Timeline

Eduardo Rocha
Head of Structure
22 Apr 2021
software

CRISPRCasFinder

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22 Apr 2021
software

PanACoTA: A modular tool for massive microbial comparative genomics

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22 Apr 2021
news

Bacteria have numerous phage–plasmids with conserved phage and variable plasmid genes

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18 Mar 2021
publication

Bacteria have numerous distinctive groups of phage-plasmids with conserved phage and variable plasmid gene repertoires.

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03 Mar 2021
news

Amandine Buffet’s first first author paper on maintenance of the capsule is out!!

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03 Mar 2021
publication

Nutrient conditions are primary drivers of bacterial capsule maintenance in Klebsiella

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01 Mar 2021
publication

The impact of genetic diversity on gene essentiality within the Escherichia coli species.

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11 Feb 2021
publication

Causes and consequences of bacteriophage diversification via genetic exchanges across lifestyles and bacterial taxa.

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31 Jul 2020
news

Our first experimental paper is out: Prophages in Klebsiella sp. And lots of them!

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30 Jul 2020
publication

Modular prophage interactions driven by capsule serotype select for capsule loss under phage predation

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17 Jul 2020
publication

Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids.

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05 Jun 2020
publication

A synthesis of bacterial and archaeal phenotypic trait data.

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01 Jun 2020
publication

Phylogenetic background and habitat drive the genetic diversification of Escherichia coli.

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08 May 2020
publication

The major subunit of widespread competence pili exhibits a novel and conserved type IV pilin fold.

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01 May 2020
publication

The Evolution of Protein Secretion Systems by Co-option and Tinkering of Cellular Machineries.

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29 Apr 2020
publication

Macromolecular crowding links ribosomal protein gene dosage to growth rate in Vibrio cholerae

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10 Feb 2020
news

Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements

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10 Feb 2020
news

Community diversity and habitat structure shape the repertoire of extracellular proteins in bacteria

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07 Feb 2020
publication

Intracellular Positioning Systems Limit the Entropic Eviction of Secondary Replicons Toward the Nucleoid Edges in Bacterial Cells.

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06 Feb 2020
publication

Community diversity and habitat structure shape the repertoire of extracellular proteins in bacteria.

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01 Feb 2020
publication

Unlinked rRNA genes are widespread among bacteria and archaea.

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24 Jan 2020
publication

Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements

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01 Jan 2020
publication

Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan.

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03 Sep 2019
news

Evolution of the type IV filament superfamily into machines for multiple functions.

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19 Jul 2019
publication

Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility

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18 Jul 2019
news

Bacteriophages benefit from generalized transduction

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13 May 2019
publication

A matter of background: DNA repair pathways as a possible cause for the sparse distribution of CRISPR-Cas systems in bacteria

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24 Apr 2019
news

Jean Cury wins the outstanding student paper of the year in MBE

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04 Feb 2019
publication

Ultrafast search of all deposited bacterial and viral genomic data

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07 Jan 2019
news

Genetic exchanges are more frequent in bacteria encoding capsules

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21 Dec 2018
publication

Genetic exchanges are more frequent in bacteria encoding capsules

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02 Jul 2018
publication

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins

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14 Jun 2018
publication

Host range and genetic plasticity explain the co-existence of integrative and extrachromosomal mobile genetic elements

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12 Jun 2018
news

Parallels between natural and experimental evolution of symbiosis

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11 Jun 2018
publication

Parallels between experimental and natural evolution of legume symbionts

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01 Jun 2018
publication

Neutral Theory, Microbial Practice: Challenges in Bacterial Population Genetics

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01 Jan 2018
publication

Bacillus subtilis, the model Gram-positive bacterium: 20 years of annotation refinement

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12 Dec 2017
publication

Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria

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15 Nov 2017
project

SPARK: Transmission of multidrug resistant Klebsiella clones and genes – a One Health approach

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11 Oct 2017
news

The treasure troves of bacterial genetic diversity

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10 Oct 2017
publication

The chromosomal organization of horizontal gene transfer in bacteria

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02 Oct 2017
publication

Metagenomic assessment of the interplay between the environment and the genetic diversification of Acinetobacter

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19 Sep 2017
event

Workshop “Recent Computational Advances in Metagenomics (RCAM)” 2017

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18 Sep 2017
publication

Recruitment of a lineage-specific virulence regulatory pathway promotes intracellular infection by a plant pathogen experimentally evolved into a legume symbiont.

