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Mount, David W. Bioinformatics: Sequence and Genome Analysis. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press, 2001. ISBN: 0879695978.
1 Introduction/Sequence Comparison and Dynamic Programming Mount. pp. 1-7, 29-35, 45-48, 51-64.
2 Multiple Sequence Alignments I Mount. pp. 8-9, 65-89, 96-115, 140-155, 161-170.
3 Multiple Sequence Alignments II Mount. pp. 139-150, 152-157, 161-171, 185-198.
4 Phylogenetic Analysis Mount. pp. 237-280, 283-286, 291-308.
5 Literature Discussion Pellegrini, M., E. M. Marcotte, M. J. Thompson, D. Eisenberg, and T. O. Yeates. "Assigning Protein Functions by Comparative Genome Analysis: Protein Phylogenetic Profiles." Proc. Natl. Acad. Sci. USA. 96, no. 8 (13 Apr 1999): 4285-8.

Suel, G. M., S. W. Lockless, M. A. Wall, and R. Ranganathan. "Evolutionarily Conserved Networks of Residues Mediate Allosteric Communication in Proteins." Nat. Struct. Biol. 10, no. 1 (Jan 2003): 59-69.
6 Genome Sequencing and DNA Sequence Analysis Woolf, Peter, Christopher Burge, Amy Keating, and Michael Yaffe. "Statistics and Probabilty Primer for Computational Biologists." MIT. BE.490/7.91 Spring 2004. (PDF)

Bork, Peer, and Richard Copley. "Genome Speak." Nature 409 (15 Feb 2001): 815.
7 DNA Sequence Comparison and Alignment Mount. Chap. 7.
8 DNA Motif Modeling and Discovery Mount. Chap. 4.
9 Markov and Hidden Markov Models for DNA Sequences Mount. Chap. 4.
10 DNA Sequence Evolution Mount. Chap. 4.
11 RNA Secondary Structure Prediction Mount. Chap. 4.
12 Literature Discussion on Predicting the Functions of DNA/RNA Sequences Kellis, M., N. Patterson, M. Endrizzi, B. Birren, and E. S. Lander. "Sequencing and Comparison of Yeast Species to Identify Genes and Regulatory Elements." Nature 423, no. 6937 (15 May 2003): 241-54.

Rivas, E., R. J. Klein, T. A. Jones, and S. R. Eddy. "Computational Identification of Noncoding RNAs in E. Coli by Comparative Genomics." Curr. Biol. 11, no. 17 (4 Sep 2001): 1369-73.
13 Midterm Exam – in class – Protein and DNA Sequence Analysis
14 Protein Secondary Structure Prediction
15 Introduction to Protein Structure and Classification
16 Comparing Protein Structures

Molecular Modeling: Methods and Applications
17 Using Computational Methods to Analyze, Predict, and Design Protein Sequences and Structures

Solving Structures using X-ray Crystallographpy and NMR
Marti-Renom, et. al. Annu. Rev. Biophys. Biomol. Struct. 29 (2000): 291-325.
18 Solving Structures using X-ray Crystallographpy and NMR (cont.)

Homology Modeling
Marti-Renom, et. al. Annu. Rev. Biophys. Biomol. Struct. 29 (2000): 291-325.
19 Methods for Protein Structure Prediction: Homology Modeling and Fold Recognition Bonneau, and Baker. Annu. Rev. Biophys. Biomol. Struct. 30 (2001): 173-189.
20 Threading and ab initio Structure Prediction

Computational Protein Design
21 Introduction to Systems Biology Ideker, and Lauffenburger. TRENDS in Biotechnology 21 (2003): 255-262.
22 Feedback Systems and Coupled Differential Equations
23 DNA Microarrays and Clustering
24 Literature Discussion on DNA Microarrays and Clustering Segal, E., et. al. "Module Networks: Identifying Regulatory Modules and their Condition-specific Regulators from Gene Expression Data." Nature Genetics (2003). 

Beer, M., and S. Tavazoie. "Predicting Gene expression from Sequence." Cell (2004). 

Background Reading

Friedman, N. "Inferring Cellular Networks Using Probabilistic Graphical Models." Science (2004).

Appendix of Probability and Statistics Primer.
25 Computational Annotation of the Proteome
26 Literature Discussion on Computational Annotation of the Proteome Bader, J. S., A. Chaudhuri, J. M. Rothberg, and J. Chant. "Gaining Confidence in High-throughput Protein Interaction Networks." Nat Biotechnol. 22, no. 1 (Jan 2004): 78-85. Epub (14 Dec 2003).

Jansen, R., H. Yu, D. Greenbaum, Y. Kluger, N. J. Krogan, S. Chung, A. Emili, M. Snyder, J. F. Greenblatt, and M. Gerstein. "A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data." Science 302, no. 5644 (17 Oct 2003): 449-53.