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MSc-level Course

Introduction to Bioinformatics,Course 27011

Spring   2002


Preliminary Course Programme


The classes will be held Tuesdays from 13:00 - 17:00 in building 208, auditorium 51.
The first lecture will be on Tuesday, February 5. The course will end on Tuesday, May 14.
Need to brush up on basic molecular biology? Select any of these on-line primers/textbooks: Genomics 101, CSH: DNA from the beginning, DNA and Molecular Genetics


Computer exercises: general instructions

Tuesday 5/2S. Brunak: Introduction.
L.J. Jensen:Sequence Comparison
L.J. Jensen: Pairwise alignment and database searches I
(Durbin et al: Chapter 2)
Tuesday 12/2 A.G.Pedersen: Multiple Alignment
(Durbin et al., chapter 6)
A.G. Pedersen: Phylogeny (Case Study: HIV)
Se lecture notes and paper on phylogeny in binder.
Tuesday 19/2L.J. Jensen: Pairwise alignment and database searches II
(Durbin et al: Chapter 2)
A. Krogh: Weight matrices, regular expressions, and hidden Markov models.
See Introduction to Hidden Markov Models in binder
Tuesday 26/2A. Krogh: Hidden Markov Models and Profile HMMs.
Tuesday 5/3A. Krogh: Genome Projects and Gene Finding.
Tuesday 12/3S. Brunak: Non-linear prediction by neural networks, sequence and category representation, internal representation of sequence space, signal peptide prediction, cross-validation and performance measures.
(Baldi and Brunak: Chapter 5 and 6.4, binder: Linjedeling med neuralt netvaerk)
Tuesday 19/3S. Brunak: Neural network model of the genetic code, intron splice site prediction, neural network weight analysis, training a neural network for protein secondary structure prediction.
(Baldi and Brunak: Chapter 6)
Ramneek Gupta: Predicting post-translational modifications using neural networks.
See slides on PTMs in binder
Performance evaluation

Passover

Tuesday 2/4S. Brunak: Prediction of protein secondary and tertiary structure, protein function
(Baldi and Brunak: Chapter 6)
Tuesday 9/4D. Ussery: DNA symmetry elements and their meanings
See binder for papers on atlases.
D. Ussery: A DNA Structural Atlas for Escherichia coli
Tuesday 16/4S. Knudsen: Analysis of DNA Microarray Data
(Baldi and Brunak: pp 5-11; Binder: Analysis of DNA Array Data.
N. Tolstrup, Exiqon A/S: Guest Lecture - Bioinformatics in an industrial setting
Tuesday 23/4Start of individual projects. Show up for lecture only if you have not yet signed up on web.
23/4 - 14/5 Individual Projects
Tuesday 14/5Reports due

Literature:


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