Events News Research CBS CBS Publications Bioinformatics
Staff Contact About Internal CBS CBS Other

Description

The course will be held at KMUTT (King Mongkut's University of Technology Thonburi) in Bangkok, Thailand. This is the third workshop on Comparative Microbial Genomics held in Thailand. (The previous two workshops were held in 2005 and in 2008). The workshop will focus on methods to compare bacterial genomes, and is a one-week version of the DTU course 27104 taught in Denmark. The general format is lectures in the morning, and computer exercises in the afternoon. The workshop will be presented by Dave Ussery, leader for the Comparative Microbial Genomics group [link to publications], and the computer exercises will be assisted by Karin Lagesin (in Oslo, Norway).

Pictures

Link to pictures from the workshop.
mangos


Course outline

  Monday, 8 March Tuesday, 9 March Wednesday, 10 March Thursday, 11 March Friday, 12 March
9:30-10:30
Introduction to Genomics
Methods to Compare Genomes
Expression of Genes and Proteins
Pan- and core-genomes
Summary
10:30-11:00
(Coffee Break)
 
11:00-12:00
Sequences as biological information
Genome Annotation
Comparison of Bacterial Proteomes
Microbial Communities
Group presentations

12:00-13:00
(Lunch break)
 
13:00-15:00
Downloading Genomes
finding RNA genes
BLAST matrices
Pan- Core-genome plots
Group presentations
15:00-15:30
(Coffee break)
 
15:30-17:00
Prediction of genes
Construction of 16S rRNA trees
Genome atlases
BLAST atlases
Group presentations, certificate presentation, closing


Book Cover The textbook is written specifically for this course:
COMPUTING FOR COMPARATIVE GENOMICS: Bioinformatics for Microbiologists
by David W. Ussery, Stefano Borini, and Trudy M. Wassenaar

Springer, published in spring, 2009.       Link to Amazon.com



Monday, 8 March, 2010: DNA and Genomics [chapters 1-5 of text]



9:30-10:30Lecture: Introduction to Genomics
Links: PDF Slides  Quiz  Genome Update: The 1000th Genome - A Cautionary Tale", Microbiology, 156:603-608, (2010).
10:30-11:00Coffee break
11:00-12:00Lecture: Sequences as biological information
Links: PDF slides  Quiz  "Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream", Nature Biotechnology, 27:627-632, (2009).
12:00-13:00Lunch break
13:00-17:00Exercise- Build your own Genomic Databases - Part 1: Downloading Genomes and Prediction of Genes
Link to Slides of wrap-up talk


Tuesday, 9 March, 2010: RNA and Transcriptomics [chapters 6-9 of text]



9:30-10:30Lecture: Methods to Compare Genomes
Links: PDF Slides  "Ten Years of Sequencing Bacterial Genomes",Functional and Integrative Genomics 6:165-185, (2006).
10:30-11:00Coffee break
11:00-12:00Lecture: Genome Annotation
Links: PDF Slides  "On the Total Number of Genes and Their Length Distribution in Complete Microbial Genomes", Trends in Genetics, 17, 425-428, (2001).
12:00-13:00Lunch break
13:00-17:00Exercise- Build your own Genomic Databases - Part 2: Finding RNA Genes and building a 16S rRNA tree
Links:   "RNAmmer: consistent and rapid annotation of ribosomal RNA genes", Nucleic Acids Research, 35, 3100-3108, (2007).


Wednesday, 10 March, 2010: Proteins and Proteomics [chapters 10-11 of text]



9:30-10:30Lecture: Expression of Genes and Proteins
Links: PDF Slides  "Prediction of highly expressed genes in microbes based on chromatin accessibility", BMC Molecular Biology, 8:, 11, (2007).
10:30-11:00Coffee break
11:00-12:00Lecture: Comparison of Bacterial Proteomes
Links: PDF slides  "The genome BLASTatlas-a GeneWiz extension for visualization of whole-genome homology", Molecular Biosystems, 4:, 363-371, (2008).
12:00-13:00Lunch break
13:00-17:00Exercise- Build your own Genomic Databases - Part 3: Genome Atlases and BLAST matrices
Link to pdf of talk


Thursday, 11 March, 2010: Microbial Communities [chapters 12-14 of text]



9:30-10:30Lecture: Bacterial Pan- and Core-genomes
Links: PDF Slides   Pan-genome family trees article
10:30-11:00Coffee break
11:00-12:00Lecture: Microbial Communities
Links: PDF slides (low resolution)  "On the Origins of Vibrio Species", Microbial Ecology, 59:, 1-13, (2009).
12:00-13:00Lunch break
13:00-17:00Exercise- Build your own Genomic Databases - Part 4: Pan- Core-genome plots and BLAST atlases
Links: PDF of slides (low resolution)
Links:   "GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes", Standards in Genomic Sciences, 1:, 204-215, (2009).


Friday, 12 March, 2010: Student Presentations



9:30-10:30Lecture: Summary
Links: pdf of talk
10:30-11:00Coffee break
11:00-12:00Presentations from Groups 1-3
Links: Group 1 - Prochlorococcus   Group 2 - Archaea and Bacteria(!)   Group 3 - E. coli and Vibrios
12:00-13:00Lunch break
13:00-14:00Presentations from Groups 4-6
Links: Group 4 - Mycobacterium   Group 5 - Extremophiles   Group 6 - Bacillus and Lactobacillus
14:00-14:30Break
14:30-15:30Presentations from Groups 7-9
Links: Group 7 - Methanococcus   Group 8 - Extremophiles   Group 9 - Spirulina genomes
15:30-16:30Certificate Presentations and Closing


talk
Link to pdf of talk