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The course will start on Thursday, 6 September, 2007 at 13:00. Lectures, journal clubs and exercises will take place at the Center for Biological Sequence Analysis, in building 208, room 61 at the Technical University of Denmark, Lyngby. The textbook for this course is Computing for Comparative Microbial Genomics, by David W. Ussery and Trudy M. Wassenaar, to be published by Springer UK. The text is currently being written, and pdfs for each chapter will be given to accompany specific lectures.
Link to pdf file of outline for the text.
Links to PDF files for relevant papers will be provided on this web page (see below). This is the sixth year for this course. Links to the course programme for
2006 ,
2005 ,
2004 ,
2003 and
2002
Also, one-week versions of the course have been taught at other locations:
Brazil, August 2007,
Oslo, Norway, October 2006,
Brazil, August 2006,
Thailand, March 2005,
Link to DNA Atlas pages
Final report due 3 December, 2007
 Thursday, 6 September, 2007
Introductory talk - Please note that the first class meets in building 303, room 49.
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- Comparative Microbial Genomics: A Brief Overview
Link to pdf file of lecture notes
Literature:
10 Years of Bacterial Genomics
Thursday, 13 September, 2007
Introduction to Bioinformatics methods for Comparison of Bacterial Genomes
Dave Ussery
- 13.00-13.45
- An Introduction to Sequences as Biological Information
Link to pdf file of lecture notes
- 13.45-14.00
- Break
- 14.00-14.45
- Guest lecture by Bill Miller,U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Albany, CA 94710, USA.
Comparative genomics of the Campylobacteraceae: insights in the biology of emerging food-borne pathogens
- 14.45-15.00
- Break
- 15.00-16.30
- Introduction to the course structure and Computer Exercises.
Literature:
Chapter 1 of textbook. (see internal web pages for chapter)
10 Years of Bacterial Genomics
Thursday, 20 September, 2007
Introduction to Microbial Genomics
- 13.00-14.30
- Lecture 1 - "20 Methods to Compare Genomes"
Link to pdf file of lecture notes
- 14.30-15.15
- Lecture 2 - "Introduction to DNA Atlases"
Link to pdf file of lecture notes
- 15.15-15.30
- Break
- 15.30-16.30
-
Computer Exercises Lesson 1 - Web-based databases for comparison of sequenced bacterial genomes
with Stefano Borini.
Three good web sites to visit: Genomes On-Line Database (GOLD)
NCBI Genomes page
CBS Atlas Pages (v3.0)
Literature:
Chapter 2 of textbook. (see internal web pages for chapter)
DNA Structure: A-, B-, and Z-DNA Families
Origins of Replication in Circular Bacterial Chromosomes
CBS Genome Atlas database
Thursday, 27 September, 2007
DNA Curvature and Flexibility in Bacterial Chromosomes
- 13.00-13.45
- A web-table of "Genome-Database" links.
Lecture 1 - "DNA Curvature and Flexibility"
Link to pdf file of lecture notes
- 13.45-14.00
- Break
- 14.00-17.00
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Computer Exercises Lesson 2 - Basic notions of Unix applied to a simple bioinformatic case
with Stefano Borini.
Literature:
Chapter 3 of textbook. (see internal web pages for chapter)
DNA Structure: A-, B-, and Z-DNA Families
Bias of purine and pyr/pur stretches
Purine bias in bacterial genomes
DNA Structural Atlases
BaseAtlas, RepeatAtlas and GenomeAtlas
The Atlas Visualisation of Genome-wide Information
Thursday, 4 October, 2007
Metagenomics
- 13.00-13.45
- Guest lecture by Paul Gilna,Executive director for CAMERA, California Institute for Telecommunications and Information Technology (Calit2), a University of California San Diego (UCSD)/University of California Irvine partnership, La Jolla, California, United States of America
The CAMERA Project; a Cyberinfrastructure for Microbial Metagenomic Research
Link to pdf file of lecture notes
- 13.45-14.00
- Break
- 14.00-14.45
- Lecture - "Replication Origins in Bacterial Genomes"
Link to pdf file of lecture notes
- 14.45-15.00
- Break
- 15.00-16.30
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Computer Exercises Lesson 3 - Finding tRNA and rRNA genes in Metagenomics projects
with Karin Lagesen.
Literature:
Chapter 4 of textbook. (see internal web pages for chapter)
"CAMERA: A Community Resource for Metagenomics"
Thursday, 11 October, 2007
Regulation of Gene Expression
- 13.00-13.45
- Lecture - "Gene Regulation in Bacteria: Sigma Factors & Transcription Factors"
Link to pdf file of lecture notes
- 13.45-14.00
- Break
- 14.00-17.00
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Computer Exercises Lesson 4 - Using the CBS GenomeAtlas database for basic data mining
with Stefano Borini.
Literature:
Chapters 5 and 6 of textbook. (see internal web pages for chapter)
Sigma Factors
Two-component signal transduction systems
Thursday, 18 October, 2007
Autumn Break
Thursday, 25 October, 2007
Protein Localization
- 13.00-13.45
- Lecture 1 - "Prediction of Membrane and Secreted Proteins"
- 13.45-14.00
- Break
- 15.00-16.30
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Computer Exercises Lesson 5 - Introduction to Atlases: a feature-rich representation of information.
with Stefano Borini.
Literature:
Chapter 7 of textbook. (see internal web pages for chapter)
rRNA comparisons
Thursday, 1 November, 2007
Proteome Comparison
- 13.00-13.45
- Lecture 1 - "BLAST Comparison of Bacterial Proteomes"
- 13.45-14.00
- Break
- 14.00-15.30
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Computer Exercises Lesson 6 - Creating atlases with GeneWiz
with Stefano Borini.
- 15.30-15.45
- Break
- 15.45-16.30
- Discussion groups - work on projects for grant proposal
Literature:
Chapter 8 of textbook. (see internal web pages for chapter)
Blast Matrices
Proteome Comparisons
Thursday, 8 November, 2007
Bacterial Speciation
- 13.00-13.45
- Guest lecture by Bill Hanage,Department of Infectious Disease Epidemiology, Faculty of Medicine, Imperial College London, St Mary's Hospital, London W2 1PG, UK
Recombination and the Nature of Bacterial Speciation
- 13.45-14.00
- Break
- 14.00-14.30
- Discussion groups - work on projects for grant proposal
- 14.30-14.45
- Break
- 14.45-16.30
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Computer Exercises Lesson 7 - Sequence alignment using BLAST at the NCBI website
with Stefano Borini.
Literature:
Chapter 9 of textbook. (see internal web pages for chapter)
Recombination and Bacterial Speciation
Modelling Bacterial Speciation
Sequences, Clusters, and Bacterial Species
"Fuzzy species among recombinogenic bacteria"
Thursday, 15 November, 2007
DNA structures
- 13.00-13.45
- Guest lecture by Valley Stewart, Section of Microbiology, University of California, Davis
Two-component signal transduction control of anaerobic respiration in Escherichia coli and Shewanella oneidensis
- 13.45-14.00
- Break
- 14.00-14.30
- Discussion group - work on projects
- 14.30-14.45
- Break
- 14.45-16.30
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Computer Exercises Lesson 8 - Using BLAST from the Unix prompt
with Stefano Borini.
Literature:
Chapter 10 of textbook. (see internal web pages for chapter)
2-D clustering
Thursday, 22 November, 2007
Thanksgiving
- 13.00-13.30
- to be announced
Thursday, 29 November, 2007
No class today; Final Reports due on 3 December, 2007!
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