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The course will start on Wednesday, 3 September, 2003 at 8:00. Lectures, journal clubs and exercises will take place at the Center for
Biological Sequence Analysis, in building 208, room 51 at the Technical University of Denmark, Lyngby.
Exam: Projects due on Thursday, 4 December, 2003.
 Wednesday, 3 September, 2003
Introduction to Bioinformatics methods for Comparison of Bacterial Genomes
- 8.00-8.45
- Introduction to Comparative Microbial Genomics
David Ussery
- 8.45-9.00
- Break
- 9.00-9.45
- "DNA Atlases for Campylobacter, Helicobacter, and Related Organisms" Link to PDF file of lecture notes
David Ussery (note: this talk was presented at the first plenary session for theCHRO2003 meeting)
- 9.45-10.00
- Break
- 10.00-10.45
- Exercises: How to make DNA atlases from a GenBank or Fasta file
- 10.45-11.00
- Break
- 11.00-12.
- Journal Club: Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica,
Julian Parkhill et al., Nature Genetics, 10 32-40, 2003.
Link to Bordetella atlases
Literature: E.coli Structure Atlas
BaseAtlas, RepeatAtlas and GenomeAtlas
DNA Structure Atlas parameters
Wednesday, 10 September, 2003
Gene Finding in Bacterial Genomes
- 9.00-9.45
- Gene Finding in Bacterial Genomes
Guest lecture by Dr. Thomas Schou Larsen, Novozymes.
- 9.45-10.00
- Break
- 10.00-11:30
- Exercises: EasyGene
GenMark
Literature: EasyGene - a prokaryotic gene finder that ranks ORFs by statistical significance, T.S. Larsen and A. Krogh, BMC Bioinformatics, 4:21, (2003)
Wednesday, 17 September, 2003
Comparative Genomics
- 8.00-8.45
- Annotation of the Lactobacillus plantarum genome.
Guest Lecture by Professor Roland Siezen, University of Nijmegen, The Netherlands
- 8.45-9.00
- Break
- 9.00-9.45
- Comparative genomics of Lactic acid Bacteria
Guest Lecture by Professor Roland Siezen, University of Nijmegen, The Netherlands
- 9.45-10.00
- Coffee Break
- 10.00-10.45
- Exercises: How to make DNA atlases Lactobacillus plantarum genome web page
- 10.45-11.00
- Coffee Break
- 11.00-12.
- Journal Club: Complete genome sequence of Lactobacillus plantarum WCFS1
M. Kleerebezem et al., Proceedings of the National Academy of Science, USA, 10:1-29, (2003)
Literature: The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403, Bolotin A, Wincker P, Mauger S, Jaillon O, Malarme K, Weissenbach J, Ehrlich SD, Sorokin A., Genome Research, 11:731-753, (2001)
Wednesday, 24 September, 2003
Taxonomy of Bacteria
- 8.00-8.45
- Modern bacterial systematics in practice : Polyphasic taxonomy of the Burkholderia cepacia complex Link to PDF file of lecture notes
Guest lecture by Dr. Tom Coenye, University of Gent, Belgium
- 8.45-9.00
- Coffee Break
- 9.00-9.45
- Use of whole-genome sequences in bacterial taxonomy Link to PDF file of lecture notes
Guest lecture by Dr. Tom Coenye, University of Gent, Belgium
- 9.45-10.00
- Coffee Break
- 10.00-10.45
- Exercises: NCBI taxonomy
- 10.45-11.00
- Coffee Break
- 11.00-12.
- Journal Club: Gene Sequences Useful for Predicting Relatedness of Whole Genomes in Bacteria. International Journal of Systematic and Evolutionary Microbiology, in press, August, 2003.