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06 Sep 2017
publication

Integrative and conjugative elements and their hosts: composition, distribution and organization

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29 Aug 2017
publication

A widespread family of polymorphic toxins encoded by temperate phages

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24 Jul 2017
publication

Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens

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24 May 2017
news

Emerging diseases: a highly mutant strain of the Elizabethkingia bacterium caused an outbreak in Wisconsin

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12 Apr 2017
event

“Microbiome evolution and function in social bees” by Nancy MORAN – Genomes & Genetics Departemental seminar co-organized with Microbiology Departement

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10 Apr 2017
publication

Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer

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28 Mar 2017
publication

Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance

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15 Mar 2017
event

Seminar “The Evolution of Bacteria Genes and Genomes”

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01 Mar 2017
publication

Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder

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01 Feb 2017
tool

CapsuleFinder

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20 Dec 2016
project

ANR SHAPE: Shaping new rhizobia by experimental evolution

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10 Oct 2016
news

A population biology study of Listeria ushers in a new era in listeriosis surveillance

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11 Sep 2016
news

Restriction modification systems as regulators of gene transfer

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27 Jul 2016
publication

Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis

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02 May 2016
publication

Regulation of genetic flux between bacteria by restriction-modification systems.

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29 Apr 2016
publication

Identification and analysis of integrons and cassette arrays in bacterial genomes.

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25 Mar 2016
publication

Genetic and life-history traits associated with the distribution of prophages in bacteria.

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17 Mar 2016
publication

Using Sex to Cure the Genome

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16 Mar 2016
publication

Identification of protein secretion systems in bacterial genomes

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01 Mar 2016
tool

TXSSdb, a database of protein secretion systems

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01 Mar 2016
publication

Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity.

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01 Mar 2016
publication

The impact of selection, gene conversion, and biased sampling on the assessment of microbial demography

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01 Feb 2016
news

Listeria: identification of hypervirulent strains with placental and cerebral tropism

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04 Jan 2016
publication

Coevolution of the Organization and Structure of Prokaryotic Genomes.

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15 Nov 2015
event

C3BI Mini Symposium – New Data, New Questions, New Methods

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10 Nov 2015
software

IntegronFinder

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09 Oct 2015
news

Olaya just got an FRM grant

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08 Oct 2015
tool

TXSScan – models and profiles for protein secretion systems

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06 Oct 2015
news

GEM paper among the all-time top10 of PLoS Genetics

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10 Sep 2015
project

ANR Magisbac : Genesis and Maintenance of Bacterial Secondary Chromosomes

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10 Sep 2015
project

ERC-2011-StG EVOMOBILOME

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05 Sep 2015
tool

Secreton – Non-Flagellar Type III Secretion Systems in sequenced genomes

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05 Sep 2015
tool

ConjDB – a database of conjugative & mobilization systems and T4SS

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05 Sep 2015
software

CONJscan-T4SSscan

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05 Sep 2015
software

T3SSscan

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05 Sep 2015
software

Repseek

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05 Sep 2015
software

Swelfe

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05 Sep 2015
software

GrowthPred

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04 Sep 2015
event

2nd Edition of the Workshop Recent computational advances in metagenomics (RCAM’15)

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04 Sep 2015
event

Bi-annual GdR Molecular Bioinformatics (BIM) meeting

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04 Sep 2015
software

MacSyFinder & MacSyView

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04 Sep 2015
software

Repeatoire

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15 Jun 2015
project

Population genomics

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15 Jun 2015
project

The imprint of growth

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15 Jun 2015
project

DNA repeats and genome dynamics

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09 Jun 2015
project

Horizontal gene transfer

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11 May 2015
team

Microbial Evolutionary Genomics

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05 May 2015
publication

Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations

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25 Feb 2015
publication

Insights on the emergence of Mycobacterium tuberculosis from the analysis of Mycobacterium kansasii

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13 Nov 2014
publication

TLR9 activation is triggered by the excess of stimulatory versus inhibitory motifs present in Trypanosomatidae DNA

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17 Oct 2014
publication

MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems

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13 Oct 2014
publication

The genomic diversification of the whole Acinetobacter genus: origins, mechanisms, and consequences.

