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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
Link to Course page
 Monday 7 March, 2005
Introduction
- 9.00-9.30
- Lecture: 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 Introduction to Biological Sequence Information
Link to pdf file of lecture notes
- 11.00-11.15
- Coffee Break
- 11.15-12.00
- Journal Club: Introductory example
- 12.00-13.00
- Lunch Break
- 13.00-14.00
- Lecture: An Overview of Microbial Genomes
Link to pdf file of lecture notes
- 14.00-14.15
- Coffee Break
- 14.15-16.00
- Computer Exercises 1: Comparative Microbial Genomics -laboratory excercises
Link to pdf file Exercise 1
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- End of the day
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
- 10.15-11.00
- Lecture: DNA Structures from A-Z
Link to pdf file of lecture notes
- 11.00-11.15
- Coffe Break
- 11.15-12.00
- Journal Club (Paper Presentation & Discussion)
- Student Group I
Link to paper (pdf file)
- 12.00-13.00
- Lunch Break
- 13.00-14.00
- Lecture: DNA curvature,melting and flexibility
Link to pdf file of lecture notes
- 14.00-14.15
- Coffe Break
- 14.15-15.30
- Computer Exercises 2: How to Make DNA Atlases from a GenBank or Fasta file
Link to pdf file Exercise 2
- 15.30-15.45
- Coffe Break
- 15.45-16.30
- Journal Club (Paper Presentation & Discussion)
- Student Group II
Link to paper (pdf file)
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- End of the day
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
- 9.00-10.00
- Lecture: DNA symmyetry elements, part 1: Local repeats
Link to pdf file of lecture notes
- 10.00-10.15
- Coffee Break
- 10.15-11.00
- Lecture : Chromatin structure and Gene Expression in E.coli
Link to pdf file of lecture notes
- 11.00-11.15
- Coffee Break
- 11.15-12.00
- Lecture : Comparison of Fungal Genomes
Link to pdf file of lecture notes
- 12.00-13.00
- Lunch Break
- 13.00-15.30
- Computer Exercises 3: Using BLAST to compare genomes
Link to pdf file Exercise 3
- 15.30-15.45
- Coffee Break
- 15.45-16.30
- Journal Club (Paper Presentation & Discussion)
- Student Group III
Link to paper (pdf file)
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- End of the day
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
Comparative Genomics
- 9.00-10.00
- Lecture: Sigma Factors in Bacterial Genomes
Link to pdf file of lecture notes
- 10.00-10.15
- Coffee Break
- 10.15-11.00
- Lecture: Bacterial pathogens "in practice" (No lecture notes)
- 11.15-12.00
- Journal Club (Paper Presentation & Discussion)
- Student Group IV
Link to paper (pdf file)
- 12.00-13.00
- Lunch Break
- 13.00-14.00
- Lecture: Comparison of Bacterial Genomes
Link to pdf file of lecture notes
- 14.00-14.15
- Coffee Break
- 14.15-15.30
- Computer Exercises 4: How to make a proteome comparison table
Link to pdf file Exercise 4
- 15.30-15.45
- Coffe Break
- 15.45-16.30
- Journal Club (Paper Presentation & Discussion)
- Student Group V
Link to paper (pdf file)
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- End of the day
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
Pathogenicity of Microbial Genomes
- 9.00-10.00
- Lecture: Secreted proteins and membrane-bound proteins- a genomic view
will be added later
- 1000.-10.15
- Coffee Break
- 10.15-11.00
- Lecture: Prediction of pathogenicity networks in bacterial genomes
Link to pdf file of lecture notes
- 11.00-11.15
- Break
- 11.15-12.00
- Discussion and course evaluation
- 12.00-13.00
- Lunch Break
- 13.00-17.00
- Discussion with other research groups (if desired)
Literature:
B. subtilus microarrays
Transcriptomics of B. subtilus
PucR regulon
ure regulon
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