Wednesday, 1 October, 2003
DNA structures and their meanings in Prokaryotic chromosomes
- 8.00-8.45
- Genomic Bias of purine and pyrimidine/purine stretches Link to PDF file of lecture notes
David Ussery
- 8.45-9.00
- Coffee Break
- 9.00-9.45
- "Prediction of Gene Expression Levels in Bacteria" Link to PDF file of lecture notes
David Ussery (note: this talk was presented at the Society of General Microbiolgy UMIST meeting, 8 - 11 September 2003)
- 9.45-10.00
- Coffee Break
- 10.00-10.45
- Journal Club - presented by Group #1 - Micheal Stangegaard, Morten Gjermansen and Mikkel Klausen
The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000
C. Robin Buell et al., Proceedings of the National Academy of Science, USA, 100:10181-10186, (2003).
Link to Pseudomonas atlases
- 10.45-11.00
- Coffee Break
- 11.00-12.
- Exercises: How to make DNA atlases from a GenBank or Fasta file
Literature: DNA Structure: A-, B-, and Z-DNA Families, David Ussery, The Encyclopedia of Life Sciences, (Macmillan Publishers, London, 2002).
Bias of Purine Stretches in Sequenced Genomes,David Ussery, Dikeos Mario Soumpasis, Søren Brunak, Hans-Henrik Stærfeldt, Peder Worning, and Anders Krogh, Computers in Chemistry, 26, 531-541, (2002).
Link to web page comparing fractions purine and pyr/pur tracts in more than 700 chromosomes
Wednesday, 8 October, 2003
Chromatin structures and Genome Organisation in Bacteria
- 8.00-8.45
- DNA Structures and their meanings in chromosomes. Link to PDF file of lectuer notes
David Ussery
- 8.45-9.00
- Coffee Break
- 9.00-9.45
- Global DNA Structural Properties in Bacterial Chromosomes. Link to PDF file of lecture notes
David Ussery
- 9.45-10.00
- Coffee Break
- 10.00-10.45
- Journal Club - presented by Group #2 - Peter Hallin and Lars Larsen and Kai Wang
Complete genome sequence and analysis of Wolinella succinogenes
Claudia Baar et al., Proceedings of the National Academy of Science, USA, 100:1169011695, (2003)
Link to Wolinella atlases
- 10.45-11.00
- Coffee Break
- 11.00-12.
- Exercises: How to make DNA atlases from a GenBank or Fasta file
Literature: "A DNA Structural Atlas for Escherichia coli", Anders Gorm Pedersen, Lars Juhl Jensen, Hans-Henrik Stærfeldt, Søren Brunak, and David W. Ussery, Journal of Molecular Biology, 299:907-930, 2000.
Wednesday, 22 October, 2003
DNA Repeats in Bacterial Genomes
- 8.00-8.45
- Local and Global Repeats Link to PDF file of lecture notes
David Ussery
- 8.45-9.00
- Coffee Break
- 9.00-9.45
- Cruciforms
David Ussery
- 9.45-10.00
- Coffee Break
- 10.00-10.45
- Journal Club - presented by Group #3 - Marcelo Bertalane, Adriano Marques, Susanne Hoyer, and Amaya Cabezon
Comparison of the genomes of two Xanthomonaspathogens with differing host specificities
Nature, 417:459-463, (2003)
Link to Xanthomonas atlases
- 10.45-11.00
- Coffee Break
- 11.00-12.
- Exercises: Link to web table comparing fractions DNA Repeats in Bacterial Chromosomes
Literature: "Three Views of Microbial Genomes", Lars Juhl Jensen, Carsten Friis, and David W. Ussery,Research in Microbiology, 150:773-777, 1999.
"The Atlas Visualisation of Genome-wide Information", Marie Skovgaard, Lars Juhl Jensen, Carsten Friis, Hans-Henrik Stærfeldt, Peder Worning, Søren Brunak, and David Ussery,Methods in Microbiology, 33:49-63, 2002.
"Strand misalignments lead to quasipalindrome correction", Vera van Noort, Peder Worning, David W. Ussery, William A. Rosche, and Richard Sinden Trends in Genetics, 19:365-369, 2003.
Wednesday, 29 October, 2003
Comparative genomics of Staphylcoccus aureus
- 8.00-8.45
- Evolutionary History of Staphylcoccus aureus multi-drug resistance
Guest lecturer, Katie Hardy, Health Protection Agency, Birmingham Heartlands Hospital, Birmingham, United Kingdom.