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08 Oct 2014
publication

The chromosomal accommodation and domestication of mobile genetic elements

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15 Sep 2014
department

Genomes and Genetics

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02 Sep 2014
publication

Transient hypermutagenesis accelerates the evolution of legume endosymbionts following horizontal gene transfer

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12 Aug 2014
publication

The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts

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04 Aug 2014
publication

Pervasive domestication of defective prophages by bacteria

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12 Mar 2014
publication

Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion

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09 Jan 2014
publication

A PNPase dependent CRISPR System in Listeria

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26 Sep 2013
publication

Manipulating or superseding host recombination functions: a dilemma that shapes phage evolvability

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01 Mar 2013
publication

Clinical trial evaluating color change and tooth sensitivity throughout and following in-office bleaching

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01 Mar 2013
publication

Evolution. With a little help from prokaryotes

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01 Jan 2013
publication

Natural selection for operons depends on genome size

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01 Jan 2013
publication

Natural genome diversity of AI-2 quorum sensing in Escherichia coli: conserved signal production but labile signal reception

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12 Dec 2012
publication

The adaptation of temperate bacteriophages to their host genomes

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26 Nov 2012
publication

Rapid evolution of the sequences and gene repertoires of secreted proteins in bacteria

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21 Nov 2012
publication

Are diabetes management guidelines applicable in ‘real life’?

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30 Oct 2012
publication

Influence of platform and abutment angulation on peri-implant bone. A three-dimensional finite element stress analysis

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11 Oct 2012
publication

Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements

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27 Sep 2012
publication

The non-flagellar type III secretion system evolved from the bacterial flagellum and diversified into host-cell adapted systems

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13 Sep 2012
publication

Evolution of conjugation and type IV secretion systems

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24 Aug 2012
publication

Characterization of novel phages isolated in coagulase-negative staphylococci reveals evolutionary relationships with Staphylococcus aureus phages

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06 Jul 2012
publication

A Single Amino Acid Substitution Changes the Self-Assembly Status of a Type IV Piliation Secretin

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29 Feb 2012
publication

After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection

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02 Feb 2012
publication

Immune subversion and quorum-sensing shape the variation in infectious dose among bacterial pathogens

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30 Nov 2011
publication

Investment in rapid growth shapes the evolutionary rates of essential proteins

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16 Sep 2011
publication

Complete genome sequence of the fish pathogen Flavobacterium branchiophilum

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18 Aug 2011
publication

The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation

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18 Mar 2011
publication

CRISPR distribution within the Escherichia coli species is not suggestive of immunity-associated diversifying selection

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24 Feb 2011
publication

Function-specific accelerations in rates of sequence evolution suggest predictable epistatic responses to reduced effective population size

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27 Jan 2011
publication

Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes

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09 Sep 2010
publication

Mutational patterns cannot explain genome composition: Are there any neutral sites in the genomes of bacteria?

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01 Sep 2010
publication

Mobility of plasmids

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15 Jun 2010
publication

The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella

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08 Apr 2010
publication

No evidence for elemental-based streamlining of prokaryotic genomes

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24 Mar 2010
publication

What traits are carried on mobile genetic elements, and why?

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15 Jan 2010
publication

The systemic imprint of growth and its uses in ecological (meta)genomics

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17 Dec 2009
publication

Genome-wide analysis of DNA repeats in Burkholderia cenocepacia J2315 identifies a novel adhesin-like gene unique to epidemic-associated strains of the ET-12 lineage

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01 Oct 2009
publication

Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence

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19 Sep 2009
publication

Alternative to homo-oligomerisation: the creation of local symmetry in proteins by internal amplification

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01 May 2009
publication

Genesis, effects and fates of repeats in prokaryotic genomes

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01 Apr 2009
publication

A novel heuristic for local multiple alignment of interspersed DNA repeats

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23 Jan 2009
publication

Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths

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04 Nov 2008
publication

The temporal dynamics of slightly deleterious mutations in Escherichia coli and Shigella spp

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17 Oct 2008
publication

The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients

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15 Oct 2008
publication

Evolutionary patterns in prokaryotic genomes

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25 Jun 2008
publication

An assessment of the impacts of molecular oxygen on the evolution of proteomes

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16 May 2008
publication

Swelfe: a detector of internal repeats in sequences and structures

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09 May 2008
publication

Comparison of stress distribution between complete denture and implant-retained overdenture-2D FEA

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26 Mar 2008
publication

The impact of the neisserial DNA uptake sequences on genome evolution and stability

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07 Jan 2008
publication

Persistence drives gene clustering in bacterial genomes

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01 Jan 2008
publication

The organization of the bacterial genome

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29 Sep 2007
publication

From GC skews to wavelets: a gentle guide to the analysis of compositional asymmetries in genomic data

