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Course Programme 2008



The course will be held from May 19 - 30, 2008 (incl.) Please note that due to the limited space, only those registered can participate in the Spring 2008 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 Monday, May 19


Pair-wise Alignment and Database Searching
Recordings:    Henrik Nielsen 1st lecture    Henrik Nielsen, 2nd. Lecture    Exercise introduction    Exercise introduction, part 2    During exercise    Exercise summary
9.00-9.45
What is Bioinformatics? [PPT] [PDF]
Henrik Nielsen
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]
Henrik Nielsen
12.00-13.00
Lunch Break
13.00-16.30
Exercises: searching databases of nucleotide and amino acid sequences
Henrik Nielsen
16.30-17.00
Discussion
Evaluation form, May 19


O Tuesday, May 20

Multiple Alignment and Phylogeny
Recordings:    Anders, 1st lecture    Anders, 2nd. Lecture    Anders, 2nd lecture, after handout    Exercise introduction    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
Evaluation form, May 20


O Wednesday, May 21

Maximum Likelihood Phylogeny
Recordings:    Anders, 1st lecture    Anders, 2nd. Lecture    Exercise introduction    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]     Handout results: [PDF]
12.00-13.00
Lunch Break
13.00-16.30
Exercises: Maximum likelihood phylogeny
Anders Gorm Pedersen
16.30-17.00
Discussion
Evaluation form, May 21


O Thursday, May 22

Hidden Markov Models and Gene Finding
Recordings:    Morten, HMM    Claus, gene finding    Gene finding exercise intro    Gene finding exercise    T cell epitope exercise intro    T cell epitope exercise    T cell epitope exercise, summary
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!)
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
Hidden Markov model and weight matrix construction
Morten Nielsen
16.30-17.00
Discussion
Evaluation form, May 22


O Friday, May 23

Gene Expression and DNA array technology
Recordings:    Hanne, micro array intro    Bjørn, analysis    Bjørn, case story    Exercises intro    Exercises, session 2    Exercises, last session
9.00-9.45
Introduction to DNA microarray technology
Hanne Jarmer
9.45-10.15
Coffee Break
10.15-12.00cd
Data analysis: pre-processing and statistics, Case story: FARO Nielsen et al., 2007
H. Bjørn Nielsen
12.00-13.00
Lunch Break
13.00-15.30
Discussion/exercise: questions answers
H. Bjørn Nielsen
Evaluation form, May 23


O Monday, May 26

Fold Recognition
Recordings:     Thomas, protein structure     Morten, secondary structure     Morten, fold recognition     Intro to exercise     Exercise summary
9.00-9.45
Protein Structure
Thomas Blicher
9.45-10.15
Coffee Break
10.15-11.00
Protein Secondary 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
Claus Lundegaard and Morten Nielsen
16.30-17.00
Discussion
Evaluation form, May 26


O Tuesday, May 27

Protein Modelling and Drug Discovery
Recordings:     Thomas Nordahl, partial recording     Thomas Blicher     Olivier Taboureau     Thomas N, Exercise-intro     Thomas N, exercise summary     Olivier, exercise intro     Olivier, exercise details     Olivier, exercise summary
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
Olivier Taboureau  
12.00-13.00
Lunch Break
13.00-16.30
Exercises: Homology modeling , Drug design
Thomas N. Petersen, Thomas Blicher & Olivier Taboureau
Evaluation form, May 27


O Wednesday, May 28

Datadriven Prediction
Recordings:    Brunak 1    Brunak 2    Brunak 3    Exercise intro    During exercise 1    Exercise 1 summary + exercise 2 intro    During exercise 2    Exercise 2 summary
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
Evaluation form, May 28


O Thursday, May 29

Systems biology
Recordings:     Chris Workman 1     Chris Workman 2     Chris Workman 3     Chris Workman 4
9:00-9:50
Overview and pre-module survey/quiz, Motivation for Systems Biology Lecture slides, Survey/Quiz
9:50-10:20
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
Evaluation form, May 29


O Friday, May 30

Immunological Bioinformatics
Recordings:    Claus, 1st lecture    Pernille, 2nd lecture    Morten, 3rd lecture    Claus, 4th lecture    B-cell exercise, intro    B-cell exercise summary    HCV vaccine exercise intro    HCV vaccine exercise summary
9.00-09.30
Introduction to the immune system
Claus Lundegaard
9.30-10.00
Antibody responses to linear and conformational epitopes
Pernille Andersen
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.
Claus Lundegaard
12.00-13.00
Lunch Break
13.00-14.00
Exercises: Predictions of B cell epitopes in proteins
Pernille Andersen
14.00-14.30
Break
14.30-16.30
Exercises: Development of vaccines against HCV
Morten Nielsen
16.30-17.00
Discussion


Evaluation form, May 30



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