BIOL61220: Theory and Algorithms in Bioinformatics, Autumn 2009
Course Unit Coordinator: Dr Magnus Rattray
Course Unit
Lecturers: Dr Simon
Whelan, Dr Jean-Marc Schwartz
Mathematical prerequisites
Here is a mathematical prerequisites sheet.
Distance learning notes
Download a copy of the associated distance
learning (DL) notes. These are from a closely related but different
course. You can ignore comments about the matlab programming language
which we use on the DL modules. Also, much of the material taught by Simon Whelan and
Jean-Marc Schwartz is not covered in the DL notes.
Lecture slides
Slides
for lectures given by Magnus Rattray
Slides
for lectures given by Jean-Marc Schwartz
Exercises
Exercise
sheet 1
and answers
Exercise
sheet 2
and answers
Exercise
sheet 3
and answers
Previous exam papers
2005
paper
2006
paper
2007
paper
Lecture timetable
- Monday October 26
- 10.00-11.00 Dover Street 0.1.6: Introduction to Probability
- 11.00-12.00 Dover Street 0.1.6: Introduction to Algorithms
- Wednesday October 28
- 10.00-11.00 University Place 2.219: Pairwise Alignment and Dynamic Programming
- 11.00-12.00 University Place 2.219: Score Matrices and Significance
- Monday November 2
- 10.00-12.00 Dover Street 0.1.6: Examples Class 1
- Wednesday November 4
- 10.00-11.00 University Place 2.219: Heuristic Alignment Methods
- 11.00-12.00 University Place 2.219: Introduction to Probabilistic Models
- Monday November 9
- 10.00-11.00 Dover Street 0.1.6: Markov Chains
- 11.00-12.00 Dover Street 0.1.6: Hidden Markov Models (HMMs)
- Wednesday November 11
- 10.00-11.00 University Place 2.219: Profile HMMs
- 11.00-12.00 University Place 2.219: Further HMM Applications
- Monday November 16
- 10.00-12.00 Dover Street 0.1.6: Examples Class 2
- Wednesday November 18 (Jean-Marc Schwartz)
- 10.00-11.00 University Place 2.219: Introduction to dynamic modelling for biology
- 11.00-12.00 University Place 2.219: Elementary differential equations, exponential growth
- Monday November 23 (Jean-Marc Schwartz)
- 10.00-11.00 Dover Street 0.1.6: Systems of first-order equations
- 11.00-12.00 Dover Street 0.1.6: Stability and periodic systems
- Wednesday November 25
- 10.00-11.00 University Place 2.219: Introduction to phylogenetics, UPGMA
- 11.00-12.00 University Place 2.219: Neighbour joining, parsimony, bootstrapping
- Monday November 30 (Simon Whelan)
- 10.00-11.00 Dover Street O.1.6: Probabilistic models of sequence change
- 11.00-12.00 Dover Street O.1.6: Inferring trees
- Wednesday December 2 (Simon Whelan)
- 10.00-11.00 University Place 2.219: Substitution models revisited
- 11.00-12.00 University Place 2.219: Applied Phylogenetics
- Monday December 7 (Simon Whelan)
- 10.00-12.00 Dover Street O.1.6: Examples Class 3
- Monday January 18
- 14.00-16.00 Dover Street O.1.6: Revision class
- Wednesday January 20
- 10.00-12.00 University Place 2.219: Exam question practice