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