BSA - Course Program 2011

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Biological Sequence Analysis >> Course Program 2011

The Biological Sequence Analysis course will be held from May 2 - May 13, 2011 (incl.) Lectures and exercises will take place at the Center for Biological Sequence Analysis, DTU, building 208, auditorium 062 (in the basement). Online students should use the links to online lectures under the header for each day.

Computer Setup: Both onsite and online students will use their own computer for the course. Please follow these instructions carefully and make sure your computer is ready well before the course starts. Please note that there will not be time to help individual students setting up computers once the course has started.

For some of the afternoon exercises you are supposed to log on to one of CBS' central servers using a User ID and password that will be provided to you.

Please note: lecturers will be working on slides and other course material until the last minute, so changes may occur!

These UNIX resources may be useful: Beginner's Guide to UNIX Another beginner's guide to UNIX

Lecture Schedule

Monday May 2: Pair-wise Alignment and Database Searching

Online lecture
Recordings First lecture Second lecture Third lecture Summing-up
9.00-9.45
Introduction to Bioinformatics PDF
Anders Gorm Pedersen
9.45-10.15
Coffee Break
10.15-12.00
Pairwise sequence alignment and database searching: 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

Tuesday May 3: Multiple Alignment and Phylogeny

Online lecture
Recordings First lecture Second lecture Third lecture Summing-up
9.00-9.45
Multiple alignment and phylogenetic reconstruction 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

Wednesday May 4: Maximum Likelihood Phylogeny

Online lecture
Recordings First lecture Second lecture + handout Summing-up
9.00-9.45
Assorted issues in multiple alignment and phylogeny PDF
Anders Gorm Pedersen
9.45-10.15
Coffee Break
10.15-12.00
Maximum likelihood phylogeny 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

Thursday May 5: Second Generation Sequencing, Genomics, Functional Variation

Online lecture
Recordings First lecture Second lecture SOLiD and Ion Torrent SNP Leukemia sequencing Summing-up
9.00-9.45
Lecture: The human genome project: a historical perspective on sequencing PDF
Dave Ussery
9.45-10.05
Coffee Break /NOTE:reduced break/
10.05-10.45
Lecture: Sequencing - 2nd and 3rd generation technologies PDF
Dave Ussery
10.45-11.00
Short break
11.00-12.00
Next Generation Sequencing Technology: SOLiD and Ion Torrent (brief)
Lifetech
12.00-13.00
Lunch Break - 20 mins. delay,
13.20-14.00 (delayed start)
Exercise-1: NGEN seq. reference_mapping.doc: (2-page document printed on A4 with Courier-New Font.)
Exercise-2: Next-gen sequencing, de-novo assembly
AssemblyPoster.xls: (one page, preferably print on A3 in colour, but A4 should work too. A pair of scissors is needed later)
Ramneek Gupta
14.00-14.45
Case story: SNP risk profiling in childhood acute lymphoblastic leukaemia PDF
Agata Wesolowska
Case story: Genotype-to-phenotype, Genes to faces
Hanne Jarmer
14.45-16.30
Genotype-to-Phenotype: The 4,000 year old 'Ancient' Genome
Exercise-3: Genotype to Phenotype
16.30-17.00
Discussion

Friday May 6: Gene and Drug Discovery

Online lecture
Recordings First lecture Second lecture Third lecture Cytoscape + ChemProt Summing-up
9.00-09.45
Gene Discovery by use of MySQL: PPT
Thomas Nordahl Petersen
09.45-10.15
Coffee Break
10.15-12.00
Chemoinformatics in Drug design: PPT
Systems Chemical Biology: PPT
Irene Kouskoumvekaki
12.00-13.00
Lunch Break
13.00-13.30
Introduction to ChemProt and Cytoscape PPT
Sonny Nielsen
13.30-16.30
Exercises: Drug design Systems Chemical Biology
Irene Kouskoumvekaki & Sonny Nielsen
16.30-17.00
Discussion


Monday May 9: Hidden Markov Models, Immunological Bioinformatics

Online lecture
Recordings First lecture Second lecture Third lecture Summing-up
9.00-9.45
Introduction to the immune system, Finding sequence motifs: consensus sequences, weight matrices, information content, sequence logos, and Hidden Markov Models: PDF
Ole Lund
9.45-10.15
Coffee Break
10.15-11.00
MHC binding and MHC polymorphism, MHC class II epitopes, B cell epitopes: PDF
Ole Lund
1.00-11.15
Coffee Break
11.15-12.00
Applications of immunological bioinformatics: PDF
Ole Lund
12.00-13.00
Lunch Break
13.00-16.30
Exercises:
Weight matrix construction and sequence logos
Ole Lund
Development of vaccines against HCV
Ole Lund
16.30-17.00
Discussion

Tuesday May 10: Analysis of gene-expression data on a genome-wide scale

Online lecture
Recordings First lecture (partial) First lecture+ (last year) Second lecture Third lecture + discussion
9.00-9.45
Introduction to the DNA microarray technology: PPT
H. Bjørn Nielsen
9.45-10.15
Coffee Break
10.15-11.00
Data analysis I: Preprocessing and statistics: PDF
H. Bjørn Nielsen
11.15-12.00
Data analysis II: Clustering and dimension reduction: PDF
H. Bjørn Nielsen
12.00-13.00
Lunch Break
13.00-14.45
Discussion/exercise I: The technology, preprocessing and statistics: PDF -> answers
H. Bjørn Nielsen
14.45-15.00
Break
15.00-16.30
Discussion/exercise II: Clustering and dimension reduction: PDF -> answers
H. Bjørn Nielsen

Wednesday May 11: Datadriven Prediction

Online lecture
Recordings First lecture Second lecture Exercises Summing-up
9.00-10.00
Neural networks for biological sequence analysis: PPT
Søren Brunak
10.00-10.30
Coffee Break
10.30-11.30
Neural network prediction systems - signal peptides and gene structure: PPT
Søren Brunak
11.30-12.00
Neural networks for prediction of diverse, systems biology related categories: PPT
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

Thursday May 12: Systems biology

Online lecture
Recordings First lecture Second lecture (partial) Second lecture (last year) Third lecture
Intro to Cytoscape Cytoscape discussion + fourth lecture Fifth lecture
9.00-10.00
Overview, Survey, Motivation for Systems Biology: PPT,
10.00-10.20
Coffee Break
10.20-10.50
Interaction networks: data and properties: PPT
10.50-11.10
Discussion: Pluses and minuses of HTP interaction data sets: PPT
Questions, von Mering et al. paper
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: PPT
13.50-14.00
Break
14.00-14.40
Functional genomics and inferring regulatory pathways: PPT
14.40-15.00
Conclusions and wrap-up

Friday May 13: Protein Homology Modeling, Psi-Blast and Fold Recognition

Online lecture
Recordings First lecture Second lecture Third lecture Exercise intro
NOTE: Exercise part of program is ok now, but talks will not be ready until Friday 13'th
9.00-9.45
Protein Structure: PDF
Thomas Holberg Blicher
9.45-10.15
Coffee Break
10.15-11.00
Homology modelling: PDF
Thomas Holberg Blicher
11.15-12.00
Fold Recognition: PDF
Thomas Holberg Blicher
12.00-13.00
Lunch Break
13.00-16.30
Exercise: Homology modeling and fold recognition.
Thomas Nordahl Petersen & Thomas Holberg Blicher
16.30-17.00
Discussion
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