Tentative Course Syllabus

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


Sequence Alignments
Homology, alignments and dynamic programming
Local alignment, heuristic local alignment and BLAST
Advanced alignment techniques: linear space, affine gaps, banded linear time alignments, time warping


Hidden Markov 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


Multiple Sequence Alignments
Definition, scoring, main alignment techniques

Multiple aligners for proteins: CLUSTALW, MUSCLE, ProbCons


Genomic Sequencing

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

Computational assembly of a genome


Applications of HMMs and Alignments: Comparative Genomics
The human genome: chromosomes, repeats, genes, and SNPs
Synteny mapping and whole-genome alignment

Finding genes and other functional elements


Microarrays and Motifs
Microarray technology, analysis, and gene clustering

Gene regulation, regulatory motifs, and computational motif finding

RNA structure

Probabilistic context free grammars and RNA structure modeling

Other topics

If time permits, we may cover phylogeny, haplotypes, or other topics