesian methods
for haplotype reconstruction from population genotype data. American
Journal of Human Genetics, 73:1162-1169.
02/28 - Readings for lecture 12
Microarray review
03/02 - Readings for lecture 13
Normalization
03/02 - Readings for lecture 14
Significance Analysis of Microarrays (SAM)
03/14 - Readings for lecture 15
Cluster analysis and display of genome-wide expression patterns
03/16 - Readings for lecture 16
Optimal leaf ordering
Clustering expression data
03/21 - Readings for lecture 17
Molecular Classification of Cancer
03/23 - Readings for lecture 18
Analyzing time series gene expression data
04/04 - Readings for lecture 21
Using Bayesian Networks to Analyze Expression Data
04/13 - Readings for lecture 24
Network motifs in the transcriptional regulation network of Escherichia coli
04/18 - Readings for lecture 25
Comparative assessment of large-scale data
sets of protein protein interactions