Timeline
Eduardo Rocha
Head of Structure
12 Mar 2024
publication
Perturbation and resilience of the gut microbiome up to 3 months after β-lactams exposure in healthy volunteers suggest an important role of microbial β-lactamases.
Read more06 Mar 2024
publication
Capsules and their traits shape phage susceptibility and plasmid conjugation efficiency
Read more20 Feb 2024
22 Jan 2024
event
GG department seminar: Tai Dagan (University of Kiel, Germany): “Multilevel drift and selection in the evolution of prokaryotic plasmids”; February 1st, 2024 @11.00am; Auditorium F. Jacob
Read more12 Jan 2024
publication
Cassette recombination dynamics within chromosomal integrons are regulated by toxin-antitoxin systems
Read more03 Jan 2024
publication
Integron cassettes integrate into bacterial genomes via widespread non-classical attG sites
Read more06 Nov 2023
news
Chance Favors the Prepared Genomes: Horizontal Transfer Shapes the Emergence of Antibiotic Resistance Mutations in Core Genes.
Read more04 Oct 2023
publication
Chance Favors the Prepared Genomes: Horizontal Transfer Shapes the Emergence of Antibiotic Resistance Mutations in Core Genes.
Read more03 Aug 2023
publication
Latent evolution of biofilm formation depends on life-history and genetic background
Read more30 May 2023
news
The parasites of parasites: identification and characterization of thousands of bacteriophage satellites across bacteria
Read more30 May 2023
06 Apr 2023
news
Highlighted paper: “Competition between lysogenic and sensitive bacteria is determined by the fitness costs of the different emerging phage-resistance strategies” ; Rendueles et al. ; eLife – March 2023
Read more28 Mar 2023
publication
Competition between lysogenic and sensitive bacteria is determined by the fitness costs of the different emerging phage-resistance strategies.
Read more03 Mar 2023
publication
Identification and characterization of thousands of bacteriophage satellites across bacteria.
Read more29 Nov 2022
publication
Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation.
Read more19 Oct 2022
publication
Structural and Genomic Evolution of RRNPPA Systems and Their Pheromone Signaling.
Read more26 Sep 2022
publication
Phage-Plasmids Spread Antibiotic Resistance Genes through Infection and Lysogenic Conversion.
Read more13 Aug 2022
publication
Adaptation to novel spatially-structured environments is driven by the capsule and alters virulence-associated traits.
Read more02 Jun 2022
publication
Evolution of Plasmid Mobility: Origin and Fate of Conjugative and Nonconjugative Plasmids.
Read more11 May 2022
17 Jan 2022
publication
To catch a hijacker: abundance, evolution and genetic diversity of P4-like bacteriophage satellites.
Read more10 Nov 2021
news
Back on: “The Ancient DNA journey: from humans to human pathogens and microbiomes” – 4/11/2021
Read more21 Oct 2021
06 Oct 2021
01 Jul 2021
publication
Interplay between the cell envelope and mobile genetic elements shapes gene flow in populations of the nosocomial pathogen Klebsiella pneumoniae.
Read more22 Apr 2021
22 Apr 2021
22 Apr 2021
news
Bacteria have numerous phage–plasmids with conserved phage and variable plasmid genes
Read more18 Mar 2021
publication
Bacteria have numerous distinctive groups of phage-plasmids with conserved phage and variable plasmid gene repertoires.
Read more03 Mar 2021
03 Mar 2021
publication
Nutrient conditions are primary drivers of bacterial capsule maintenance in Klebsiella
Read more01 Mar 2021
publication
The impact of genetic diversity on gene essentiality within the Escherichia coli species.
Read more11 Feb 2021
publication
Causes and consequences of bacteriophage diversification via genetic exchanges across lifestyles and bacterial taxa.
Read more31 Jul 2020
30 Jul 2020
publication
Modular prophage interactions driven by capsule serotype select for capsule loss under phage predation
Read more17 Jul 2020
publication
Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids.
Read more05 Jun 2020
01 Jun 2020
publication
Phylogenetic background and habitat drive the genetic diversification of Escherichia coli.
Read more08 May 2020
publication
The major subunit of widespread competence pili exhibits a novel and conserved type IV pilin fold.
Read more01 May 2020
publication
The Evolution of Protein Secretion Systems by Co-option and Tinkering of Cellular Machineries.
Read more29 Apr 2020
publication
Macromolecular crowding links ribosomal protein gene dosage to growth rate in Vibrio cholerae.
Read more10 Feb 2020
news
Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements
Read more10 Feb 2020
news
Community diversity and habitat structure shape the repertoire of extracellular proteins in bacteria
Read more07 Feb 2020
publication
Intracellular Positioning Systems Limit the Entropic Eviction of Secondary Replicons Toward the Nucleoid Edges in Bacterial Cells.
Read more06 Feb 2020
publication
Community diversity and habitat structure shape the repertoire of extracellular proteins in bacteria.
