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Advanced Bioinformatics - #27614

Course Programme - Fall 2005

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.


O 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)

O Friday, September 2

09.00-12.00
Exercises: searching databases of nucleotide and amino acid sequences
Anders Gorm Pedersen

O 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

O Friday, September 9

09.00-12.00
Exercises:
Hidden Markov model and weight matrix construction
Morten Nielsen
Gene finding in eukaryotes.
Nikolaj Blom

O 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.

O Friday, September 16

09.00-12.00
Exercises: multiple alignments, construction of phylogenetic trees
Rasmus Wernersson and Claus Lundegaard

O 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.

O 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.

O 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

O Friday, September 30

09.00-12.00
Exercises: Homology modeling
Thomas N. Petersen, Anne Mølgaard

O 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

O Friday, October 7

09.00-12.00
Exercises: Fold recognition using web servers
Claus Lundegaard and Morten Nielsen

O 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

O Friday, October 14

09.00-12.00
Exercises: signal peptide prediction, neural network training, performance measures and evaluation of prediction quality
Søren Brunak

O 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)

O 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

O 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)

O Friday, November 4

09.00-12.00
Exercises:
Classification of array data

Inferring regulatory networks , Lecture
Carsten Friis

O 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)

O Friday, November 11

09.00-12.00
Exercises: Exercise in Data Integration and Systems Biology
Carsten Friis


O 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)

O Friday, November 18

09.00-12.00
Exercises: Comparative Bacterial Genomics
David Ussery

O 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.

O Friday, November 25

Work through of last year exam
9.00-12.00
Exercise: exercise notes, Larst year exam part I
Rasmuss Wernersson

O Tuesday, November 29
13.00-17.00
Exercise: exercise notes, Larst year exam part II
H. Bjørn  Nielsen

O 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

O 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