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 |
|
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