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The course will start on Wednesday, 1 September, 2004 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. 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 third year for this course. Links to the course programme for 2003 and 2002
Exam: Projects due on Monday, 6 December, 2004.
Link to DNA Atlas pages
 Wednesday, 1 September, 2004
Introduction to Bioinformatics methods for Comparison of Bacterial Genomes
Dave Ussery
- 8.00-8.45
- An Overview of Microbial Genomes
Link to pdf file of lecture notes
- 8.45-9.00
- Break
- 9.00-9.45
- An Introduction to Bioinformatic Methods: AT content in bacterial genomes
Link to pdf file of lecture notes
- 9.45-10.00
- Break
- 10.30-11.30
- Exercises: Using BLAST to compare genomes
Literature:
Genome update: 161 prokaryotic genomes sequenced, and counting
Genome update: Length distributions of sequenced prokaryotic genomes
Genome Update: AT content in sequenced prokaryotic genomes
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
Genome Update: chromosome atlases
Wednesday, 8 September, 2004
DNA Structures and Their Functions in Genomes
- 8.00-8.45
- Lecture 1 - DNA Structures from A to Z
Link to pdf file of lecture notes
- 8.45-9.00
- Break
- 9.00-9.45
- Lecture 2 - DNA curvature, melting, and flexibility
Link to pdf file of lecture notes
- 9.45-10.00
- Break
- 10.00-10.45
- Computer Exercises
- 10.45-11.00
- Break
- 11.00-12.
- Journal Club:
"The Complete Genome and Proteome of Mycoplasma mobile",
Jaffe et al., Genome Research, 14:1447-1461, 2004.
Link to Mycoplasma atlases
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
Wednesday, 15 September, 2004
We will meet in room 007 (building 208) this morning.
DNA Repeats in Bacterial Chromosomes
- 8.00-8.45
- Lecture 1 - local repeats
Link to pdf file of lecture notes
- 8.45-9.00
- Break
- 9.00-9.45
- Lecture 2 - global repeats
Link to pdf file of lecture notes
Literature:
BaseAtlas, RepeatAtlas and GenomeAtlas
The Atlas Visualisation of Genome-wide Information
Strand misalignments lead to quasipalindrome correction
Short Simple Repeats
Wednesday, 22 September, 2004
Pathogenicity of Microbial Genomes
- 8.00-8.45
- Lecture 1 - Computational Prediction of Pathogenicity Networks in Bacterial Genomes
Link to pdf file of lecture notes
- 8.45-9.00
- Break
- 9.00-9.45
- Journal Club: Group 1 - Claus, Camilla, Marc
"Complete Genome Sequence of Yersinia pestis Strain 91001, an Isolate Avirulent to Humans", DNA Research, 11:179-197 (2004).
Link to Yersinia genome atlases
- 9.45-10.00
- Break
- 10.00-11.45
- Exercises: How to make DNA atlases from a GenBank or Fasta file
Literature:
Classification of Virulence Genes
Prediction of virulence genes
Wednesday, 29 September, 2004
Transcriptomics of Bacteria
- 8.00-8.45
- Lecture 1 - Genomic properties of genes
Link to pdf file of lecture notes
- 8.45-9.00
- Break
- 9.00-9.45
- Lecture 2 - Hanne Jarmer, special guest lecturer
Transcriptome analysis of the TnrA regulon in Bacillus subtilis
Link to pdf file of lecture notes
- 9.45-10.00
- Break
- 10.00-10.45
- 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
Wednesday, 6 October, 2004
Sigma factors and a "Genome Update"
- 8.00-8.45
- Lecture 1 - Sigma Factors in Bacterial Genomes
Link to pdf file of lecture notes
- 8.45-9.00
- Break
- 9.00-9.45
- Lecture 2 - Genome Update - 12 genomes publised in 2 weeks!
Link to pdf file of lecture notes
- 9.45-10.00
- Break
- 10.00-10.45
- Computer Exercises: How to make a proteome comparison table
- 10.45-11.00
- Break
- 11.00-12.
- Journal Club: Group 5 - Heng Wu, Natascha, Asger.
"Complete genome sequence of the industrial bacterium Bacillus licheniformis, and comparisons with closely related Bacillus species", Genome Biology, 5:R77 (2004).
Link to Bacillus genome atlases
Literature:
Sigma Factors Encyclopedia Article
Clostridium sporulation sigma factors
[Sigma Factors] in E.coli
Wednesday, 20 October, 2004
Bacterial pathogenesis
- 8.00-8.45
- Lecture - Evolution of bacterial pathogens
Link to pdf file of lecture notes
Guest lecturer Trudy Wassenar, Zotzenheim, Germany
- 8.45-9.00
- Coffee Break
- 9.00-9.30
- Tutorial 1 - How Pathogens Evolve
- 9.30-9.45
- Coffee Break
- 9.45-10.15
- Tutorial 2 - How to Make a Pathogen
- 10.15-10.30
- Coffee Break
- 10.30-11.00
- Exercises - Lessons from Real Life
- 11.00-11.15
- Break
- 11.15-12
- Journal Club: Group 2 - Dorthe, Jakob, Gen.
"The genome sequence of the filamentous fungus Neurospora crassa", Nature, 422:859-868 (2003).
