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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.
 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
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
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
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
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
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
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
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
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
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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