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Course Programme 2006



The course will be held from May 8 - 19, 2006 (incl.)
Please note that due to the limited space, only those registered can participate in the Spring 2006 course.

Lectures and exercises will take place at the Center for Biological Sequence Analysis at the Technical University of Denmark, building 208, room 007, in Lyngby.

DAILY SCHEDULE:
Lectures will be from 9 - 12 am,
Lunch from 12 - 13, and,
Exercises from 13 - 16.30 pm.
Discussion from 16.30 - 17.00 pm.


O Monday, May 8


Pair-wise Alignment and Database Searching
9.00-9.45
Introduction to bioinformatics and systems biology
Søren Brunak
9.45-10.15
Coffee Break
10.15-12.00
Pairwise sequence alignment and database searching: global and local alignments, substitution matrices, gap penalties, statistical significance
Anders Gorm Pedersen Handout (PDF)
12.00-13.00
Lunch Break
13.00-16.30
Exercises: searching databases of nucleotide and amino acid sequences
Anders Gorm Pedersen
16.30-17.00
Discussion

O Tuesday, May 9

Multiple Alignment and Phylogeny
9.00-9.45
Resources of biomolecular data: sequences, structures and functionality - with emphasis on the human genome
Nikolaj Blom
9.45-10.15
Coffee Break
10.15-12.00
Multiple alignment and phylogenetic reconstruction
Anders Gorm Pedersen Handout (PDF)
12.00-13.00
Lunch Break
13.00-16.30
Exercises: multiple alignments, construction of phylogenetic trees
Anders Gorm Pedersen
16.30-17.00
Discussion

O Wednesday, May 10

Immunology and Phylogeny
9.00-9.45
Immunological bioinformatics
Claus Lundegaard
9.45-10.15
Coffee Break
10.15-12.00
Maximum likelihood phylogeny
Anders Gorm Pedersen
Handout (PDF)
12.00-13.00
Lunch Break
13.00-16.30
Exercises: Maximum likelihood phylogeny
Anders Gorm Pedersen and Rodrigo Oliveira
16.30-17.00
Discussion

O Thursday, May 11

Gene Expression and DNA array technology
9.00-9.45
Introduction to DNA microarray technology
Carsten Friis  
9.45-10.15
Coffee Break
10.15-11.00
PCA, clustering and classification
Agnieszka S. Juncker
11.15-12:00
Epistasis analysis by microarray data
Chris Workman
12.00-13.00
Lunch Break
13.00-16.30
Exercise: Probe design using OligoWiz 2.0    Lecture Notes
Rasmus Wernersson

Exercise: Classification of array data
Agnieszka S. Juncker
16.30-17.00
Discussion

O Friday, May 12

No class ("Store bededags" holiday).


O Monday, May 15

DNA Structure
9.00-9.45
Introduction to Comparative Genomics
David Ussery
9.45-10.15
Coffee Break
10.15-11.00
Chromatin and Gene Expression in E.coli
David Ussery
11.00-11.15
Break
11.15-12.00
Comparative Microbial Genomics
David Ussery
12.00-13.00
Lunch Break
13.00-16.30
Exercises: Comparative Bacterial Genomics
David Ussery
16.30-17.00
Discussion

O Tuesday, May 16

Hidden Markov Models and Gene Finding
9.00-10.00
Finding sequence motifs: consensus sequences, weight matrices, information content,
sequence logos, and Hidden Markov Models

Ole Lund
10.00-10.30
Coffee Break
10.30-12.00
Eukaryotic gene finding
Nikolaj Blom   Handout (PDF) ONLINE PARTICIPANTS: PLEASE PRINT BEFORE LECTURE
12.00-13.00
Lunch Break
13.00-16.30
Exercises:
Hidden Markov model and weight matrix construction
Ole Lund
Gene finding in eukaryotes.
Nikolaj Blom
16.30-17.00
Discussion

O Wednesday, May 17

Fold Recognition
9.00-9.45
Protein Structure
Thomas Blicher
9.45-10.15
Coffee Break
10.15-11.00
Protein Secondary Structure Prediction
Pernille Andersen
11.15-12.00
Fold Recognition
Ole Lund
12.00-13.00
Lunch Break
13.00-16.30
Exercises: Fold recognition using web servers
Claus Lundegaard and Ole Lund
16.30-17.00
Discussion

O Thursday, May 18

Datadriven Prediction
9.00-10.00
Datadriven prediction methods and neural networks
Søren Brunak
10.00-10.30
Coffee Break
10.30-11.30
Applications: learning from evolution to predict protein structure
Søren Brunak
11.30-12.00
Application: prediction of post-translational modifications and protein function
Søren Brunak
12.00-13.00
Lunch Break
13.00-16.30
Exercises: signal peptide prediction, neural network training, performance measures and evaluation of prediction quality
Søren Brunak
16.30-17.00
Discussion

O Friday, May 19

Protein Modelling and Drug Discovery
9.00-09.45
Gene Discovery by use of MySQL
Thomas Nordahl Petersen   Lecture notes
09.45-10.15
Coffee Break
10.15-11.00
Computational decision support for drug design. Profilling of small molecule compound libraries
Anne Marie Munk Jørgensen   Lecture notes
11.15-12.00
Homology modeling and model evaluation
Thomas Blicher   Lecture notes
12.00-13.00
Lunch Break
13.00-15.00
Exercises: Homology modeling
Thomas N. Petersen, Thomas Blicher
15.00-16.00
Course Evaluation and perspectives for the future


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