- 8.45-9.00
- Coffee Break
- 9.00-9.45
- Comparison of nine Staphylcoccus genomes.
David Ussery
- 9.45-10.00
- Coffee Break
- 10.00-10.45
- Journal Club - presented by Group #4 - Rikke Rothmann, Maria van Gennip, Mikael R. Andersen, Frederik Lundberg
Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica,
Julian Parkhill et al., Nature Genetics, 10 32-40, 2003.
Link to Bordetella atlases
- 10.45-11.00
- Coffee Break
- 11.00-11.45.
- Journal Club - presented by Group #7 - Long Zhang, Halfdan Beck, Kasper Nielsen, and Christina Andersen
The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria,
Timothy Reed et al., Nature, 423 381-86, 2003.
Link to Bacillus atlases
Wednesday, 5 November, 2003
Origin of Replication
- 8.00-8.45
- Finding the Origin of Replication in Bacterial Chromosomes Link to ppt file of lecture notes
Guest lecturer, Dr. Peder Worning, CBS
- 8.45-9.00
- Coffee Break
- 9.00-9.45
- Comparison of five Clostridium genomes Link to PDF file of lecture notes
David Ussery (note: this talk was presented at the second open meeting of the EU concerted action group on the genus Clostridium, DIAGNOSIS, EPIDEMIOLOGY AND ANTIBIOTIC RESISTANCE OF THE GENUS CLOSTRIDIUM, 17 - 18 October 2003)
- 9.45-10.00
- Coffee Break
- 10.00-10.45
- Journal Club - presented by Group #5 - Dorte Friis, Jan Lønstrup, Lifang Liu and Li Jiang
The complete genome sequence of the avian pathogen Mycoplasma gallisepticum strain Rlow
Leka Papazisi et al., Microbiology, 149:2307-2316, (2003).
- 10.45-11.00
- Coffee Break
- 11.00-12.
- Exercises: How to make DNA atlases from a GenBank or Fasta file
Wednesday, 12 November, 2003
DNA Supercoiling, DNA Structures, and DNA Information in Bacterial Chromosomes
- 8.00-8.45
- Introduction to computation of DNA Structures Link to PDF file of lecture notes (both lectures)
Guest lecture by Professor Craig Benham, U.C. Davis Genome Center, California, USA
- 8.45-9.00
- Coffee Break
- 9.00-9.45
- DNA Structures, part II
Guest lecture by Professor Craig Benham, U.C. Davis Genome Center, California, USA
- 9.45-10.00
- Coffee Break
- 10.00-10.45
- Journal Club - presented by Group #6 - Jimmy Hoffmann Hansen and Paiman Kh-Jamal
The genome sequence of Clostridium tetani, the causative agent of tetanus disease
Holger Brüggemann et al., Proceedings of the National Academy of Science, USA, 100:1316-1321, (2003)
- 10.45-11.00
- Coffee Break
- 11.00-12.
- Exercises: How to make DNA atlases from a GenBank or Fasta file
Wednesday, 19 November, 2003
Sigma Factors
- 9.00-9.45
- Sigma Factors in Bacterial Genomes Link to PDF file of lecture notes
David Ussery
- 9.45-10.00
- Coffee Break
- 10.00-10.45
- Journal Club - presented by Group #7 - Gudmundur Albert Hardarson, Binici Cengiz, Ye Xiuxiu
Tropheryma whipplei Twist: A Human Pathogenic Actinobacteria With a Reduced Genome
D. Raoult et al., Genome Research, 13:1800-1809, (2003)
Wednesday, 26 November, 2003
ncRNAs
- 9.00-9.45
- Prediction of non-coding RNAs in Bacterial Genomes Link to PDF file of lecture notes
- 9.45-10.00
- Coffee Break
- 10.00-10.45
- Journal Club - presented by Group #8 - Michael Christiansen
The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism.
Elizabeth Waters et al., Proceedings of the National Academy of Science, USA, 100:12984-12988, (2003)
Thursday, 4 December, 2003
Final Reports DUE
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