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04 Sep 2007
publication

Causes for the intriguing presence of tRNAs in phages

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10 Jul 2007
publication

Reconstructing the ancestor of Mycobacterium leprae: the dynamics of gene loss and genome reduction

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23 Jan 2007
publication

Causes of insertion sequences abundance in prokaryotic genomes

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15 Jan 2007
publication

Erosion of interaction networks in reduced and degraded genomes

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26 Oct 2006
publication

Similar compositional biases are caused by very different mutational effects

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11 Oct 2006
publication

Repseek, a tool to retrieve approximate repeats from large DNA sequences

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24 Aug 2006
publication

Protein evolution: causes of trends in amino-acid gain and loss

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01 Jul 2006
publication

Intrastrain heterogeneity of the mgpB gene in Mycoplasma genitalium is extensive in vitro and in vivo and suggests that variation is generated via recombination with repetitive chromosomal sequences

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30 Jun 2006
publication

The quest for the universals of protein evolution

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15 May 2006
publication

An integrative method for accurate comparative genome mapping

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10 Mar 2006
publication

Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages

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01 Mar 2006
publication

Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes

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09 Nov 2005
publication

Inference and analysis of the relative stability of bacterial chromosomes

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18 Oct 2005
publication

Comparisons of dN/dS are time dependent for closely related bacterial genomes

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16 Sep 2005
publication

Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125

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26 Aug 2005
publication

Comparative and evolutionary analysis of the bacterial homologous recombination systems

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13 Jul 2005
publication

How essential are nonessential genes?

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18 Feb 2005
publication

The unusually large Plasmodium telomerase reverse-transcriptase localizes in a discrete compartment associated with the nucleolus

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12 Oct 2004
publication

Codon usage bias from tRNA’s point of view: redundancy, specialization, and efficient decoding for translation optimization

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01 Oct 2004
publication

Order and disorder in bacterial genomes

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01 Jun 2004
publication

Cytosine methylation is not the major factor inducing CpG dinucleotide deficiency in bacterial genomes

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01 Jun 2004
publication

The replication-related organization of bacterial genomes

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15 Nov 2003
publication

Gene essentiality determines chromosome organisation in bacteria

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01 Nov 2003
publication

DNA repeats lead to the accelerated loss of gene order in bacteria

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31 Oct 2003
publication

An analysis of determinants of amino acids substitution rates in bacterial proteins

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01 Aug 2003
publication

Associations between inverted repeats and the structural evolution of bacterial genomes

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01 Aug 2003
publication

A strand-specific model for chromosome segregation in bacteria

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01 Aug 2003
publication

Essentiality, not expressiveness, drives gene-strand bias in bacteria

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12 May 2003
publication

An appraisal of the potential for illegitimate recombination in bacterial genomes and its consequences: from duplications to genome reduction

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15 Oct 2002
publication

A new family of highly variable proteins in the Chlamydophila pneumoniae genome

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01 Sep 2002
publication

Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes?

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01 Jul 2002
publication

Origin and fate of repeats in bacteria

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01 Jun 2002
publication

Base composition bias might result from competition for metabolic resources

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01 May 2002
publication

Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution

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01 May 2002
publication

Over-representation of repeats in stress response genes: a strategy to increase versatility under stressful conditions?

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01 Sep 2001
publication

Ongoing evolution of strand composition in bacterial genomes

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01 Jun 2001
publication

Evolutionary role of restriction/modification systems as revealed by comparative genome analysis

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15 May 2001
publication

The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis

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01 Jul 2000
publication

The DB case: pattern matching evidence is not significant

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30 Jun 2000
publication

Sulphur islands in the Escherichia coli genome: markers of the cell’s architecture?

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31 Mar 2000
publication

Implication of gene distribution in the bacterial chromosome for the bacterial cell factory

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01 Nov 1999
publication

Functional and evolutionary roles of long repeats in prokaryotes

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01 Oct 1999
publication

Codon usage and lateral gene transfer in Bacillus subtilis

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01 Sep 1999
publication

Analysis of long repeats in bacterial genomes reveals alternative evolutionary mechanisms in Bacillus subtilis and other competent prokaryotes

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01 Sep 1999
publication

Translation in Bacillus subtilis: roles and trends of initiation and termination, insights from a genome analysis

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01 Aug 1999
publication

Bacterial DNA strand compositional asymmetry: response

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01 Apr 1999
publication

Universal replication biases in bacteria

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15 Jun 1998
publication

Oligonucleotide bias in Bacillus subtilis: general trends and taxonomic comparisons

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