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Course Programme 2010



The course will be held from May 31 - June 11, 2010 (incl.) Please note that due to the limited space, only those registered can participate in the Spring 2010 course.

Lectures and exercises will take place at the Center for Biological Sequence Analysis, DTU, building 208, auditorium 062 (in the basement).

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 some of 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
Another beginner's guide to UNIX


O Monday, May 2


Pair-wise Alignment and Database Searching
9.00-9.45
Introduction to 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 Tuesday, May 3

Multiple Alignment and Phylogeny
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 Wednesday, May 4

Maximum Likelihood Phylogeny
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 Thursday, May 5

Second Generation Sequencing, Genomics, Functional Variation
9.00-10.30
Lecture: Cautionary Tales of Next-generation Sequencing (Dave Ussery) (incl. 20-30min break)
Dave Ussery [PDF]
9.45-10.15
Coffee Break
10.30-11.00
Exercise: NGEN seq. reference_mapping.doc: (2-page document printed on A4.)
Dave Ussery, Ramneek Gupta
11.00-12.00
Next Generation Sequencing Technology: HiSeq
Illumina [PDF]
12.00-13.00
Lunch Break
13.00-16.30
Case story: The ancient genome sequencing project
Ramneek Gupta
Exercise: Genotype to Phenotype
AssemblyPoster.xls: (one page, preferably print on A3 in colour, but A4 should work too. A pair of scissors is needed later)
Ramneek Gupta, Thomas Sicheritz-Ponten
16.30-17.00
Discussion

O Friday, May 6

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
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 Monday, May 9

Hidden Markov Models, Immunological Bioinformatics
9.00-10.00
Introduction to the immune system
Ole Lund
10.00-10.30
Coffee Break
10.30-11.15
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
How to estimate pseudo counts (Answers)
11.15-12.00
MHC binding and MHC polymorphism
Morten Nielsen
12.00-13.00
Lunch Break
13.00-16.30
Exercises:
Weight matrix construction and sequence logos
Morten Nielsen
Development of vaccines against HCV
Morten Nielsen, and Ole Lund
16.30-17.00
Discussion

O Tuesday, May 10

Analysis of gene-expression data on a genome-wide scale
9.00-9:45
Introduction to the DNA microarray technology
Hanne Jarmer
9.45-10.15
Coffee Break
10.15-11.00
Data analysis I: Preprocessing and statistics
Hanne Jarmer
11.15-12.00
Data analysis II: Clustering and dimension reduction
Hanne Jarmer
12.00-13.00
Lunch Break
13.00-14.45
Discussion/exercise I: The technology, preprocessing and statistics -> answers
Hanne Jarmer
14:45-15:00
Break
15.00-16.30
Discussion/exercise II: Clustering and dimension reduction -> answers
Hanne Jarmer

O Wednesday, May 11

Datadriven Prediction
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 Thursday, May 12

Systems biology
Recordings:    Workman: Session 1    Workman: survey + session 2    Workman: Session 3    Workman: session 3 continued    Workman: von mering+cyctoscape    Workman:brief intro to exercise    Workman:exercise continued    Workman:session 4
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
13:00-13:50
Transcription factor binding location analysis (chIP-chip), Active modules approach
13:50-14:00
Break
14:00-14:40
Functional genomics and inferring regulatory pathways
14:40-15:00
Conclusions and wrap-up

O Friday, May 13

Fold Recognition
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
Handout exercise
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