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Course Programme 2009



The course will be held from April 17 - 30, 2009 (incl.) Please note that due to the limited space, only those registered can participate in the Spring 2009 course.

Lectures and exercises will take place at the Center for Biological Sequence Analysis at the Technical University of Denmark, building 208, auditorium 062.

DAILY SCHEDULE:
09:00 - 12:00 Lectures
12:00 - 13:00 Lunch
13:00 - 16:30 (approximately): Exercises
16:30 - 17:00 (approximately): Discussion

For the afternoon exercises you are supposed to log on to one of CBS' central servers using the User ID and password that will be forwarded to you in an email.

Please note: lecturers will be working on powerpoints and handouts until the last minute, so changes may occur!

Setting up your own computer for the course

Beginner's Guide to UNIX


O Friday, April 17


Pair-wise Alignment and Database Searching
Recordings:    Anders: What is Bioinformatics    Anders: Pairwise alignment and database searching    Anders: Exercise summary
9.00-9.45
What is Bioinformatics? [PPT] [PDF]
Anders Gorm Pedersen
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
Slides: [PPT] [PDF]
Handout: [PDF]
Anders Gorm Pedersen
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 Monday, April 20

Multiple Alignment and Phylogeny
Recordings:    Anders: 1st lecture    Anders: 2nd. Lecture    2nd lecture, after handout    Exercise introduction    During Exercise    Exercise summary
9.00-9.45
Multiple alignment and phylogenetic reconstruction [PPT] [PDF]
Anders Gorm Pedersen
9.45-10.15
Coffee Break
10.15-12.00
Multiple alignment and phylogenetic reconstruction (continued)
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 Tuesday, April 21

Maximum Likelihood Phylogeny
Recordings:    Anders: "Assorted issues"    Anders: Max likelihood phylogeny    Exercise introduction + during    Exercise summary
9.00-9.45
Assorted issues in multiple alignment and phylogeny [PPT] [PDF]
Anders Gorm Pedersen
9.45-10.15
Coffee Break
10.15-12.00
Maximum likelihood phylogeny [PPT] [PDF]
Anders Gorm Pedersen
Handout [PDF]    
12.00-13.00
Lunch Break
13.00-16.30
Exercises: Maximum likelihood phylogeny
Anders Gorm Pedersen
16.30-17.00
Discussion

O Wednesday, April 22

Hidden Markov Models and Gene Finding
Recordings:    Morten: HMMs etc. lecture    Claus: gene finding lecture        Gene finding exercise intro    During gene finding exercise    Gene finding exercise summary    Weight matrix + logos exercise
9.00-10.00
Finding sequence motifs: consensus sequences, weight matrices, information content,
sequence logos, and Hidden Markov Models
Handout for the lecture: How to estimate pseudo counts (online students please print out before lecture!)
How to estimate pseudo counts (Answers)
Morten Nielsen
10.00-10.30
Coffee Break
10.30-11.15
Prokaryotic gene finding
Claus Lundegaard
11.15-12.00
Eukaryotic gene finding
Claus Lundegaard   Handout (PDF)
12.00-13.00
Lunch Break
13.00-16.30
Exercises:
Gene finding in eukaryotes
Claus Lundegaard
Weight matrix construction and sequence logos
Morten Nielsen
16.30-17.00
Discussion

O Thursday, April 23

Gene Expression and DNA array technology
Recordings:     H. Bjørn: Introduction     H. Bjørn: Data analysis     Exercise     Exercise 2
9.00-9.45
Introduction to DNA microarray technology
H. Bjørn Nielsen
9.45-10.15
Coffee Break
10.15-12.00
Data analysis: pre-processing and statistics,
H. Bjørn Nielsen
Case story: FARO, Nielsen et al., 2007
H. Bjørn Nielsen
12.00-13.00
Lunch Break
13.00-15.30
Discussion/exercise: questions
H. Bjørn Nielsen

