| Main |
| CS/ST480 |
| Instructors |
| Asa Ben-Hur |
| Hari Iyer |
| Course Materials |
| Outline |
| Detailed Syllabus |
| Homework |
detailed course syllabus
| Week | Topic | References |
|---|---|---|
| 1 |
Course overview, biological preliminaries Gene finding in prokaryotes |
Introduction to molecular biology for computer scientists: First chapter of "Kernel methods in computational biology" [pdf] Book chapter from Larry Hunter [pdf] Martin Tompa's notes [pdf] |
| 2 |
Concepts: Homology, sequence similarity, and sequence alignment Dynamic programming algorithms |
Chapter 6 of Jones and Pevzner [pdf] |
| 3 |
Pairwise sequence alignment: global and local Amino acid scoring matrices Handling affine gap penalties Alignment with linear memory |
Chapter 6 of Jones and Pevzner [pdf] Chapter 7 of Jones and Pevzner |
| 4 |
Heuristic alignment methods: FASTA and
BLAST Multiple sequence alignment | |
| 5 | Motif finding in DNA and proteins |
Sections 4.4-4.8, Chapter 12 of Jones and Pevzner Motif finding by Gibbs sampling |
| 6 | Markov models and hidden Markov models | Chapter 3 or Durbin, Eddy, Krogh, and Mitchison |
| 7 |
HMMs: algorithms (forward, backward, Viterbi, Baum-Welch) Applications: CpG islands Midterm |
Chapter 3 of Durbin, Eddy, Krogh, and Mitchison |
| 8 |
Gene finding with HMMs Profile HMMs Pair HMMs |
Chapters 4,5 of Durbin, Eddy, Krogh, and Mitchison |
| 9 |
Graph algorithms in bioinformatics Genome assembly |
Chapter 8 of Jones and Pevzner |
| 10 |
Comparative genomics: genome rearragements |
Chapter 5 of Jones and Pevzner |
| 11 |
Comparative genomics: Gene finding Gene regulation |
Chapter 6 of Jones and Pevzner CREME: A framework for identifying cis-regulatory modules in human-mouse conserved segments. [pdf] Creme server |
| 12 |
Phylogeny Neighbor-joining |
|
| 13 |
Phylogeny (cont) Parsimony methods Maximum likelihood models A lecture on microarray data analysis |
|
| 15 |
Mass-spectrometry, ChIP-Chip and other sources of high-throughput data Review for final exam |