| 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. |
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