Chapters refer to Eidhammer, Jonassen and Taylor if not otherwise stated.
Lecture slides and papers will be accessible in the Student portal (for copyright reasons).
| Week | Date | Topic | Reference |
|---|---|---|---|
| 3 | Mon 16/1 | Orientation meeting. INF280 review: Pairwise alignment by dynamic programming |
Ch. 1 and 2.3 |
| Thu 19/1 | Multiple alignment | Ch. 4 | |
| 4 | Mon 23/1 | Multiple alignment and phylogenetic trees | Ch. 4 |
| Thu 26/1 | Multiple alignment and phylogenetic trees | Ch. 4 | |
| 5 | Mon 30/1 | Scoring matrices | Ch. 5 |
| Thu 2/2 | Profiles | Ch. 6 | |
| 6 | Mon 6/2 | Markov chains | Ewens & Grant Ch. 4.4-4.9 |
| Thu 9/2 | Hidden Markov Models | Ewens & Grant Ch. 11 | |
| 7 | Mon 13/2 | Hidden Markov Models | Ewens & Grant Ch. 11 |
| Thu 16/2 | HMM profiles, patterns | Ch. 6, 7 | |
| 8 | Mon 20/2 | Patterns | Ch. 7 |
| Thu 23/2 | Patterns | Ch. 7 | |
| 9 | Mon 27/2 |
Work on compulsory assignment No lectures! |
|
| Thu 2/3 | |||
| 9 | Mon 6/3 | Introduction to Gene Prediction | |
| Thu 9/3 | Gene prediction: Hidden Markov Models | Krogh et al. (1994) Burge & Karlin (1997) (GENSCAN) |
|
| 10 | Mon 13/3 | Gene prediction: Artificial Neural Networks | Uberbacher & Mural (1991) (GRAIL) Pedersen & Nielsen (1997) Hatzigeorgiou (2002) |
| Thu 16/3 | Evaluation of gene prediction methods | Burset & Guigo (1996) Claverie (1997) |
|
| 11 | Mon 20/3 | Protein structures Review of assignment |
Ch. 8 |
| Thu 23/3 | Protein structures Review of assignment (cont.) |
Ch. 8 | |
| 12 | Mon 27/3 | Superposition and Dynamic Programming | Ch. 9 |
| Thu 30/3 | Classification of protein structures | Ch. 14 | |
| 14 | Mon 3/4 | Structure prediction | Ch. 15 |
| Thu 6/4 | Structure prediction | Ch. 15 | |
| 15-16 | Easter holidays | ||
| 16 | Thu 20/4 | Annotation and Gene Ontology | Gene Ontology Consortium (2000, 2004) |
| 17 | Mon 24/4 | Cancelled | |
| Thu 27/4 | Introduction to proteomics By Ingvar Eidhammer |
||
| 18 | Mon 1/5 | Public holiday | |
| Thu 4/5 | Summing up | ||
| 19 | Mon 8/5 | More summing up (please suggest topics!) | |
| Thu 11/5 10:00-11:30 |
Introduction to microarray data analysis By Inge Jonassen |
Note the time! | |
Oral exam: Tue, May 23