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The course will start on Monday, 7 March, 2005 at 9:00. Lectures, journal clubs and exercises will take place at Room no. 127, BIOTEC Building, Science Park, Pathumthani, Thailand
There is no textbook for this course. Links to PDF files for relevant papers will be provided on this web page (see below).
Link to DNA Atlas pages
 Monday 7 March, 2005
Introduction
- 9.00-9.30
- Introduction to CBS and the workshop
Link to pdf file of lecture notes
- 9.30-10.00
- Coffee Break and informal discussion
- 10.00-11.00
- Lecture: An Overview of Microbial Genomes
Link to pdf file of lecture notes
- 11.00-11.15
- Break
- 11.15-12.00
- Journal Club: Introductory example by Tim Binnewies and Dave Ussery
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- 12.00-13.00
- Lunch Break
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- 13.00-14.00
- Lecture: An Introduction to Biological Sequence Information
Link to pdf file of lecture notes
- 14.00-14.15
- Break
- 14.15-16.30
- Computer Exercises: How to Make DNA Atlases from a GenBank of Fasta file: Using BLAST to compare genomes
- 16.30-17.00
- Discussion of results from Computer Excercises.
Literature:
Genome update: 161 prokaryotic genomes sequenced, and counting
Genome update: Length distributions of sequenced prokaryotic genomes
Genome Update: chromosome atlases
Tuesday 8 March, 2005
DNA Structures and Their Functions in Genomes
- 9.00-10.00
- Lecture: An Introduction to Bioinformatic Methods: AT content in bacterial genomes
Link to pdf file of lecture notes
- 10.00-10.15
- Coffee Break
- 10.00-10.45
- DNA repeats and structures in bacterial genomes
Link to pdf file of lecture notes
- 10.45-11.00
- Break
- 11.00-12.00
- Discussion
-
- 12.00-13.00
- Lunch
-
- 13.00-17.00
- Computer Exercises
Literature:
DNA Structure: A-, B-, and Z-DNA Families
Bias of purine stretches in sequenced chromosomes
DNaseI hypersensitive sites in the cystic fibrosis gene
Environmental Influences on DNA Curvature
DNA Denaturation
DNA bendability and nucleosome positioning in transcriptional regulation
E.coli Structure Atlas
BaseAtlas, RepeatAtlas and GenomeAtlas
DNA Structure Atlas parameters
Genome Update: AT content in sequenced prokaryotic genomes
Wednesday 9 March, 2005
DNA Repeats in Bacterial Chromosomes
- 9.00-9.45
- Promoters in bacteria
Link to pdf file of lecture notes
- 9.45-10.00
- Break
- 10.00-10.45
- Sigma factors and transcriptional regulation
Link to pdf file of lecture notes
- 10.45-11.00
- Break
- 11.00-12.00
- Discussion
-
- 12.00-13.00
- Lunch
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- 13.00-17.00
Literature:
BaseAtlas, RepeatAtlas and GenomeAtlas
The Atlas Visualisation of Genome-wide Information
Strand misalignments lead to quasipalindrome correction
Short Simple Repeats
Thursday 10 March, 2005
Pathogenicity of Microbial Genomes
- 9.00-9.45
- Chromatin organization and gene expression in bacteria
Link to pdf file of lecture notes
- 9.45-10.00
- Break
- 10.00-10.45
- Microarrays of bacterial genomes
Link to pdf file of lecture notes
- 10.45-11.00
- Break
- 11.00-12.00
- Discussion
-
- 12.00-13.00
- Lunch
-
- 13.00-17.00
- Exercises: How to make DNA atlases from a GenBank or Fasta file
Literature:
Classification of Virulence Genes
Prediction of virulence genes
Genome update: rRNAs in sequenced microbial genomes
Genome update: tRNAs in sequenced microbial genomes
Genome Update: annotation quality in sequenced microbial genomes
Genome Update: alignment of bacterial chromosomes
Genome Update: promoter profiles
Friday 11 March, 2005
Transcriptomics of Bacteria
- 9.00-9.45
- Bacterial proteomics
Link to pdf file of lecture notes
- 9.45-10.00
- Break
- 10.00-10.45
- Secretion systems in bacteria
Link to pdf file of lecture notes
- 10.45-11.00
- Break
- 11.00-12.00
- Discussion
-
- 12.00-13.00
- Lunch
-
- 13.00-17.00
- Computer Exercises: How to make compare gene properties in genomes
- 10.45-11.00
- Break
- 11.00-12.
- Journal Club: Group 3 - Morten, Jesper, Nis
"The genome of Desulfotalea psychrophila, a sulfatereducing bacterium from permanently cold Arctic sediments", Environmental Microbiology, 6:887-902 (2004).
Link to Desulfotalea genome atlases
Literature:
B. subtilus microarrays
Transcriptomics of B. subtilus
PucR regulon
ure regulon
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