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Course Programme 2005




The course will be held from April 4 - 15, 2005 (incl.)
Please note that due to the limited space, only those registered can participate in the Spring 2005 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.

The Bulletin Board - YaBB is now up and running at http://www.cbs.dtu.dk/cgi-bin/yabb/YaBB.cgi.
You need to register the first time you go in there. When you've registered, you will receive an email confirmation including a password.

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

EVALUATION FORMS



O Monday, April 4


Pair-wise Alignment and Database Searching
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   Handout (PDF)   Lecture notes
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, April 5

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 PDF 
10.00-10.30
Coffee Break
10.30-12.00
Eukaryotic gene finding
Nikolaj Blom   Handout (PDF)   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 Wednesday, April 6

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 Handout (PDF)   Lecture notes
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 Thursday, April 7

Immunology and Phylogeny
9.00-9.45
Immunological bioinformatics
Ole Lund  Lecture notes
9.45-10.15
Coffee Break
10.15-12.00
Maximum likelihood phylogeny
Anders Gorm Pedersen   Handout (PDF)   Lecture notes
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 Friday, April 8

Datadriven Prediction
9.00-10.00
Datadriven prediction methods and neural networks
Søren Brunak   Lecture notes
10.00-10.30
Coffee Break
10.30-11.30
Applications: learning from evolution to predict protein structure
Søren Brunak   Lecture notes
11.30-12.00
Application: prediction of post-translational modifications and protein function
Søren Brunak   Lecture notes
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 Monday, April 11

Fold Recognition
9.00-10.00
Protein Structure
Anne Mølgaard   Lecture notes
10.00-10.30
Coffee Break
10.30-11.15
Fold Recognition
Morten Nielsen   Lecture notes
11.15-12.00
Homology modeling and model evaluation
Anne Mølgaard   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 12

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
11.00-12.00
Protein Secondary Structure: Classification and Prediction
Pernille Andersen   Lecture notes
12.00-13.00
Lunch Break
13.00-16.30
Exercises: Homology modeling
Thomas N. Petersen, Anne Mølgaard
16.30-17.00
Discussion

O Wednesday, April 13

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   Lecture notes
12.00-13.00
Lunch Break
13.00-16.30 Exercises:
13.00 GenePublisher
Steen Knudsen
14.00 Probe design using OligoWiz 2.0 (Exercise introduction)
Rasmus Wernersson   Exercise guide   OligoWiz 2.0 server
16.30-17.00
Discussion

O Thursday, April 14

Gene Expression and DNA array technology
9.00-10.00
PCA, clustering and classification (Chapter 5, 6, 10)
Steen Knudsen   Lecture notes
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: Using Microarrays to Study Cell Cycle Regulation
Ulrik de Lichtenberg Lecture notes
12.00-13.00
Lunch Break
13.00-16.00
Exercises:
Classification of array data
Inferring regulatory networks
Steen Knudsen
16.30-17.00
Discussion

O Friday, April 15

DNA Structure
9.00-9.45
Introduction to Comparative Genomics
David Ussery   Lecture notes
9.45-10.15
Coffee Break
10.15-11.00
Chromatin and Gene Expression in E.coli
David Ussery   Lecture notes
11.00-11.15
Break
11.15-12.00
Comparative Microbial Genomics
David Ussery   Lecture notes
12.00-13.00
Lunch Break
13.00-15.00
Exercises: Comparative Bacterial Genomics
David Ussery
15.00-17.00
Course Evaluation and perspectives for the future





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