Read more01 Feb 2020
24 Jan 2020
publication
Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements
Read more01 Jan 2020
publication
Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan.
Read more03 Sep 2019
19 Jul 2019
publication
Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility
Read more18 Jul 2019
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
Read more24 Apr 2019
12 Feb 2019
04 Feb 2019
07 Jan 2019
21 Dec 2018
02 Jul 2018
publication
CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins
Read more14 Jun 2018
publication
Host range and genetic plasticity explain the co-existence of integrative and extrachromosomal mobile genetic elements
Read more12 Jun 2018
11 Jun 2018
01 Jun 2018
publication
Neutral Theory, Microbial Practice: Challenges in Bacterial Population Genetics
Read more01 Jan 2018
publication
Bacillus subtilis, the model Gram-positive bacterium: 20 years of annotation refinement
Read more12 Dec 2017
11 Oct 2017
10 Oct 2017
02 Oct 2017
publication
Metagenomic assessment of the interplay between the environment and the genetic diversification of Acinetobacter
Read more19 Sep 2017
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.
Read more06 Sep 2017
publication
Integrative and conjugative elements and their hosts: composition, distribution and organization
Read more29 Aug 2017
24 Jul 2017
publication
Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens
Read more24 May 2017
news
Emerging diseases: a highly mutant strain of the Elizabethkingia bacterium caused an outbreak in Wisconsin
Read more12 Apr 2017
event
“Microbiome evolution and function in social bees” by Nancy MORAN – Genomes & Genetics Departemental seminar co-organized with Microbiology Departement
Read more10 Apr 2017
publication
Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer
Read more28 Mar 2017
publication
Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance.
Read more15 Mar 2017
01 Mar 2017
publication
Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder
Read more01 Feb 2017
20 Dec 2016
10 Oct 2016
news
A population biology study of Listeria ushers in a new era in listeriosis surveillance
Read more11 Sep 2016
27 Jul 2016
publication
Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis
Read more02 May 2016
publication
Regulation of genetic flux between bacteria by restriction-modification systems.
Read more29 Apr 2016
publication
Identification and analysis of integrons and cassette arrays in bacterial genomes.
Read more25 Mar 2016
publication
Genetic and life-history traits associated with the distribution of prophages in bacteria.
Read more17 Mar 2016
16 Mar 2016
01 Mar 2016
01 Mar 2016
publication
Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity.
Read more01 Mar 2016
publication
The impact of selection, gene conversion, and biased sampling on the assessment of microbial demography
Read more01 Feb 2016
news
Listeria: identification of hypervirulent strains with placental and cerebral tropism
Read more04 Jan 2016
15 Nov 2015
10 Nov 2015
09 Oct 2015
08 Oct 2015
06 Oct 2015
10 Sep 2015
10 Sep 2015
05 Sep 2015
05 Sep 2015
05 Sep 2015
05 Sep 2015
05 Sep 2015
05 Sep 2015
04 Sep 2015
04 Sep 2015
04 Sep 2015
04 Sep 2015
15 Jun 2015
15 Jun 2015
11 May 2015
05 May 2015
publication
Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations
Read more25 Feb 2015
publication
Insights on the emergence of Mycobacterium tuberculosis from the analysis of Mycobacterium kansasii
Read more13 Nov 2014
publication
TLR9 activation is triggered by the excess of stimulatory versus inhibitory motifs present in Trypanosomatidae DNA
Read more17 Oct 2014
publication
MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems
Read more13 Oct 2014
publication
The genomic diversification of the whole Acinetobacter genus: origins, mechanisms, and consequences.
Read more08 Oct 2014
02 Sep 2014
publication
Transient hypermutagenesis accelerates the evolution of legume endosymbionts following horizontal gene transfer
Read more12 Aug 2014
publication
The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts
Read more04 Aug 2014
12 Mar 2014
publication
Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion
Read more09 Jan 2014
26 Sep 2013
publication
Manipulating or superseding host recombination functions: a dilemma that shapes phage evolvability
Read more01 Mar 2013
publication
Clinical trial evaluating color change and tooth sensitivity throughout and following in-office bleaching
Read more01 Mar 2013
01 Jan 2013
01 Jan 2013
publication
Natural genome diversity of AI-2 quorum sensing in Escherichia coli: conserved signal production but labile signal reception
Read more12 Dec 2012
26 Nov 2012
publication
Rapid evolution of the sequences and gene repertoires of secreted proteins in bacteria
Read more21 Nov 2012
30 Oct 2012
publication
Influence of platform and abutment angulation on peri-implant bone. A three-dimensional finite element stress analysis
Read more11 Oct 2012
publication
Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements
Read more27 Sep 2012
publication
The non-flagellar type III secretion system evolved from the bacterial flagellum and diversified into host-cell adapted systems
Read more13 Sep 2012
24 Aug 2012
publication
Characterization of novel phages isolated in coagulase-negative staphylococci reveals evolutionary relationships with Staphylococcus aureus phages
Read more06 Jul 2012
publication
A Single Amino Acid Substitution Changes the Self-Assembly Status of a Type IV Piliation Secretin
Read more29 Feb 2012
publication
After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection
Read more02 Feb 2012
publication
Immune subversion and quorum-sensing shape the variation in infectious dose among bacterial pathogens
Read more30 Nov 2011
publication
Investment in rapid growth shapes the evolutionary rates of essential proteins
Read more16 Sep 2011
18 Aug 2011
publication
The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation
Read more18 Mar 2011
publication
CRISPR distribution within the Escherichia coli species is not suggestive of immunity-associated diversifying selection
Read more24 Feb 2011
publication
Function-specific accelerations in rates of sequence evolution suggest predictable epistatic responses to reduced effective population size
Read more27 Jan 2011
publication
Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes
Read more09 Sep 2010
publication
Mutational patterns cannot explain genome composition: Are there any neutral sites in the genomes of bacteria?
