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
Lecture: Models of Sequence Evolution
Student Activity: Article preparation
Lecture: Statistical Alignment
Lecture: Phylogenies and The Tree of Life
Student Activity: Article discussion
Student Activity: Project preparation
Student Activity: Project discussion
Lecture: Inferring Recombination Histories
Grammar Evolution: Biological and Linguistics
Evolution of Biological Networks
Articles to read
Acknowledgements. Rune Lyngsø, Garrett Hellenthal, Istvan Miklos, Adam Novak and Yun Song are thanked for help with the practicals.