| Week | Date | Lecture | Topic | Slides | Readings |
|---|
| 1 |
1/22 |
1 |
Course overview |
slides |
|
| 1/24 |
2 |
The trees of life |
slides
|
Hunter2004 (if you didn't read it for 576),
Watson1953
|
| 2 |
1/29 |
3 |
Homology forests |
slides |
Chapter 1 handout (1/24) |
| 1/31 |
4 |
Probabilistic graphical models |
slides |
Murphy2001 (or related Web site) |
| 3 |
2/5 |
5 |
Models of sequence evolution |
slides |
handout (1/31) |
| 2/7 |
6 |
Inference of ancestral nucleotides |
slides |
Text 8.1-8.3, Pupko2000 |
| 4 |
2/12 |
7 |
Biological text mining (guest lecture by Mark Craven) |
slides |
|
| 2/14 |
8 |
Motif models - EM algorithm |
slides |
Bailey1995, Text ch. 11 (recommended) |
| 5 |
2/19 |
9 |
Motif models - EM algorithm (continued) |
|
|
| 2/21 |
10 |
Motif models - Gibbs sampling |
slides |
Lawrence1993, Text ch. 11 (recommended) |
| 6 |
2/26 |
11 |
Prokaryotic gene finding |
slides |
Salzberg1998, Text 3.1,3.5 |
| 2/28 |
12 |
Eukaryotic gene finding |
slides |
Burge1997, Text 3.2-3.4 |
| 7 |
3/4 |
13 |
Statistical global alignment |
slides |
Text 4.1-4.2 |
| 3/6 |
14 |
Comparative gene finding |
slides |
Pachter2001, Korf2001 |
| 8 |
3/11 |
15 |
Alignment combinatorics |
slides |
Edgar2004a (optional: Edgar2004b) |
| 3/13 |
16 |
Multiple alignment |
slides |
Schwartz2007 |
| Spring Break |
| 9 |
3/25 |
17 |
Pattern matching - Suffix trees/arrays |
slides |
(optional: Ukkonen1995) |
| 3/27 |
18 |
Pattern matching - Locality-sensitive hashing |
slides |
Buhler2001 |
| 10 |
4/1 |
19 |
Alignment of long sequences |
slides |
(recommended: Brudno2003, Bray2003, Delcher2001) |
| 4/3 |
20 |
Whole-genome alignment |
slides |
Darling2004
(optional: chapter 3 of Dewey2006) |
| 11 |
4/8 |
21 |
RNA |
slides |
Text ch. 10.1-10.2 |
| 4/10 |
22 |
SCFGs |
slides |
Text ch. 9 (optional: Sakakibara1994) |
| 12 |
4/15 |
23 |
SCFGs for RNA |
slides |
Klein2003, Rivas2001 |
| 4/17 |
24 |
Cellular networks introduction |
slides |
(recommended: Barabasi2004) |
| 13 |
4/22 |
25 |
Comparative network algorithms |
slides |
(optional: Sharan2006) |
| 4/24 |
26 |
Parameters & polytopes |
slides |
|
| 14 |
4/29 |
27 |
Parametric Inference |
slides |
(optional: Dewey2006) |
| 5/1 |
28 |
Discriminative models |
slides |
Do2006 (optional: Bernal2007) |
| 15 |
5/6 |
29 |
Insertion/deletion models |
slides |
Thorne1991 |
| 5/8 |
30 |
Genotypes & Haplotypes |
slides |
|