O Friday, April 24

Fold Recognition
Recordings:     Thomas: protein structure     Thomas: protein structure, 2     Morten: structure prediction     Morten: Fold recognition     Exercise summary
9.00-9.45
Protein Structure
Thomas Blicher
9.45-10.15
Coffee Break
10.15-11.00
Protein Local Structure Prediction
Morten Nielsen
11.15-12.00
Fold Recognition
Morten Nielsen
12.00-13.00
Lunch Break
13.00-16.30
Exercises: Fold recognition using web servers
Morten Nielsen
16.30-17.00
Discussion

O Monday, April 27

Datadriven Prediction
Recordings:    Brunak: 1st lecture    Brunak: 2nd lecture    Anders: exercise intro    Exercise 2 summary (2008)
9.00-10.00
Neural networks for biological sequence analysis
Søren Brunak
10.00-10.30
Coffee Break
10.30-11.30
Neural network prediction systems - signal peptides and gene structure
Søren Brunak
11.30-12.00
Neural networks for prediction of diverse, systems biology related categories
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 and Henrik Nielsen
16.30-17.00
Discussion

O Tuesday, April 28

Protein Modelling and Drug Discovery
Recordings:     Thomas Nordahl: 1st lecture     Thomas Blicher: 2nd lecture     Irene: Drug design     Exercise 1     Drug design exercise intro     Drug design, during exercise
9.00-09.45
Gene Discovery by use of MySQL
Thomas Nordahl Petersen  
09.45-10.15
Coffee Break
10.15-11.00
Homology modeling and model evaluation
Thomas Blicher  
11.15-12.00
Drug design
Irene Kouskoumvekaki  
12.00-13.00
Lunch Break
13.00-16.30
Exercises: Homology modeling , Drug design
Thomas N. Petersen, Thomas Blicher & Irene Kouskoumvekaki

O Wednesday, April 29

Systems biology
Recordings:     Chris: overview     Chris: survey     Chris: biological networks     Chris: exercise discussion     Chris: cytoscape introduction and TF binding location analysis     Chris: Cytoscape session and conclusion
9:00-10:00
Overview, Survey, Motivation for Systems Biology Lecture slides, *** Click Here to take survey ***
10:00-10:20
Coffee Break
10:20-10:50
Interaction networks: data and properties
10:50-11:10
Discussion: Pluses and minuses of HTP interaction data sets Questions, von Mering et al., Slides
11:10-11:20
Break
11:20-12:00
Exercise: Protein interaction networks and network properties , RUAL.subset.sif , RUAL.subset.names.tab
12:00-13:00
Lunch Break
13:00-13:30
Transcription factor binding location analysis (chIP-chip), Active modules approach
13:30-14:30
Exercise: Integrating gene expression data with protein interaction data (Active Modules)
14:30-14:45
Break
14:45-15:15
Functional genomics and inferring regulatory pathways
15:15-15:45
Finish Cytoscape exercises 1 and 2, explore more advanced usage
15:45-16:00
Conclusions and wrap-up

O Thursday, April 30

Immunological Bioinformatics
Recordings:    Ole, 1st lecture    Morten, 2nd lecture    Ole, 3rd lecture    Exercise 1 intro    During exercise 1    Exercise 1 summary    Exercise 2 intro    During exercise 2    Exercise 2 summary
9.00-09.30
Introduction to the immune system
Ole Lund
9.30-10.00
Antibody responses to linear and conformational epitopes
Ole Lund
10.00-10.30
Coffee Break
10.30-11.15
MHC binding and MHC polymorphism
Morten Nielsen
11.15-12.00
Processing, prediction integration, and rational epitope selection.
Ole Lund
12.00-13.00
Lunch Break
13.00-14.00
Exercises: Predictions of B cell epitopes in proteins
Ole Lund
14.00-14.30
Break
14.30-16.30
Exercises: Development of vaccines against HCV
Morten Nielsen
16.30-17.00
Discussion




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