There will be no seminar on 12.11.2012 but the next seminar will be 19.11.2012.

Due to opening of the academic year in University of Helsinki, there is no teaching on 3.9.2012. The first meeting of the seminar is on 10.9.2012.

General

The expected schedule of each presentation session is 60 minutes of presentation, 15 minutes of opponent comments and 15 minutes of audience comments. These times are subject to change and active discussion during the presentations is expected.  Second and third Monday (17. and 24. September) of the course is reserved for one-to-one 20 minute meetings with teacher to discuss about individual topics.

Bellow are possible topics for presentations but the participants are welcomed to propose their own topic. While most of the proposed topics have long histories, the presentations should concentrate on recent whole genome approaches to the problems:

1. Phylogenetic Inference

   1. Estimating Phylogeny

   2. Finding functional sequences by evolutionary conservation

2. Multiple genome alignment

3. Population genetic inference / coalescent theory

   1. Inferring human population history from autosomal genome

      1. Out of Africa

      2. Neanderthal admixture (ABBA-BABA test)

      3. Incomplete Lineage Sorting

   2. Admixture and recent ancestry of an individual

   3. Identifying genomic regions under positive or negative selection

4. Genome Wide Association Studies, Linkage Disequilibrium and genetic architectures

   1. Hypothesis testing, Bayesian analysis

   2. Correcting population stratification

   3. Estimating genetic architecture of a trait (In humans and non-human species)

   4. Genomic Prediction of traits

5. Haplotyping and genotype imputation

   1. Recombination and haplotypes in population

   2. Methods for haplotype inference

   3. Haplotype based association and linkage studies

   4. Haplotype based genotype imputation and improvement (IMPUTE2, Beagle, low-coverage sequencing)

6. Somatic evolution

   1. History of a tumor and timing of somatic mutations

   2. Identifying driver mutations in cancer

7. Heritability

   1. 'Missing' heritability

 Schedule

No seminar on 15. or 22. October

• 10.9. in C220.  Introduction and scheduling. Choosing topics and presentation dates.
• 17.9 One-to-one meetings with students and teacher, in C220
  • 14:00 Kirti and Jian 
  • 14:30 Kristiina
  • 15:00 Hailin
  • 15:30 Juhana
  • On Tuesday 18.9. in Meilahti around B526 Poojitha
• 24.9 One-to-one meetings with students and teacher, 20 minutes each. SLOTS AVAILABLE
  • 14:15 Kristiina
  • 14:45 Juhana(?)
• 1.10 Presentations
  • Anna: Identifying driver mutations in cancer (opp: Poojitha)
• 8.10 Presentations
  • Poojitha: History of a tumor and timing of somatic mutations (opp: Anna)
• 29.10 in C222 Presentations
  • Kristiina: Genome wide disease genetics (opp: Hailin)
• 5.11.Presentations
  • Hailin: Population genetics (needs coordination with Juhana) (opp: Juhana)
• 12.11. Presentations
  • No Seminar!
• 19.11. Presentations
  • Jian: Phylogenetic inference in microbes/animals (opp: Kristiina)
• 26.11. Presentations
  • Juhana: Ancient DNA and history of populations (opp: Jian)