Graduate course: Analysis of sequence data (in two parts).

Part I: Basic coalescent theory (Paul Joyce, University of Idaho, USA, and Martin Lascoux, EBC). September 6-10 2004
Part II: Applications (Gil McVean, University of Oxford, UK and Martin Lascoux, EBC). Spring 2005. Tentative date: 14/3-17/3 (this may change later on).

Credits: 4 points (2 for attendance + 2 for homework). If only one part is attended 2 points.

Aim of the course: Introduce the necessary theoretical background to carry out the analysis of DNA sequence data (part 1) and go through various applications (estimation of population recombination rate, detection of recombination hotspots, detection of selection, estimation of past demographics, part 2).

Target group: Students studying evolutionary biology in general, especially those using genetics. The course will also be relevant for students working in gene mapping.

Recommended background: Basic knowledge of genetics, basic knowledge of  basic probability and statistics

Content: Lectures, Exercises, Computer based assignments. Simulation and analysis of empirical datasets.

Preliminary outline:

Part I
Intro, basic probability, stochastic processes, statistics.
The standard coalescent
Estimation of parameters. Computationally simple methods.
Estimation of parameters.  Computationally intensive methods
Extension of the coalescent: Recombination and selection graphs

Part II
The coalescent: a reminder
Modelling and detecting selection
Recombination: Estimating the population recombination rate
LD and haplotypes. Haplotype blocks
Association mapping

Registration: Send an email to Martin Lascoux at Martin.Lascoux@ebc.uu.se before August 1. You can register for only one part, but I strongly recommend attending both as they complement each other. For those coming from other universities please note that we do not arrange housing.

Both Paul and Gil are outstanding teachers. Paul already gave a course at the EBC a few years ago along the same lines. Here is one of the many positive comments on the course: "cheers for a great course which gave me lots of ideas for analysing data and thinking about polymorphism.  As I mentioned at the time, I really wish I had gone to such a course when I was a postgrad" (one of the postdoctoral fellow that attended the course).

Welcome!

Martin

Martin Lascoux
Program in Conservation Biology & Genetics
Evolutionary Biology Centre
Uppsala University
Norbyvägen 18D 752 36 UPPSALA
SWEDEN

Tel: 46 18 471 64 16
Fax: 46 18 471 64 24