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Course Programme 2004




The course will be held from April 19 - 30, 2004 (incl.)
Please note that due to the limited space, only those registered can participate in the Spring 2004 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 19



Pair-wise Alignment
9.00-9.45
Introduction to bioinformatics with focus on the human, mouse and rat genomes
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   Lecture notes
12.00-13.00
Lunch Break
13.00-16.30
Exercises: searching databases of nucleotide and amino acid sequences
Anders Gorm Pedersen and Lars Kiemer
16.30-17.00
Discussion

O Tuesday, April 20


Multiple Alignment and Phylogeny
9.00-9.45
Resources of biomolecular data: sequences, structures and functionality - with emphasis on the human genome
Nikolaj Blom   Lecture notes
9.45-10.15
Coffee Break
10.15-12.00
Multiple alignment and phylogenetic reconstruction
Anders Gorm Pedersen
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, April 21


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 Thursday, April 22


Immunology and Phylogeny
9.00-9.45
Immunological bioinformatics
Ole Lund  Lecture notes
9.45-10.15
Coffee Break
10.15-12.00
Bayes and maximum likelihood phylogeny
Anders Gorm Pedersen
12.00-13.00
Lunch Break
13.00-16.30
Exercises: Phylogenetic analysis of viral evolution
Anders Gorm Pedersen and Ole Lund
16.30-17.00
Discussion

O Friday, April 23


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
Morten Nielsen   Lecture notes
10.00-10.30
Coffee Break
10.30-12.00
Eukaryotic gene finding
Nikolaj Blom   Lecture notes
12.00-13.00
Lunch Break
13.00-16.30
Exercises:
Hidden Markov model and weight matrix construction
Morten Nielsen
Gene finding in eukaryotes.
Nikolaj Blom
16.30-17.00
Discussion

O Monday, April 26


Fold Recognition
9.00-10.00
Fold recognition
Ole Lund
Lecture notes:   Classification of protein structure   Fold recognition  Comparative modelling
10.00-10.30
Coffee Break
10.30-11.15
Homology building
Ole Lund
11.15-12.00
Evaluation modelling accuracy (CASP/LiveBench/Eva)
Morten Nielsen   Lecture notes
12.00-13.00
Lunch Break
13.00-16.30
Exercises: Fold recognition using web servers
Claus Lundegaard and Morten Nielsen
16.30-17.00
Discussion

O Tuesday, April 27


Protein Modelling and Drug Discovery
9.00-09.45
Gene Discovery by use of MySQL
Thomas Nordahl Petersen
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
11.00-12.00
Classification of protein structures (secondary structure prediction and topology)
Claus Lundegaard   Lecture notes
12.00-13.00
Lunch Break
13.00-16.30
Exercises: Homology modeling
Thomas N. Petersen, Ole Lund and Lars Kiemer
16.30-17.00
Discussion

O Wednesday, April 28


DNA Arrays
9.00-9.45
Introduction to DNA microarray technology
Steen Knudsen   Lecture notes (Chapter 1-3)
9.45-10.15
Coffee Break
10.15-11.00
Normalisation and significance of array data
Steen Knudsen   Lecture notes (Chapter 4)
11.00-12.00
Developmental disorders and gene expression
Niels Tommerup
12.00-13.00
Lunch Break
13.00-16.30
Exercises:
Probe design
Probe design II - notes
GenePublisher
Steen Knudsen, Henrik Bjørn Nielsen, Rasmus Wernersson
16.30-17.00
Discussion

O Thursday, April 29


Gene Expression and DNA array technology
9.00-10.00
PCA, clustering and classification (Chapter 5, 6, 10)
Agnieszka S. Juncker
10.00-10.30
Coffee Break
10.30-11.15
Promoter analysis, pathway analysis and inference of regulatory networks (Chapter 7, 8, 9)
Steen Knudsen
11.15-12:00
Case story: Arabidopsis transcriptomics
Henrik Bjørn Nielsen
12.00-13.00
Lunch Break
13.00-16.00
Exercises:
Classification of array data
Inferring regulatory networks
Carsten Friis, Hanne Jarmer, Hanni Willenbrock, Agnieszka S. Juncker
16.30-17.00
Discussion

O Friday, April 30


DNA Structure
9.00-10.30
Bioinformatics of Microbial Genomes
David Ussery   Lecture notes
10.30-11.00
Coffee Break
11.00-12.00
Bacterial cromatin, genome organisation and gene expression of E.coli
David Ussery   Lecture notes
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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