Gulbenkian
Comparative and Integrative Biology
This is a one-week course taught by Jotun Hein and Rune Lyngsø. Examples of projects can be found at Projects. Preparation of the project discussion will take 4-8 hours. Beyond this the course should be self-contained.
Day 1: Molecular Evolution
9.00-10.15 Lecture: Models of Sequence Evolution and Statistical Alignment
10.30-12.00 Practical: Molecular Evolution (Phylogenies – PHYLIP+)
2.00-3.30 Lecture: Molecular Evolution & Comparative Genomics
3.30-5.00 Student Activity: Prepare projects
Day 2: Population Biology and Mapping
9.00-10.00 Lecture: Population Genetics and Gene Genealogies
10.00-11.00 Exercise: Jukes-Cantor and Rate Matrix
11.00-12.00 Lecture: Inferring Recombination Histories
2.00-3.30 Practical: DNA Sequence Analysis (PAML Phase +)
3.30-5.00 Student Activity: Prepare projects
Day 3: Integrative Genomics (IG)
9.00-10.15 Lecture: High Throughput Data, the structure of IG, GF
10.30-12.00 Practical: Statistical Alignment & Footprinting
2.00-3.30 Lecture (L): Grammars and RNA Prediction
3.30-5.00 Student Activity: Prepare projects
Day 4: Integrative Genomics (IG)
9.00-10.00 Lecture: Networks and other concepts
10.00-11.00 Exercise: Stochastic Context Free Grammars
11.00-12.00 Lecture: Concepts, Data Analysis and Functional Studies
2.00-3.30 Practical: Detecting Recombinations
3.30-5.00 Student Activity: Prepare projects
Day 5: Project Discussion/Presentation
9.00-10.00 Project 1 – Population Genomics: 1000 genomes
11.00-12.00 Project 2 – Comparative Genomics: Signals
2.00-3.00 Project 3 – Integrative Genomics: Basic data types
3.00-4.00 Exercise: Statistical Alignment
4.00-5.00 Project 4 – Comparative Biology: Networks
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