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Comparative Microbial Genomics Workshop
7 - 11 March, 2005 Pathumthani, Thailand



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



O 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
 
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




O 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)
 
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     




O 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)
 
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




O 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)
 
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     




O 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     








Course Organizers

Tim T. Binnewies       and       David W. Ussery