Introduction to Computational Molecular Biology

Calendar

LEC #	TOPICS	KEY Dates
Introduction to Biology
1	The Central Dogma: Some Algorithms Introduction
Enumerative Solutions: Partial Digest Problem and Median Strings
2	Partial Digest Problem	Problem set 1 out
3	Motifs and Median Strings
Dynamic Programming: Sequence Alignments
4	Global Alignment	Problem set 2 out
5	Local Alignment
6	Spliced Alignment
7	More Efficient Alignment
Graph Theory: Sequencing Genes and Proteins
8	Genomics and SBH Graphs	Problem set 3 out
9	Peptide Graphs
Pattern Matching: Exact Matches, Gapless Alignments, and BLAST
10	Exact Pattern Matching	Problem set 4 out
11	Suffix Trees
12	Suffix Arrays and BWTs
13	BLAST
Clustering: Microarrays and Phylogeny
14	Clustering (Guest Lecturer)	Problem set 5 out
15	Trees
Neighbor Joining
16	Review of Phylogenetic Analysis Coalescent Theory in Biology
17	Application: Microarrays (Guest Lecturer)
Probabilistic Models and Machine Learning: Gene Annotation and Evolution
18	Hidden Markov Models I	Problem set 6 out
19	Hidden Markov Models II
20	Gibbs Sampling
21	Random Projections
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.)