Jotun Hein: Topics in Evolutionary Biology of Genomes 18-20.2.08


  The plan for the three days arranged by me are as follows.  Every item last 90 minutes.  I will lecture 2 times 90 minutes every day.  There will be 2 computer practicals, 2 periods where you discuss/prepare 3 articles and 3 projects.  There will be 1 period for presenting the 3 articles and 1 period for discussion of projects.


Lectures: There are no lecture notes, so you should download the lectures and go through them on your computer and prepare questions that you can ask during the lecture.  You are welcome to email me suggestions/questions, as I have a little to improve/correct the material.


Practicals – instructions can be downloaded at the above link.


Article discussion/presentation will be done in 3 groups that you make.  The are focussed on three major topics


Project discussion/presentation will be done in 3 groups that you make – not necessarily the same as for articles. It should be a critical discussion.  Do you like the ideas in the project?  Are they realistic?  Have they been done before? Do you have your own suggestions?

    Read Evolving Biological Grammars. Other projects of relevance to this could be, Artifacts from Combining Hidden Markov Models and possibly the report Combining different grammars to make multiple annotations of a single sequence.

    Read Identifiability of a Simple Biological System. Other projects of possible relevance Parameter and Sensitivity Analysis for Large System of ODEs, Evolving Dynamical Systems – case study: Cell Cycle and The Structure of the Computational Biosciences.  The last is very drafty.

    Read MCMC Integration over Evolutionary Histories of Metabolic Networks.  Possible other projects of relevance Evolving Dynamical Systems – case study: Cell Cycle and the report Evolution of metabolic networks





Monday 18th

Lecture: Models of Sequence Evolution

Student Activity: Article preparation

Lecture: Statistical Alignment

Practical: Statistical alignment (Statistical Alignment Programs)


Tuesday 19th

Lecture: Phylogenies and The Tree of Life

Student Activity: Article discussion

Lecture: Molecular Evolution & Comparative Genomics

Student Activity: Project preparation


Wednesday 20th

Lecture: Coalescent Theory & Population Genetics

Student Activity: Project discussion

Lecture: Inferring Recombination Histories

Practical: Recombination (Beyond Phylogenies Programs)


Projects to discuss

Grammar Evolution: Biological and Linguistics

Systems Identifiability

Evolution of Biological Networks


Articles to read

Coalescent HMM

Drosophila paper  discussion

Avian Flu paper  discussion



Genome Analysis & Bioinformatics Group

Summer project paper

Bioinformatics workshop


Acknowledgements.  Rune Lyngsø, Garrett Hellenthal, Istvan Miklos, Adam Novak and Yun Song are thanked for help with the practicals.