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
á
Comparative Genomics of
Drosophila
á
Evolutionary Analysis of
Avian Flu
á
Results of the Encode
Project
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
Schedule
Monday 18th
Lecture: Models
of Sequence Evolution
Student Activity: Article preparation
Lecture: Statistical
Alignment
Practical: Statistical alignment
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
Grammar Evolution: Biological and Linguistics
Systems Identifiability
Evolution of Biological Networks
Articles to read
Encode paper
discussion
Drosophila paper discussion
Avian Flu paper
discussion
Acknowledgements. Rune Lyngs¿, Garrett Hellenthal, Istvan Miklos, Adam Novak
and Yun Song are thanked for help with the practicals.