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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 quite a lot of material under each topic. The idea is to concentrate on the most important matters and not to present all algorithmic details and variations. (Note, however, that some algorithmic details are important!)

The length of the presentations should be 20 min. (Maximally a total of 30 min, including the discussion.) Note that the time limit is strict when there are three presentations within 90 min!

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. Raul Lozano
SSK, Ch.4 (20p.)+ DEKM, Ch.3 (34p.), (supplementary material BB, Ch.7-8 (58p.)): An introduction to hidden Markov models for biological sequences (an overview of the methods)
  Jouni Seppänen DEKM, Ch.4: Pairwise alignment using HMMs (20p.)
10.10. Anne Patrikainen
DEKM, Ch.5: Profile HMMs for sequence families (34p.)
  Juha Alaluusua DEKM, Ch.6: Multiple sequence alignment methods (26p)
17.10. Eero Vaarnas
SM, Ch.4: Fragment assembly of DNA (38p.)
  Jukka Laurila SM, Ch.5: Physical mapping of DNA (32p.)
24.10. Janne Sinkkonen
SM, Ch.6: Phylogenetic trees (40p.),(supplementary material DEKM: Ch.7 (32p.))
  Jarkko Salojärvi DEKM, Ch.8: Probabilistic approaches to phylogeny (41p.), (supplementary material BB, Ch.10 (12p.))
31.10. Olli-Pekka Rinta-Koski
SM, Ch.7: Genome rearrangements (30p.)
  Markku Roiha SM, Ch.8: Molecular structure prediction (16p.)
7.11. Antonio Villena
DEKM, Ch.9: (Stochastic) transformational grammars (27p.), (supplementary material BB, Ch.11 (22p.)
  Ismo Haanaho DEKM, Ch.10: (Probabilistic) RNA structure analysis (39p.)
14.11. Jarkko Venna
SSK, Ch.11: Statistical analysis of protein structures (20p.)
  Jörkki Hyvönen SSK, Ch.12: Analysis and algorithms for protein sequence-structure alignment (For a group of 2 people) (58p.)
21.11. (NOTE! Read the introduction papers to micro array methods before this day!) Satu Nahkuri Microarrays and gene regulatory networks

Chen et al.: Identifying gene regulatory networks from experimental data, ACM RECOMB 1999, pp.94-103
Brazma et al.: Predicting gene regulatory elements in silico on a genomic scale, Brazma et al., Genome, vol 8, pp.1202-1215, 1998))
  Mika Inki SSK, Ch.14: From computer vision to protein structure and association (22p.)
  Vesa Siivola SSK, Ch.15: Modeling biological data and structure with probabilistic networks (20p)
28.11. (time has changed!) Invited speakers
Symposium on bioinformatics
5.12. Petri Loukasmäki
Microarrays and gene expression clustering

Ben-Dor:Clustering gene expression patterns , ACM recomb 1999, pp.33-42
Tamayo et al.: Interpreting patterns of gene exspression with self-organizing maps: Methods and application to hetopoietic differentiation, Proc.Natl.Acad.Sci.USA, vol96,pp.2907-2912,1999
Eisen et al.: Cluster analysis and display of genome-wide expression patterns PNAS USA, vol95, pp. 14863-14868,1998)
  Matti Aksela SSK, Ch.7: Computational gene prediction using neural networks and similarity search (20p.)
  Harri Laakso SSK, Ch.10: Decision trees and Markov chains for gene finding (20p.)
12.12. Julian Cobos Microarrays and gene expression analysis and classification

Brown et al.: Knowledge-based analysis of microarray gene expression data by using support vector machines, PNAS 2000, vol 97.,pp.262-267
Alter et al.: Singular Value decomposition for genome-wide expression data processing and modeling, PNAS 2000, vol.97,pp.10101-10106
  Ville Könönen
SSK, Ch.13: THREADER: protein sequence threading by double dynamic programming (28p.)

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Tuesday, 21-Nov-2000 16:26:05 EET