| Week | Date | Lecture | Topic | Slides | Readings |
|---|
| 1 |
1/23 |
1 |
Course overview |
slides |
|
| 1/25 |
2 |
The trees of life |
slides,
handout figures
|
Watson1953,
Fitch2000,
handout
|
| 2 |
1/30 |
3 |
Models of sequence evolution |
slides |
Text 8.1-8.2, handout |
| 2/1 |
4 |
Inference of ancestral nucleotides |
slides |
Pupko2000, Text 8.3 |
| 3 |
2/6 |
5 |
Motif models - EM algorithm |
slides |
Bailey1995, Text ch. 11 (recommended) |
| 2/8 |
6 |
Motif models - Gibbs sampling |
slides, Gibbs sampling example |
Lawrence1993, Text ch. 11 (recommended) |
| 4 |
2/13 |
7 |
Prokaryotic gene finding |
slides |
Salzberg1998, Text 3.1,3.5 |
| 2/15 |
8 |
Eukaryotic gene finding |
slides |
Burge1997, Text 3.2-3.4 |
| 5 |
2/20 |
9 |
Eukaryotic gene finding (cont.) |
horizontal models |
|
| 2/22 |
10 |
Alignment combinatorics |
slides |
(review 2.1-2.4, if needed) |
| 6 |
2/27 |
11 |
Statistical global alignment |
slides | Text 4.1-4.2 |
| 3/1 |
12 |
Insertion/deletion models |
slides |
Thorne1991 |
| 7 |
3/6 |
13 |
Comparative gene finding |
slides |
Pachter2001, Korf2001 |
| 3/8 |
14 |
Multiple alignment - MUSCLE |
slides |
Edgar2004a (optional: Edgar2004b) |
| 8 |
3/13 |
15 |
Multiple alignment - ProbCons |
slides |
Do2005 |
| 3/15 |
16 |
Multiple alignment - AMAP |
slides |
Schwartz2007 |
| 9 |
3/20 |
17 |
Pattern matching - Suffix trees/arrays |
slides |
(optional: Ukkonen1995) |
| 3/22 |
18 |
Pattern matching - Locality-sensitive hashing |
slides |
Buhler2001 |
| 10 |
3/27 |
19 |
Alignment of long sequences |
slides |
(recommended: Brudno2003, Bray2003, Delcher2001) |
| 3/29 |
20 |
Whole-genome alignment |
slides |
Darling2004
(optional: chapter 3 of Dewey2006) |
| Spring Break |
| 11 |
4/10 |
21 |
RNA |
slides |
Text ch. 10.1-10.2 |
| 4/12 |
22 |
SCFGs |
slides |
Text ch. 9 (optional: Sakakibara1994) |
| 12 |
4/17 |
23 |
SCFGs for RNA |
slides |
Klein2003, Rivas2001 |
| 4/19 |
24 |
Discriminative models |
slides |
Do2006 (optional: Bernal2007) |
| 13 |
4/24 |
25 |
Parameters & polytopes |
slides |
|
| 4/26 |
26 |
Parametric Inference |
slides |
(optional: Dewey2006) |
| 14 |
5/1 |
27 |
Cellular networks introduction |
slides |
(recommended: Barabasi2004) |
| 5/3 |
28 |
Network Inference from Co-Occurrences |
(Guest lecture by Rob Nowak) |
(optional: Rabbat2006) |
| 15 |
5/8 |
29 |
Comparative network algorithms |
slides |
(optional: Sharan2006) |
| 5/10 |
30 |
Biomedical text mining |
slides |
|
