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Tik-61.181 Timetable
The first topics will be assigned on 19.9., and the rest on 26.9.There is a relatively lot material under each topic so the idea is not to present all algorithmic details and variations. The details will be considered in the exercises.
References to books:
SM: Setubal & Meidanis
SSK: Salzberg, Searls, Kasif
DEKM: Durbin, Eddy, Krogh, Mitchison
BB: Baldi & Brunak - this is only complementary material
| Date | Speaker | Topic |
|---|---|---|
| 19.9. | Heikki Mannila, Sami Kaski | Opening lecture, general information. |
| 26.9. |
The topics and the rest of the timetable will be fixed. Homework: read Ch. 1-2 of Setubal & Meidanis (S&M) |
|
| Teemu Karevaara | Sequence comparison. S&M: Ch. 3.1-3.4. | |
| Ville Viitaniemi | Database search + other issues. S&M: Ch. 3.5-3.6. | |
| 3.10. | SSK, Ch.4 + DEKM, Ch.3, myös BB, Ch.7-8: An introduction to hidden Markov models for biological sequences (1 presentation: an overview of the methods + exercise) (20p.+34p.+58p.) |
|
| DEKM, Ch.4: Pairwise alignment using HMMs (20p.) | ||
| 10.10. | DEKM, Ch.5: Profile HMMs for sequence families (34p.) |
|
| DEKM, Ch.6: Multiple sequence alignment methods (26p) | ||
| 17.10. | SM, Ch.4: Fragment assembly of DNA (38p.) |
|
| SM, Ch.5: Physical mapping of DNA (32p.) | ||
| 24.10. | SM, Ch.6: Phylogenetic trees (also DEKM: Ch.7) (40p.+32p.) |
|
| DEKM, Ch.8: Probabilistic approaches to phylogeny, myös BB, Ch.10 (41p.+12p.) ("comparison of probabilistic and non-probabilistic methods": exercise) | ||
| 31.10. | SM, Ch.7: Genome rearrangements (30p.) |
|
| SM, Ch.8: Molecular structure prediction (16p.) | ||
| 7.11. | DEKM, Ch.9: (Stochastic) transformational grammars, myös BB, Ch.11 (27p.+22p.) |
|
| DEKM, Ch.10: (Probabilistic) RNA structure analysis (39p.) | ||
| 14.11. | SSK, Ch.11: Statistical analysis of protein structures (20p.) |
|
| SSK, Ch.12: Analysis and algorithms for protein sequence-structure alignment (For 2 people together!) (58p.) | ||
| 21.11. | SSK, Ch.13: THREADER: protein sequence threading by double dynamic programming (28p.) |
|
| SSK, Ch.14: From computer vision to protein structure and association (22p.) | ||
| SSK, Ch.15: Modeling biological data and structure with probabilistic networks (20p) | ||
| 28.11. | SSK, Ch.5: Case-based reasoning driven gene annotation (22p.) |
|
| SSK, Ch.7: Computational gene prediction using neural networks and similarity search (20p.) | ||
| SSK, Ch.10: Decision trees and Markov chains for gene finding (20p.) | ||
| 5.12. (time may change!) | Invited speakers | Symposium on bioinformatics |
12.12. | Microarrays |
jnikkila@mail.cis.hut.fi
Friday, 22-Sep-2000 08:36:09 EEST