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Advanced Bioinformatics - #27614Course Programme - Fall 2006
The course starts on September 05, 2006 at 13:00. Lectures will be held Tuesday afternoons and exercises Friday mornings. Please fill in the course evaluation on Campusnet Some information about the exam ... (last changed 2006-12-10 23:45:38) Tuesday, September 05 Alignments, Phylogeny and Database Searching Anders Gorm Pedersen 13.00-13.45 Introduction to bioinformatics with focus on the human, mouse and rat genomes 13.45-14.00 Coffee break 14.00-15.30 Pairwise sequence alignment and database searching: global and local alignments, substitution matrices, gap penalties, statistical significance Handout (PDF), Lecture notes Friday, September 08 09.00-12.00 Tuesday, September 12 13.00-16.00 Multiple alignment and phylogenetic reconstruction Handout (PDF) Lecture notes (PPT)
Friday, September 15 09.00-12.00 Tuesday, September 19 13.00-16.00 Maximum likelihood phylogenyHandout (PDF) Lecture notes (PPT) Anders Gorm Pedersen Friday, September 22 09.00-12.00 Exercise: Maximum likelihood phylogeny Tuesday, September 26 Gene Expression and DNA array technology Henrik Bjoern Nielsen 13.00-13.45 Introduction to DNA microarray technology Array group 13.45-14.00 Coffee break 14.00-17.00 Data analysis: pre-processing and statistics slides (pdf) Friday, September 29 09.00-10.00 Case story 10.00-12:00 Microarray discussion (group work) (answers to exercise) Tuesday, October 03 --- As the Array block has been compressed to one week, there will be no lectures and exercises this week Friday, October 06 --- no exercise Tuesday, October 10 Protein Modelling, Drug Discovery and Fold recognition Ole Lund 13.00-13.45 Protein Secondary Structure: Classification and Prediction (slides) 13.45-14.00 Coffee break 14.00-14.45 Industry lecture: Computational decision support for drug discovery. Property profiling and virtual screening of small molecule libraries (slides) Anne Marie Munk Jørgensen Friday, October 13 09.00-12.00 Exercise: Homology modeling Thomas N. Petersen, Thomas Blicher Tuesday, October 17 13.00-13.45 Efterårsferie Friday, October 20 09.00-12.00 Efterårsferie Tuesday, October 24 13.00-13.45 Protein Structure (slides) 13.45-14.00 Coffee break 14.00-15.30 Fold Recognition 15.30-17.00 Homology modeling and model evaluation (slides) Friday, October 27 09.00-12.00 Exercise: Fold recognition using web servers Claus Lundegaard, Ole Lund Tuesday, October 31 Datadriven Predictions and gene finding with Hidden Markov Models and Neural Networks Thomas Nordahl Petersen 13.00-13.45 Datadriven prediction methods and neural networks (slides) 13.45-14.00 Coffee break 14.00-15.30 Applications: learning from evolution to predict protein structure (slides) 15.30-17.00 Application: prediction of post-translational modifications and protein function Friday, November 03 09.00-12.00 Exercise: Signal peptide prediction, neural network training, performance measures and evaluation of prediction quality Tuesday, November 07 13.00-13.45 Immunological bioinformatics (slides) 13.45-14.00 Coffee break 14.00-15.30 Eukaryotic gene finding (slides) Friday, November 10 09.00-12.00 Exercise: Gene finding in eukaryotes Tuesday, November 14 13.00-13.45 The essential role of biological hypothesis in microarray based
research - Meaningful data integration in high throughput biology 14.00-16.00 Jens Viktor Noergaard Friday, November 17 10.00-12.00 Finding sequence motifs: consensus sequences, weight matrices, information content, sequence logos, and Hidden Markov models (slides) Tuesday, November 21 Systems Biology and Comparative Genomics Dave Ussery 13.00-13.45 20 Methods to Compare Microbial Genomes (slides) 13.45-14.00 Coffee break 14.00-15.30 Global Regulation of Gene Expression in Microbial Genomes(slides) Friday, November 24 09.00-09:45 Industrial lecture: Peder Worming, Astra (slides) 10.00-12.00 Exercise: Comparative Bacterial Genomics(slides) Tuesday, November 28 13.00-13.45 Introduction to Systems Biology(slides) 13.45-14.00 Coffee break 14.00-14.45 Proteomics technologies and protein-protein interaction(slides) 15.00-16.00 Disease gene finding(slides) Friday, December 01 09.00-12.00 Exercise: Data Integration and Systems Biology Carsten Friis Tuesday, December 05 --- No lectures. The students are encouraged to go over last years exam and prepare ev. questions to the teachers on Friday 8/12. Friday, December 08 09.00-12.00 Questions to last year exam Tuesday, December 19 15.00-19.00 Exam |