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.

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
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.