Readings are from the textbook: Jones, Neil C., and Pavel A. Pevzner. An Introduction to Bioinformatics Algorithms (Computational Molecular Biology), Bradford Books. Cambridge, MA: MIT Press, August 1, 2004. ISBN: 0262101068.
| LEC # | TOPICS | READINGS |
|---|---|---|
| Introduction to Biology | ||
| 1 | The Central Dogma: Some Algorithms Introduction | |
| Enumerative Solutions: Partial Digest Problem and Median Strings | ||
| 2 | Partial Digest Problem | Chapter 4 |
| 3 | Motifs and Median Strings | Chapter 4 |
| Dynamic Programming: Sequence Alignments | ||
| 4 | Global Alignment | Chapter 6 |
| 5 | Local Alignment | Chapter 6 |
| 6 | Spliced Alignment | Chapter 6 |
| 7 | More Efficient Alignment | Chapter 7 |
| Graph Theory: Sequencing Genes and Proteins | ||
| 8 | Genomics and SBH Graphs | Chapter 8 |
| 9 | Peptide Graphs | Chapter 8 |
| Pattern Matching: Exact Matches, Gapless Alignments, and BLAST | ||
| 10 | Exact Pattern Matching | Chapter 9 |
| 11 | Suffix Trees | |
| 12 | Suffix Arrays and BWTs | Chapter 9 |
| 13 | BLAST | Chapter 9 |
| Clustering: Microarrays and Phylogeny | ||
| 14 | Clustering (Guest Lecturer) | Chapter 10 |
| 15 | Trees | Chapter 10 |
| Neighbor Joining | ||
| 16 | Review of Phylogenetic Analysis Coalescent Theory in Biology |
|
| 17 | Application: Microarrays (Guest Lecturer) | Chapter 10 |
| Probabilistic Models and Machine Learning: Gene Annotation and Evolution | ||
| 18 | Hidden Markov Models I | Chapter 11 |
| 19 | Hidden Markov Models II | Chapter 11 |
| 20 | Gibbs Sampling | Chapter 12 |
| 21 | Random Projections | Chapter 12 |
| 22 | MCMC and Bayesian Networks | |
| Horizons | ||
| 23 | The Future: Protein Structure (Guest Lecturer) | |
| 24 | The Future: Haplotype Mapping (Guest Lecturer) | |
| 25 | Presentations of Final Projects | |
| 26 | Presentations of Final Projects (cont.) | |
Recommended Readings
The following list of books will give greater understanding on specific topics.
Setubal, Carlos, and Joao Meidanis. Introduction to Computational Molecular Biology. 1st ed. Boston, MA: PWS Publishing, January 16, 1997. ISBN: 0534952623.
Durbin, Richard, Sean R. Eddy, Anders Krogh, and Graeme Mitchison. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge, UK: Cambridge University Press, Reprint edition, July 1, 1999. ISBN: 0521629713.
Gusfield, Dan. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. 1st ed. Cambridge, UK: Cambridge University Press, January 15, 1997. ISBN: 0521585198.
Lodish, Harvey, David Baltimore, Arnold Berk, S. Lawrence Zipursky, Paul Matsudaira, and James Darnell. Molecular Cell Biology. New York, NY: W. H. Freeman & Company, 3rd Package edition, March 1, 1995. ISBN: 0716736861.
Branden, Carl-Ivar, and John Tooze. Introduction to Protein Structure. 2nd ed. New York, NY: Garland Publishing, January 15, 1999. ISBN: 0815323050.
Clote, Peter, and Rolf Backofen. Computational Molecular Biology: Introduction. 1st ed. New York, NY: John Wiley & Sons, September 22, 2000. ISBN: 0471872520.