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Course Programme 2002

Biological Sequence Analysis and Protein Modelling

The course will be held from April 8 - 19, 2002 (incl.)
Please note that due to the limited space, only those registered can participate in the Spring 2002 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.

Beginner's Guide to UNIX is available on-line.


O Monday, April 8

Pair-wise Alignment

9.00-9.30
Introduction to bioinformatics with focus on the human genome
Søren Brunak
9.30-10.00
Alignment of biological sequences
Anders Gorm Pedersen
10.00-10.30
Coffee Break
10.30-12.00
Global and local pair-wise alignment, similarity scores, statistical significance, and substitution matrix entropies
Anders Gorm Pedersen
Transparencies etc.
12.00-13.00
Lunch Break
13.00-16.30
Exercises: searching databases of nucleotide and amino acid sequences - choice of substitution matrices and gap penalties
Anders Gorm Pedersen and Nikolaj Blom
16.30-17.00
Discussion

O Tuesday, April 9

Databases, World Wide Web and Hidden Markov Models

9.00-10.00
Resources of biomolecular data: sequences, structures and functionality - with emphasis on the human genome
Nikolaj Blom
10.00-10.30
Coffee Break
10.30-12.00
Finding sequence motifs: consensus sequences, weight matrices, information content, sequence logos, and Hidden Markov Models
Anders Krogh
12.00-13.00
Lunch Break
13.00-16.30
Exercises: Exploring Ensembl
Thomas Sicheritz Ponten and Nikolaj Blom
16.30-17.00
Discussion

O Wednesday, April 10

Multiple Alignment and Phylogeny

9.00-10.00
Multiple alignment, sequence profiles, complex evolutionary events
Anders Gorm Pedersen
10.00-10.30
Coffee Break
10.30-12.00
Phylogenetic reconstruction, molecular evolution, parsimony, distance matrix, maximum likelihood, boot-strapping
Anders Gorm Pedersen
12.00-13.00
Lunch Break
13.00-16.30
Exercises: multiple alignments, construction of phylogenetic trees
Anders Gorm Pedersen and Peder Worning
16.30-17.00
Discussion

O Thursday, April 11

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, April 12

Gene Finding

9.00-10.00
Coding and non-coding regions in DNA
Anders Krogh
10.00-10.30
Coffee Break
10.30-12.00
Gene finding in prokaryotes and eukaryotes
Anders Krogh
12.00-13.00
Lunch Break
13.00-16.30
Exercises: Computational gene finding in prokaryotes and eukaryotes
Anders Krogh and Thomas Schou
16.30-17.00
Discussion

O Monday, April 15

Fold Recognition

9.00-10.00
Classification of protein structures (secondary structure prediction and topology)
Ole Lund
10.00-10.30
Coffee Break
10.30-11.15
Fold recognition
Arne Elofsson
11.15-12.00
Evaluation modelling accuracy (CASP/LiveBench/Eva)
Arne Elofsson
12.00-13.00
Lunch Break
13.00-16.30
Exercises: Fold recognition using web servers
Ole Lund and Arne Elofsson
16.30-17.00
Discussion

O Tuesday, April 16

Protein Modelling and Drug Discovery

9.00-09.45
Prediction of drug likeness
Søren Brunak
09.45-10.15
Coffee Break
10.15-11.00
Drug discovery and protein modelling in an industrial setting
Jan Thorleif Pedersen
11.00-12.00
Homology building
Ole Lund
12.00-13.00
Lunch Break
13.00-16.30
Exercises: Homology building using Modeller and SwissModel
Ole Lund and Lars Kiemer
16.30-17.00
Discussion

O Wednesday, April 17

DNA Arrays

9.00-9.45
Introduction to DNA microarray technology (Chapter 1)
Steen Knudsen
9.45-10.15
Coffee Break
10.15-11.00
Normalisation and significance of array data (Chapter 2-5)
Steen Knudsen
11.00-12.00
Developmental disorders and gene expression
Niels Tommerup
12.00-13.00
Lunch Break
13.00-16.30
Exercises:
Normalization of array data
Cluster analysis of array data
Steen Knudsen, Chris Workman, Henrik Bjørn Nielsen
16.30-17.00
Discussion

O Thursday, April 18

Gene Expression and DNA array technology

9.00-10.00
Reverse engineering of array data (Chapter 7)
Steen Knudsen
10.00-10.30
Coffee Break
10.30-12.00
Classification and integration of array data (Chapter 6, 8, 9)
Steen Knudsen
12.00-13.00
Lunch Break
13.00-16.00
Exercises:
Classification of array data
Inferring regulatory networks
Steen Knudsen, Carsten Friis, Hanne Jarmer
16.00-16.30
Discussion

O Friday, April 19

DNA Structure

9.00-10.30
Bioinformatics of Microbial Genomes
Lecture notes
David Ussery
10.30-11.00
Coffee Break
11.00-12.00
Bacterial cromatin, genome organisation and gene expression of E.coli
Lecture notes
David Ussery
12.00-13.00
Lunch Break
13.00-15.00
Exercises: Analysis and visualisation of DNA structures
David Ussery
15.00-17.00
Course Evaluation and perspectives for the future


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