Introduction to Computational Molecular Biology

Readings

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.