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The course will start on Thursday, 7 September, 2006 at 13:00. Lectures, journal clubs and exercises will take place at the Center for Biological Sequence Analysis, in building 210, room 48 at the Technical University of Denmark, Lyngby. There is no textbook for this course. Links to PDF files for relevant papers will be provided on this web page (see below). This is the fifth year for this course. Links to the course programme for
Oslo, Norway, October 2006,
Brazil, August 2006,
Autumn semester 2005,
Thailand, March 2005,
Autumn semester 2004,
2003 and
2002.
Link to DNA Atlas pages
Final report due 30 November, 2006
 Thursday, 14 September, 2006
Introduction to Bioinformatics methods for Comparison of Bacterial Genomes
Dave Ussery
- 13.00-13.45
- An Introduction to Sequences as Biological Information
Link to pdf file of lecture notes (preliminary, fra Brazil wkshp)
- 13.45-14.00
- Break
- 14.00-14.45
- An Introduction to Comparative Genomics
Link to pdf file of lecture notes (preliminary, fra Brazil wkshp)
- 14.45-15.00
- Break
- 15.00-16.30
- Introduction to the course structure and Computer Exercises.
Literature:
10 Years of Bacterial Genomics
Thursday, 21 September, 2006
Introduction to DNA Structures in Genomes
- 13.00-14.30
-
Computer Exercises - Introduction to UNIX; From DNA Sequence information to gene information
with Kristoffer Kiil.
- 14.30-15.15
- Lecture 1 - "DNA Structures from A- to Z."
Link to pdf file of lecture notes (preliminary, fra Brazil wkshp)
- 15.15-15.30
- Break
- 15.30-16.30
- Lecture 2 - "Finding Replication Origins"
Link to pdf file of lecture notes (preliminary, fra Brazil wkshp)
Literature:
DNA Structure: A-, B-, and Z-DNA Families
Origins of Replication in Circular Bacterial Chromosomes
CBS Genome Atlas database
Thursday, 28 September, 2006
DNA Curvature and Flexibility in Bacterial Chromosomes
- 13.00-13.45
- Lecture 1 - "DNA Curvature and Flexibility"
Link to pdf file of lecture notes (preliminary, fra Brazil wkshp)
- 13.45-14.00
- Break
- 14.00-15.30
-
Computer Exercises - Constuction of Chromosome Atlases
with Kristoffer Kiil.
- 15.30-15.45
- Break
- 15.45-17.00
- Lecture 2 - "Global Regulation of Gene Expression"
Link to pdf file of lecture notes (preliminary, fra Brazil wkshp)
Literature:
DNA Structure: A-, B-, and Z-DNA Families
Bias of purine and pyr/pur stretches
Purine bias in bacterial genomes
DNA Structural Atlases
BaseAtlas, RepeatAtlas and GenomeAtlas
The Atlas Visualisation of Genome-wide Information
Thursday, 5 October, 2006
Comparative Genomics
- 13.00-13.45
- Lecture 1 - "20 Methods to Compare Genomes"
Link to pdf file of lecture notes (preliminary, fra Brazil wkshp)
- 13.45-14.00
- Break
- 14.00-14.45
- Lecture 1 - "Pan-Genomics of Escherichia coli"
Link to pdf file of lecture notes (preliminary, fra Brazil wkshp)
- 14.45-15.00
- Break
- 15.00-16.30
-
- Computer Exercises - Codon Usage and AT content
with Kristoffer Kiil.
Literature:
10 Years of Bacterial Genomics
CBS Genome Atlas database
Thursday, 12 October, 2006
Regulation of Gene Expression
- 13.00-13.45
- Lecture 2 - "Sigma Factors"
- 13.45-14.00
- Break
- 14.00-14.45
- Lecture 1 - "Transcription Factors"
- 14.45-15.00
- Break
- 15.00-16.30
-
- Computer Exercises - Finding Sigma-Factors and Two-Component Signal Transduction Systems
with Kristoffer Kiil.
Literature:
Sigma Factors
Two-component signal transduction systems
Thursday, 19 October, 2006
Autumn Break
Thursday, 26 October, 2006
Bacterial Taxonomy
- 13.00-13.45
- Lecture 1 - "Prediction of Membrane and Secreted Proteins"
- 13.45-14.00
- Break
- 14.00-16.30
-
- Computer Exercises - Consruction of 16S rRNA Trees
with Kristoffer Kiil.
Literature:
rRNA comparisons
Thursday, 2 November, 2006
Proteome Comparison
- 13.00-13.45
- Lecture 1 - "BLAST Comparison of Bacterial Proteomes"
- 13.45-14.00
- Break
- 14.00-15.30
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- Computer Exercises - Constuction of BLAST Matrices and BLAST Atlases
with Kristoffer Kiil.
- 15.30-15.45
- Break
- 15.45-16.30
- Journal Club - Group 2
Literature:
Blast Matrices
Proteome Comparisons
Thursday, 9 November, 2006
Bacterial Pathogenesis
- 13.00-13.45
- Lecture 1 - "Bacterial Virulence Networks"
Guest lecture by Tim Binnewies
- 13.45-14.00
- Break
- 14.00-14.30
- Journal Club - Group 1
"Comparison between avian and human influenza A virus reveals a mutational bias on the viral genomes"
Journal of Virology in the pressNovember, 2006. PubMed
- 14.30-14.45
- Break
- 14.45-16.30
-
- Computer Exercises - Protein Localisation
with Kristoffer Kiil.
Literature:
Membrane Proteins
Secreted Proteins
TMHMM
Thursday, 16 November, 2006
Metagenomics
- 13.00-13.45
- Lecture 1 - "Metagenomics"
Link to pdf file of lecture notes (preliminary, fra Brazil wkshp)
- 13.45-14.00
- Break
- 14.00-14.30
- Journal Club - Group 2
- 14.30-14.45
- Break
- 14.45-16.30
-
- Computer Exercises - 2-Dimensional Clustering of Bacterial Chromosomal Properties
with Kristoffer Kiil.
Literature:
2-D clustering
Thursday, 23 November, 2006
Thanksgiving
- 13.00-13.30
- Journal Club - Group 3
Thursday, 30 November, 2006
No class today; Final Reports due!
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