Literature (recommended by Trudy):
Common Themes in Pathogenicity (1989)
Common Themes in Pathogenicity Revisited (1997)
A Fresh Look at Bacterial Chromosomes
Yersinia pestis emerged from Yersinia pseudotuberculosis NOTE: Erratum was published the next year
More refs (fra Dave)
Classification of Bacterial Virulence Genes
Prediction of Bacterial Virulence Genes
Expression of Bacterial Virulence Genes
Mechanisms of Bacterial Pathogenesis
Genomic Analysis of Bacterial Secretion Systems
Wednesday, 27 October, 2004
Pseudomonas comparative genomics
- 8.00-8.45
- Lecture 1
Guest lecturer Burkhard Tuemmler, Medizinische Hochschule Hannover, Germany
"Comparative genomics of Pseudomonads"
- 8.45-9.00
- Break
- 9.00-9.45
- Lecture 2 - "Comparison of Genomes from four Pseudomonas species"
- 9.45-10.00
- Break
- 10.00-10.45
- Computer Exercises
- 10.45-11.00
- Break
- 11.00-12.
- Journal Club: Group 6 - Qiyuan Li, Zhang, - cyanobacteria
Literature:
Wednesday, 3 November, 2004
Global Properties of Bacterial Chromosomes
- 8.00-8.45
- Lecture 1 - Guest lecture by Dr. Peder Worning, AstraZeneca, Lund, Sweden
DNA periodicity in chromosomes
- 8.45-9.00
- Break
- 9.00-9.45
- Lecture 2 - Guest lecture by Dr. Peder Worning, AstraZeneca, Lund, Sweden
On Finding the Origin of Replication in Circular Bacterial Chromosomes
- 9.45-10.00
- Break
- 10.00-10.45
- Computer Exercises
- 10.45-11.00
- Break
- 11.00-12.
- Journal Club: Group 4 - Tim, Marie, Niels - Yersinia pseudotuberculosis
Literature:
Wednesday, 10 November, 2004
Genomics and Taxonomy of Burkholderia
- 8.00-8.45
- Lecture 1 - Guest lecture by Dr. Tom Coenye, Laboratorium voor Microbiologie, Universiteit Gent, Belgium
Searching for ncRNA in Burkholderia
Link to pdf file of lecture notes
- 8.45-9.00
- Break
- 9.00-9.45
- Lecture 2 - Guest lecture by Dr. Tom Coenye, Laboratorium voor Microbiologie, Universiteit Gent, Belgium
The use of Comparative Microbial Genomics to Study Microbiological Diversity and Taxonomy
Link to pdf file of lecture notes
- 9.45-10.00
- Break
- 10.00-10.45
- Computer Exercises
- 10.45-11.00
- Break
- 11.00-12.
- Journal Club: Group 7 - Agnaeszka, Mgada, Irina - bacteria GC rich
Literature:
Wednesday, 17 November, 2004
non-coding RNAs in Bacteria
- 8.00-8.45
- Lecture 1 - Guest lecture by Karin Lagesen, Centre for Molecular Biology and Neuroscience (CMBN) at Rikshospitalet University Hospital (RH) and the University of Oslo, Norway
ncRNAs
- 8.45-9.00
- Break
- 9.00-9.45
- Lecture 2 - more on ncRNAs by Karin Lagesen
- 9.45-10.00
- Break
- 10.00-10.45
- Computer Exercises
- 10.45-11.00
- Break
- 11.00-12.
- Journal Club: Group 9 - Martin, Yizi Yang and Rolf
"Genetic exchange and plasmid transfers in Borrelia burgdorferi sensu stricto revealed by three-way genome comparisons and multilocus sequence typing", PNAS, 101:14150-14155 (2004).
Link to Borrelia genome atlases
Literature:
Wednesday, 24 November, 2004
Horizontal Gene Transfer
- 8.00-8.45
- Lecture 1 - Guest lectuer by Cecilia Alsmark, Newcastle University, UK
Detection of horizontally transferred genes to protists.
- 8.45-9.00
- Break
- 9.00-9.45
- Lecture 2 - Guest lectuer by Cecilia Alsmark, Newcastle University, UK
Horizontal Gene Transfer and the Entamoeba histolytica genome
- 9.45-10.00
- Break
- 10.00-10.30.
- Journal Club: Group 9 - Ondrej Valina, Daniel Paul Cappiello and Line Thorsen
"The Genomic Sequence of the Accidental Pathogen Legionella pneumophilaits", Science, 305:1966-1968 (2004).
Link to Legionella genome atlases
Literature (recommended by Cecilia):
Horizontal Gene Transfer in Protists
Lateral Gene Transfer
The Tip of the Iceberg?
Wednesday, 1 December, 2004
Comparative Genomics of Staphylococcus aureus and Campylobacter jejuni
- 9.00-9.45
- Lecture 1 - Guest lecture by Professor Hanne Ingmer, Microbial Food Safety and Hygiene, Department of Veterinary Pathobiology, Royal Veterinary & Agricultural University, Copenhagen
Stress Induced Genes in Campylobacter jejuni
- 9.45-10.00
- Break
- 10.00-10.45
- Lecture 2 - Guest lecture by Professor Hanne Ingmer, Microbial Food Safety and Hygiene, Department of Veterinary Pathobiology, Royal Veterinary & Agricultural University, Copenhagen
Comparative Genomics of Staphylococcus aureus
Literature:
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