Advanced Bioinformatics - #27614

The course starts on August 30, 2005 at 13:00. Lectures will be held Tuesday afternoons and exercises Friday mornings. Lectures and exercises will take place at the Center for Biological Sequence Analysis at the Technical University of Denmark, building 208, Auditorium 051, in Lyngby.

Evaluation: written examination, 4 hours without books (pocket calculator is allowed). Scale of marks (0-13), internal examiner.

Tuesday, August 30 Pair-wise Alignment and Database Searching 13.00-13.45 Introduction to bioinformatics with focus on the human, mouse and rat genomes Søren Brunak 13.45-14.00 Coffee Break 14.00-17.00 Pairwise sequence alignment and database searching: global and local alignments, substitution matrices, gap penalties, statistical significance Anders Gorm Pedersen   Handout (PDF)  , Lecture notes, Compendium: Alignment (Volume 1) Friday, September 2 09.00-12.00 Exercises: searching databases of nucleotide and amino acid sequences Anders Gorm Pedersen Tuesday, September 6 Hidden Markov Models and Gene Finding 13.00-13.45 Finding sequence motifs: consensus sequences, weight matrices, information content, sequence logos, and Hidden Markov Models Morten Nielsen   Lecture notes PDF  13.45-14.00 Coffee Break 14.00-17.00 Eukaryotic gene finding Nikolaj Blom   Handout (PDF)   Lecture notes Compendium: Computational Prediction of Eukaryotic Protein-coding Genes, Michael Q. Zhang, Nature Reviews Genetics, 2002. Methods Applied in Immunological Bioinformatics, in Immunological Bioinformatics, O. Lund, M. Nielsen, C. Lundegaard, C. Kesmir, S. Brunak, 2005. An Introduction to Hidden Markov Models for Biological Sequence Analysis, Anders Krogh, in Computational Methods in Molecular Biology, S. Salzberg, D. Searls and S. Kasif (eds.), 1998 Friday, September 9 09.00-12.00 Exercises: Hidden Markov model and weight matrix construction Morten Nielsen Gene finding in eukaryotes. Nikolaj Blom Tuesday, September 13 Multiple Alignment and Phylogeny 13.00-13.45 Resources of biomolecular data: sequences, structures and functionality - with emphasis on the human genome Nikolaj Blom   Lecture notes 13.45-14.00 Coffee Break 14.00-17.00 Multiple alignment and phylogenetic reconstruction Anders Gorm Pedersen Handout (PDF)   Lecture notes Compendium: User's Guide, Question 1, Supplement to Nature Genetics, 2002. Friday, September 16 09.00-12.00 Exercises: multiple alignments, construction of phylogenetic trees Rasmus Wernersson and Claus Lundegaard Tuesday, September 20 Phylogeny 14.00-17.00 Maximum likelihood phylogeny Anders Gorm Pedersen   Handout (PDF)   Lecture notes Compendium: Class 20: Likelihood Methods and Estimation of Model Parameters, Paul O. Lewis, 2002. Friday, September 23 09.00-12.00 Exercises: Maximum likelihood phylogeny Anders Gorm Pedersen and Rodrigo Oliveira Compendium: Phylogenetic Methods Come of Age: Testing Hopotheses in an Evolutionary Context, J.P. Huelsenbeck and B. Rannala, Science, 1997. Inference of selection from multiple species alignments, Ziheng Yang, Current Opinion in Genetics and Development, 2002. Tuesday, September 27 Protein Modelling and Drug Discovery 13.00-13.45 Protein Secondary Structure: Classification and Prediction Claus Lundegaard Lecture notes 13.45-14.00 Coffee Break 14.00-15.30 Computational decision support for drug design. Profilling of small molecule compound libraries Anne Marie Munk Jørgensen   Lecture notes 15.30-17.00 Gene Discovery by use of MySQL Thomas Nordahl Petersen   Lecture notes Compendium: Bioinformatics: The Machine Learning Approach, Søren Brunak and Pierre Baldi 120-133 Friday, September 30 09.00-12.00 Exercises: Homology modeling Thomas N. Petersen, Anne Mølgaard Tuesday, October 4 Fold Recognition 13.00-13.45 Protein Structure Anne Mølgaard   Lecture notes 13.45-14.00 Coffee