Monday, August 13	Tuesday, August 14	Wednesday, August 15	Thursday, August 16	Friday, August 17
1 Introduction to the workshop Fabiano Thompson	7 20 Methods to compare bacterial genomes David Ussery	13 Genome annotation: Gene finding, rRNA and tRNA Carsten Friis	19 Transcriptional regulation in Bacterial Genomes David Ussery	25 Metagenomics: principles and approaches Gilna	9:00-10:00
					10:00-10:30 (Break)
2 An Overview of Microbial Genomes David Ussery	8 Genome evolution Dirk Gevers	14 Ex: Genome annotation Kristoffer Kiil	20 Secreted proteins and membrane-bound proteins - a genomic view Carsten Friis	26 Ex: Bioinformatics tools for understanding and mining metagenomic data Gilna	10:30-11:30
3 Ex: Comparative Microbial Genomics Kristoffer Kiil	9 The Prokaryotic species in a genomic era Dirk Gevers	15 Recombination Bill Hanage	21 Bacterial Pan-Genomics David Ussery	27 Summary of the workshop David Ussery Fabiano Thompson Dirk Gevers Kristoffer Kiil Carsten Friis Bill Hanage Gilna	11:30-12:30
					12:30-13:30 (Lunch break)
4 An Introduction to Bioinformatic Methods. Carsten Friis	10 Ex: From comparative genomics to a sequence-based taxonomy I Dirk Gevers	16 Ecology Bill Hanage	22 Ex: Pan-Genomics from a practical perspective Kristoffer Kiil		13:30-14:30
5 AT content: DNA Structures, curvature, melting and flexibility in bacterial genomes Carsten Friis	11 Ex: From comparative genomics to a sequence-based taxonomy II Dirk Gevers	17 Introduction to atlases Carsten Friis	23 MLST Bill Hanage		14:30-15:30
					15:30-16:00 (Break)
6 Ex: DNA structures + AT content Kristoffer Kiil	12 Ex: From comparative genomics to a sequence-based taxonomy III Dirk Gevers	18 Ex: Configuring and analysing genome atlases Kristoffer Kiil	24 Ex: The 'A' bit of MLSA - final locus selection, tree building and analysis Bill Hanage		16:00-17:00

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• Monday, August 13, 2006


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9:00-10:00  M1 Fabiano Thompson
: Introduction to the workshop

10:00-10:30 
Break
10:30-11:30  M2 David Ussery
Lecture: An Overview of Microbial Genomes

Links: Lecture M2
11:30-12:30  M3 Kristoffer Kiil
Exercise: Ex: Comparative Microbial Genomics

Links: Exercise M3
12:30-13:30 
Lunch break
13:30-14:30  M4 Carsten Friis
Lecture: An Introduction to Bioinformatic Methods.

14:30-15:30  M5 Carsten Friis
Lecture: AT content: DNA Structures, curvature, melting and flexibility in bacterial genomes

15:30-16:00 
Break
16:00-17:00  M6 Kristoffer Kiil
Exercise: Ex: DNA structures + AT content

Links: Exercise M6

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• Tuesday, August 14, 2006


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9:00-10:00  M7 David Ussery
Lecture: 20 Methods to compare bacterial genomes

Links: Lecture M7
10:00-10:30 
Break
10:30-11:30  M8 Dirk Gevers
Lecture: Genome evolution

Links: Lecture M8
Literature:
Bordetella Genomes

Cole Nature

Jensen GB

Ochman Nature 2000

Rost 1999

Woese PNAS 2000

Eisen GB

Koonin ARG

Phydbac

Siev Structure

Mischegian TiG

Gevers TiM

Kunin GB

Puscher GB

Tamames GB

Casjens ARG

Hacker EMBOrep

Li 2001

Rocha TiG

Tama Science
11:30-12:30  M9 Dirk Gevers
Lecture: The Prokaryotic species in a genomic era

Links: Lecture M9
Literature:
CJMreview

EMreview

Poltax-Vandamme
12:30-13:30 
Lunch break
13:30-14:30  M10 Dirk Gevers
Exercise: Ex: From comparative genomics to a sequence-based taxonomy I

Links: Exercise M10
14:30-15:30  M11 Dirk Gevers
Exercise: Ex: From comparative genomics to a sequence-based taxonomy II

15:30-16:00 
Break
16:00-17:00  M12 Dirk Gevers
Exercise: Ex: From comparative genomics to a sequence-based taxonomy III


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• Wednesday, August 15, 2006


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9:00-10:00  M13 Carsten Friis
Lecture: Genome annotation: Gene finding, rRNA and tRNA

10:00-10:30 
Break
10:30-11:30  M14 Kristoffer Kiil
Exercise: Ex: Genome annotation

Links: Exercise M14
11:30-12:30  M15 Bill Hanage
Lecture: Recombination

12:30-13:30 
Lunch break
13:30-14:30  M16 Bill Hanage
Lecture: Ecology

14:30-15:30  M17 Carsten Friis
Lecture: Introduction to atlases

15:30-16:00 
Break
16:00-17:00  M18 Kristoffer Kiil
Exercise: Ex: Configuring and analysing genome atlases

Links: Exercise M18

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• Thursday, August 16, 2006


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9:00-10:00  M19 David Ussery
Lecture: Transcriptional regulation in Bacterial Genomes

Links: Lecture M19
10:00-10:30 
Break
10:30-11:30  M20 Carsten Friis
Lecture: Secreted proteins and membrane-bound proteins - a genomic view

11:30-12:30  M21 David Ussery
Lecture: Bacterial Pan-Genomics

Links: Lecture M21
12:30-13:30 
Lunch break
13:30-14:30  M22 Kristoffer Kiil
Exercise: Ex: Pan-Genomics from a practical perspective

Links: Exercise M22
14:30-15:30  M23 Bill Hanage
Lecture: MLST

15:30-16:00 
Break
16:00-17:00  M24 Bill Hanage
Exercise: Ex: The 'A' bit of MLSA - final locus selection, tree building and analysis


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• Friday, August 17, 2006


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9:00-10:00  M25 Gilna
Lecture: Metagenomics: principles and approaches

Links: Lecture M25
10:00-10:30 
Break
10:30-11:30  M26 Gilna
Exercise: Ex: Bioinformatics tools for understanding and mining metagenomic data

11:30-12:30  M27 David Ussery Fabiano Thompson Dirk Gevers Kristoffer Kiil Carsten Friis Bill Hanage Gilna
Lecture: Summary of the workshop

12:30-13:30 
Lunch break
13:30-14:30  M28 
:

14:30-15:30  M29 
:

15:30-16:00 
Break
16:00-17:00  M30 
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