Introduction
DNA, RNA, proteins, the central dogma in molecular biology, splicing, gene structure

PART 1: Basic Algorithms

Sequence Alignment, Dynamic Programming, and Trees
Homology, alignments and dynamic programming
Local alignment, heuristic local alignment and BLAST
Advanced alignment techniques: linear space, affine gaps, Four Russians algorithm

Phylogeny trees

Multiple Sequence Alignment  -- scoring, profiles, progressive alignment

Sparse Dynamic Programming -- Chaining of Local Alignments

Hidden Markov Models & Other Graphical Models
Markov chains and hidden Markov models
Parsing: Viterbi, Posterior Decoding, other alternatives
Parameter estimation for HMMs: maximum likelihood, expectation maximization
Connection between pair HMMs and alignments

Conditional Random Fields

Context Free Grammars & RNA structure

Part 2: More Algorithms, Systems, and Applications

Genomic Sequencing

Sequencing methods: Sanger sequencing, cloning, shotgun sequencing, new technologies

Computational assembly of a genome

Comparative Genomics & Annotation
The human genome: chromosomes, repeats, genes, and SNPs
Synteny mapping and whole-genome alignment

Gene Finding

Detection of elements that are selectively preserved

Protein Families, and Alignment

Protein evolution & classification

Current protein aligners

Gene Regulation: Experimental Technologies, Regulatory Elements, Networks
Microarrays, ChIP-Chip experiments, other technologies

Regulatory Elements & Motif Finding

Networks of gene regulation and protein interactions