Monday, August 14	Tuesday, August 15	Wednesday, August 16	Thursday, August 17	Friday, August 18
Opening Talk by Fabiano Thompson					8:45-9:00
1 An Introduction to Biological Sequence Information and Microbial Genomes David Ussery	5 Introduction to Prokaryotic Taxonomy Tom Coenye	9 20 Methods to Compare Bacterial Genomes David Ussery	13 Stepping stones towards a new electronic prokaryotic taxonomy: MLSA Dirk Gevers	17 Protein localization, function, and networks David Ussery	9:00-10:30
					10:30-11:00 (Break)
2 Exercises: Introduction to UNIX + From DNA Sequence information to gene information Peter Hallin	6 The bacterial species in the genomic era Dirk Gevers	10 Novel approaches for assessing taxonomic relationships using whole-genome sequences Tom Coenye	14 Interspecies diversity + exercises Tom Coenye	18 Wrapping it up: Exercise on 2D clustering, Blast Matrices and genome comparison Peter Hallin	11:00-12:30
					12:30-14:00 (Lunch break)
3 Genome Dynamics & Evolution Dirk Gevers	7 Prokaryotic Taxonomy Computer exercises Tom Coenye Dirk Gevers	11 Exercises on Codon Usage and AT content Peter Hallin	15 Gene regulation on a global scale David Ussery	19 Meta-genomics and Pan-Genomics David Ussery	14:00-15:30
					15:30-16:00 (Break)
4 Genome Dynamics & Evolution computer exercises Dirk Gevers	8 DNA structures in bacterial chromosomes and their biological meanings David Ussery	12 Taxonomy exercises Tom Coenye	16 Exercise on predicting T.C.S. and Sigma factors Peter Hallin	20 Summary of the workshop David Ussery Peter Hallin Fabiano Thompson Tom Coenye Dirk Gevers	16:00-17:30

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• Monday, August 14, 2006


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9:00-10:30  M1 David Ussery
Lecture: An Introduction to Biological Sequence Information and Microbial Genomes

Links: Lecture M1-1 | Lecture M1-2
Literature:
Genome update: 161 prokaryotic genomes sequenced, and counting.

Genome update: Length distributions of sequenced prokaryotic genomes.
10:30-11:00 
Break
11:00-12:30  M2 Peter Hallin
Exercise: Exercises: Introduction to UNIX + From DNA Sequence information to gene information

Links: Brief Unix Guide | Exercise M2
Literature:
Large-scale prokaryotic gene prediction and comparison to genomeannotation.

Genome Update: annotation quality in sequenced microbial genomes.

EasyGene--a prokaryotic gene finder that ranks ORFs by statistical significance.

The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAsand snoRNAs.

Genome update: rRNAs in sequenced microbial genomes.

tRNAscan-SE: a program for improved detection of transfer RNA genes ingenomic sequence.

Genome update: tRNAs in sequenced microbial genomes.
12:30-14:00 
Lunch break
14:00-15:30  M3 Dirk Gevers
Lecture: Genome Dynamics & Evolution

Links: Lecture M3
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
15:30-16:00 
Break
16:00-17:30  M4 Dirk Gevers
Lecture: Genome Dynamics & Evolution computer exercises

Links: Exercise M4

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• Tuesday, August 15, 2006


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9:00-10:30  M5 Tom Coenye
Lecture: Introduction to Prokaryotic Taxonomy

Links: Lecture M6
Literature:
CJMreview

EMreview

Poltax-Vandamme
10:30-11:00 
Break
11:00-12:30  M6 Dirk Gevers
Lecture: The bacterial species in the genomic era

Links: Lecture M5
Literature:
bapteste BMCEB

kolisnychenko GR

mushegian PNAS

boucher COiM

konstantinidis PNAS

susko MBE

charlebois GR

koonin NRM

tettelin PNAS

ciccarelli

lawrence COiM

wolf TiG

daubin GR

lerat PLOS

harris GR

medini COiGD
12:30-14:00 
Lunch break
14:00-15:30  M7 Tom Coenye Dirk Gevers
Exercise: Prokaryotic Taxonomy Computer exercises

Links: Exercise M7
15:30-16:00 
Break
16:00-17:30  M8 David Ussery
Lecture: DNA structures in bacterial chromosomes and their biological meanings

Links: Lecture M8-1 | Lecture M8-2 | Introduction to ComputerExercises
Literature:
Origin of replication in circular prokaryotic chromosomes.