Break 14.00-15.30 Fold Recognition Morten Nielsen   Lecture notes 15.30-17.00 Homology modeling and model evaluation Anne Mølgaard   Lecture notes Compendium: Homology Modelling, E. Krieger, S.B. Nabuurs, G. Vriend in Structural Bioinformatics, 2003 Friday, October 7 09.00-12.00 Exercises: Fold recognition using web servers Claus Lundegaard and Morten Nielsen Tuesday, October 11 Datadriven Prediction 13.00-13.45 Datadriven prediction methods and neural networks Søren Brunak   Lecture notes 13.45-14.00 Coffee Break 14.00-15.15 Applications: learning from evolution to predict protein structure Søren Brunak   Lecture notes 15.15-17.00 Application: prediction of post-translational modifications and protein function Søren Brunak   Lecture notes Friday, October 14 09.00-12.00 Exercises: signal peptide prediction, neural network training, performance measures and evaluation of prediction quality Søren Brunak Tuesday, October 25 DNA Arrays 13.00-13.30 Introduction to DNA microarray technology H. Bjørn  Nielsen; Lecture notes 13.30-13.45 Coffee Break 13.45-14.15 Normalisation of microarray data H. Bjørn  Nielsen; Lecture notes 14.15-17.00 Statistical alalysis of microarray data H. Bjørn  Nielsen; Lecture notes Curriculum: Knudsen, S. (2004) Guide to Analysis of DNA Microarray Data, 2nd edition (Chapter 1-4) Friday, October 28 09.00-10.00 GenePublisher Carsten Friis 10.15-12.00 Probe design using OligoWiz 2.0 (Exercise introduction) Rasmus Wernersson   Exercise guide   OligoWiz 2.0 server Tuesday, November 1 Gene Expression and DNA array technology 13.00-13.45 PCA, clustering and classification Agnieszka S. Junker Lecture notes 13.45-14.00 Coffee Break 14.00-16.00 Case story: Using Microarrays to Study Cell Cycle Regulation Ulrik de Lichtenberg Lecture notes Curriculum: Knudsen, S. (2004) Guide to Analysis of DNA Microarray Data, 2nd edition (Chapter 5, 6, 10) Friday, November 4 09.00-12.00 Exercises: Classification of array data Inferring regulatory networks , Lecture Carsten Friis Tuesday, November 8 Systems Biology 13.00-13.30 Introduction to Systems Biology Søren Brunak  13.30-14.00 Coffee Break 14.00-14.45 Proteomics technologies and protein-protein interaction Anders Hinsby   Lecture notes 14.45-15.00 Break 15.00-16.00 Disease gene finding Kasper Lage Hansen   Lecture notes Compendium: Systems Biology (section) Friday, November 11 09.00-12.00 Exercises: Exercise in Data Integration and Systems Biology Carsten Friis Tuesday, November 15 Comparative Bacterial Genomics 13.00-13.45 Introduction to Comparative Genomics David Ussery   Lecture notes (pdf) (ppt) 13.45-14.00 Coffee Break 14.00-16.00 Chromatin and Gene Expression in E.coli David Ussery   Lecture notes (pdf) (ppt) Friday, November 18 09.00-12.00 Exercises: Comparative Bacterial Genomics David Ussery Tuesday, November 22 Industrial Bioinformatics 13.00-14.00 Bioinformatics at Novozymes A/S Peter Bjarke Olsen 14.00-14.15 Coffee Break 14.15-15.00 Bioinformatics at AstraZeneca Peder Worning 15.15-16.00 Immunological bioinformatics Ole Lund  Lecture notes Compendium: Identifying cytotoxic T cell epitopes from genomic and proteomic information: The human MHC project, S.L. Lauemoller et al., Reviews in Immunogenetics, 2001. Friday, November 25 Work through of last year exam 9.00-12.00 Exercise: exercise notes, Larst year exam part I Rasmuss Wernersson Tuesday, November 29 13.00-17.00 Exercise: exercise notes, Larst year exam part II H. Bjørn  Nielsen Friday, December 2 09.00-10.00 Questions to last year exam Some answers and statistics from last years exam H. Bjørn  Nielsen, Morten Nielsen and David Ussery Monday, December 19 Exam 09.00-13.00 Exam ('Lokale 116/19 + 40') You may bring: books, notes and pocket calculator Scale of marks (0-13), internal examiner

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