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Bioinformatics: In-Depth (Spring 2012)
Open Positions
Research
- Current status of the Orthologous Matrix Project
- OMA browser
- Lecture
Wed 15-17 Uni Zurich Irchel, Y35-F-32 - Exercises
Wed 17-19 Uni Zurich Irchel, Y35-F-32 - (If you will be using a terminal from windows on your own computer, please get a ssh client such as putty.exe as the department does not allow insecure connections such as that provided from the Windows terminal program.)
Please also consult the other webpage of the course!
| Week/Date | Topic | Slides | Exercise | Lecturer |
|
PART I: Probabilities and Statistics |
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| 22.02 | Basic Probabilities and Statistics |
bi12lec1.pdf |
bi10ex1.pdf |
SM |
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29.02 |
Statistical Estimation and Testing |
|
SM | |
|
07.03 |
Markov Chains |
SM | ||
|
14.03 |
Evolutionary Models and Substitution Matrices |
SM |
||
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21.03 |
Sequence Comparison and Statistical Theory Behind BLAST |
SM | ||
| PART II: Systems Biology | ||||
|
28.03 |
Biochemical reaction network modeling I | IO | ||
|
04.04 |
Biochemical reaction network modeling II |
lec0404.pdf ExampleEpo.pdf |
Ex1matlab.zip Ex2.pdf |
IO |
|
18.04 |
Bayesian networks I |
Lec1804.pdf |
Ex3.pdf |
IO |
|
25.04 |
Bayesian networks II |
lec2504.pdf |
IO | |
| PART III: Sequence Analysis and Phylogenetics | ||||
|
02.05 |
Multiple Sequence Alignments |
BioInf2_MSA.pdf |
Exercise | MG |
|
09.05 |
Orthology, Paralogy, Xenology |
BioInf2_Orthology.pdf |
Exercise |
MG |
|
16.05 |
Basic Phylogenetic Tree Reconstruction |
PhylogenyInferenceMaria2011_part1.pdf |
Exercise Quizz |
MA |
|
23.05 |
Advanced topics in Phylogenetics |
PhylogenyInferenceMaria2011_part2.pdf |
Exercise |
MA |
|
30.05 |
Positive Selection with Codon Models |
Positive selection lecture |
Exercise |
MA |
Resources
Recommended Readings
- Ewens and Grant: Statistical methods in bioinformatics. Springer (2001)
- Durbin, Eddy, Krogh and Michison: Biological sequence analysis. CUP (1998)
- Yang Z: Computational Molecular Evolution. OUP (2006)
New Book describing the state-of the art in statistical methodology for Evolutionary Genomics (Springer):
vol. 1: ISBN 978-1-61779-581-7
vol. 2: ISBN 978-1-61779-584-8
Buy with a 25-35% discount from MA
Darwin
- Getting started with Darwin
- Darwin Online Help
- Introduction to Darwin bio-recipe
- Darwin Quick Reference
- Download darwin (new URL!) to install it on your own computer.
- The SwissProt database which can be used for larger analyses, e.g. the Dayhoff matrix bio-recipe.
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