Genome update: base skews in 200+ bacterial chromosomes.

Bias of purine stretches in sequenced chromosomes.

Strand misalignments lead to quasipalindrome correction.

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• Wednesday, August 16, 2006


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9:00-10:30  M9 David Ussery
Lecture: 20 Methods to Compare Bacterial Genomes

Links: Lecture M9-1 | Lecture M9-2 | Evolution of Reduced Genomes in Escherichia coli
Literature:
Ten years of bacterial genome sequencing: comparative-genomics-baseddiscoveries.

The genomic code: inferring Vibrionaceae niche specialization.
10:30-11:00 
Break
11:00-12:30  M10 Tom Coenye
Lecture: Novel approaches for assessing taxonomic relationships using whole-genome sequences

Links: Lecture M10-1
Literature:
Genomic Signature

Extracting Phylogenetic Information...

Towards a prokaryotic genomic taxonomy

Comparative Assessment

Prokaryotic Species
12:30-14:00 
Lunch break
14:00-15:30  M11 Peter Hallin
Exercise: Exercises on Codon Usage and AT content

Links: Exercise M11
Literature:
CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data.

Genome Update: AT content in sequenced prokaryotic genomes.

Genome update: tRNAs in sequenced microbial genomes.
15:30-16:00 
Break
16:00-17:30  M12 Tom Coenye
Exercise: Taxonomy exercises

Links: Exercise M12
Literature:
SD Article

HGT

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• Thursday, August 17, 2006


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9:00-10:30  M13 Dirk Gevers
Lecture: Stepping stones towards a new electronic prokaryotic taxonomy: MLSA

Links: Lecture M13
10:30-11:00 
Break
11:00-12:30  M14 Tom Coenye
Lecture+Exercise: Interspecies diversity + exercises

Links: Exercise M14
12:30-14:00 
Lunch break
14:00-15:30  M15 David Ussery
: Gene regulation on a global scale

Links: Lecture M15-1 | Lecture M15-2
Literature:
Regulation of bacterial virulence by two-component systems.

Two-component signal transduction.

Extracytoplasmic function sigma factors in Pseudomonas syringae.

Chromatin architecture and gene expression in Escherichia coli.
15:30-16:00 
Break
16:00-17:30  M16 Peter Hallin
Exercise: Exercise on predicting T.C.S. and Sigma factors

Links: Exercise M16
Literature:
Genome update: distribution of two-component transduction systems in 250bacterial genomes.

Genome update: sigma factors in 240 bacterial genomes.

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• Friday, August 18, 2006


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9:00-10:30  M17 David Ussery
Lecture: Protein localization, function, and networks

Links: Lecture M17-1 | Lecture M17-2
Literature:
Genome update: prediction of membrane proteins in prokaryotic genomes.

Genome update: prediction of secreted proteins in 225 bacterial proteomes.

Genome Update: Protein secretion systems in 225 bacterial genomes.
10:30-11:00 
Break
11:00-12:30  M18 Peter Hallin
Exercise: Wrapping it up: Exercise on 2D clustering, Blast Matrices and genome comparison

Links: Exercies M18 | Heatmap of Amino Acids | Blast Matrix | Heatmap of Properties | Blast Atlas
Literature:
Genome update: 2D clustering of bacterial genomes.

Genome Update: proteome comparisons.

Genome update: correlation of bacterial genomic properties.

Genome update: chromosome atlases.
12:30-14:00 
Lunch break
14:00-15:30  M19 David Ussery
Lecture: Meta-genomics and Pan-Genomics

Links: Lecture M17-1 | Opening the pan-genomics box
Literature:
Phosphate acquisition genes in Prochlorococcus ecotypes: evidence forgenome-wide adaptation.

Bioinformatics for whole-genome shotgun sequencing of microbialcommunities.

Environmental genome shotgun sequencing of the Sargasso Sea.

Crystal ball. Systems biology: in the broadest sense of the word.
15:30-16:00 
Break
16:00-17:30  M20 David Ussery Peter Hallin Fabiano Thompson Tom Coenye Dirk Gevers
Lecture: Summary of the workshop



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