Read more01 Sep 2010
15 Jun 2010
publication
The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella
Read more08 Apr 2010
24 Mar 2010
15 Jan 2010
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
Read more01 Oct 2009
publication
Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence
Read more19 Sep 2009
publication
Alternative to homo-oligomerisation: the creation of local symmetry in proteins by internal amplification
Read more01 May 2009
01 Apr 2009
23 Jan 2009
publication
Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths
Read more04 Nov 2008
publication
The temporal dynamics of slightly deleterious mutations in Escherichia coli and Shigella spp
Read more17 Oct 2008
publication
The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients
Read more15 Oct 2008
25 Jun 2008
publication
An assessment of the impacts of molecular oxygen on the evolution of proteomes
Read more16 May 2008
09 May 2008
publication
Comparison of stress distribution between complete denture and implant-retained overdenture-2D FEA
Read more26 Mar 2008
publication
The impact of the neisserial DNA uptake sequences on genome evolution and stability
Read more07 Jan 2008
01 Jan 2008
29 Sep 2007
publication
From GC skews to wavelets: a gentle guide to the analysis of compositional asymmetries in genomic data
Read more04 Sep 2007
10 Jul 2007
publication
Reconstructing the ancestor of Mycobacterium leprae: the dynamics of gene loss and genome reduction.
Read more23 Jan 2007
15 Jan 2007
26 Oct 2006
11 Oct 2006
24 Aug 2006
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
Read more30 Jun 2006
15 May 2006
10 Mar 2006
publication
Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages
Read more01 Mar 2006
publication
Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes
Read more09 Nov 2005
18 Oct 2005
16 Sep 2005
publication
Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125
Read more26 Aug 2005
publication
Comparative and evolutionary analysis of the bacterial homologous recombination systems
Read more13 Jul 2005
01 Jan 2005
publication
The unusually large Plasmodium telomerase reverse-transcriptase localizes in a discrete compartment associated with the nucleolus.
Read more12 Oct 2004
publication
Codon usage bias from tRNA’s point of view: redundancy, specialization, and efficient decoding for translation optimization
Read more01 Oct 2004
01 Jun 2004
01 Jun 2004
publication
Cytosine methylation is not the major factor inducing CpG dinucleotide deficiency in bacterial genomes
Read more15 Nov 2003
01 Nov 2003
31 Oct 2003
publication
An analysis of determinants of amino acids substitution rates in bacterial proteins
Read more01 Aug 2003
publication
Associations between inverted repeats and the structural evolution of bacterial genomes
Read more01 Aug 2003
01 Aug 2003
12 May 2003
publication
An appraisal of the potential for illegitimate recombination in bacterial genomes and its consequences: from duplications to genome reduction
Read more15 Oct 2002
publication
A new family of highly variable proteins in the Chlamydophila pneumoniae genome
Read more01 Sep 2002
publication
Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes?
Read more01 Jul 2002
01 Jun 2002
01 May 2002
01 May 2002
publication
Over-representation of repeats in stress response genes: a strategy to increase versatility under stressful conditions?
Read more01 Sep 2001
01 Jun 2001
publication
Evolutionary role of restriction/modification systems as revealed by comparative genome analysis
Read more15 May 2001
publication
The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis
Read more01 Jul 2000
30 Jun 2000
publication
Sulphur islands in the Escherichia coli genome: markers of the cell’s architecture?
Read more31 Mar 2000
publication
Implication of gene distribution in the bacterial chromosome for the bacterial cell factory
Read more01 Nov 1999
01 Oct 1999
01 Sep 1999
publication
Analysis of long repeats in bacterial genomes reveals alternative evolutionary mechanisms in Bacillus subtilis and other competent prokaryotes
Read more01 Sep 1999
publication
Translation in Bacillus subtilis: roles and trends of initiation and termination, insights from a genome analysis
Read more01 Aug 1999
01 Apr 1999
15 Jun 1998
publication