List of works by Eduardo Rocha

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

scientific article published on 01 May 2019

A module located at a chromosomal integration hot spot is responsible for the multidrug resistance of a reference strain from Escherichia coli clonal group A.

scientific article published on 13 April 2009

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

scientific article

A novel heuristic for local multiple alignment of interspersed DNA repeats

scientific article

A simple, reproducible and cost-effective procedure to analyse gut phageome: from phage isolation to bioinformatic approach

scientific article published on 05 August 2019

A strand-specific model for chromosome segregation in bacteria.

scientific article published on August 2003

A widespread family of polymorphic toxins encoded by temperate phages.

scientific article published on 29 August 2017

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

scientific article

Adaptation to novel spatially-structured environments is driven by the capsule and alters virulence-associated traits

scientific article published in 2022

Alternative to Homo-oligomerisation: The Creation of Local Symmetry in Proteins by Internal Amplification

scientific article published on 19 September 2009

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

scientific article published on 31 October 2003

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

scientific article

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

scientific article published on 25 June 2008

An integrative method for accurate comparative genome mapping

scientific article

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

scientific article published on 11 October 2012

Assembly of a unique membrane complex in type VI secretion systems of Bacteroidota

scientific article published in 2024

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

scientific article published on 01 January 2020

Author Correction: Parallels between experimental and natural evolution of legume symbionts

scientific article published in Nature Communications

Author Correction: The impact of genetic diversity on gene essentiality within the Escherichia coli species

correction of a scholarly article

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

scientific article published in January 2018

Bacterial cooperation controlled by mobile elements: kin selection and infectivity are part of the same process.

scientific article published on 27 July 2011

Bacteriophages benefit from generalized transduction ⬇️

scientific article published on 05 July 2019

Base composition bias might result from competition for metabolic resources.

scientific article published in June 2002

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

scientific article published on 18 March 2011

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

scientific article published in July 2018

Causes of insertion sequences abundance in prokaryotic genomes

scientific article published on 23 January 2007

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

scientific article published on 24 August 2012

Coevolution of the Organization and Structure of Prokaryotic Genomes.

scientific article published on 04 January 2016

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

scientific article published on 06 February 2020

Comparative and evolutionary analysis of the bacterial homologous recombination systems

scientific article published in August 2005

Comparative genomic analysis of Acinetobacter strains isolated from murine colonic crypts

scientific article published on 11 July 2017

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

scientific article

Complete genome sequence of the fish pathogen Flavobacterium branchiophilum

scientific article published on 16 September 2011

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

scientific article published in June 2004

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

article

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

scientific article published on 28 March 2017

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

scientific article published on 19 July 2019

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

scientific article

Environmental structure drives resistance to phages and antibiotics during phage therapy and to invading lysogens during colonisation

scientific article published on 28 February 2019

Erosion of interaction networks in reduced and degraded genomes.

scientific article published in January 2007

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

scientific article published in August 2003

Evolution of ColE1-like plasmids across γ-Proteobacteria: From bacteriocin production to antimicrobial resistance

scientific article published on 30 November 2021

Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain

scientific article

Evolutionary patterns in prokaryotic genomes

scientific article published on 15 October 2008

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

scientific article published on 01 June 2001

Experimental evolution of rhizobia may lead to either extra- or intracellular symbiotic adaptation depending on the selection regime.

scientific article

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

scientific article

Functional and evolutionary roles of long repeats in prokaryotes.

scientific article

Genesis, effects and fates of repeats in prokaryotic genomes.

scientific article

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

scientific article published on 25 March 2016

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

scientific article published on 17 December 2009

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

scientific article published on 27 July 2016

HflXr, a homolog of a ribosome-splitting factor, mediates antibiotic resistance

article published in the Proceedings of the National Academy of Sciences of the United States of America

Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages

scientific article

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

scientific article published on October 2009

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

scientific article

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

scholarly article by Jean Cury published in June 2018

How essential are nonessential genes?

scientific article

Human commensal gut Proteobacteria withstand type VI secretion attacks through immunity protein-independent mechanisms

scientific article published on 01 October 2021

Identification and analysis of integrons and cassette arrays in bacterial genomes

scientific article published on 29 April 2016

Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder

scientific article

Identification of protein secretion systems in bacterial genomes

scientific article published on 16 March 2016

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

scientific article published on 2 February 2012

Inference and Analysis of the Relative Stability of Bacterial Chromosomes

article

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

scientific article published on 12 December 2017

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

scientific article published on September 2017

Interplay between the cell envelope and mobile genetic elements shapes gene flow in populations of the nosocomial pathogen Klebsiella pneumoniae

scientific article published on 06 July 2021

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

scientific article

Investment in rapid growth shapes the evolutionary rates of essential proteins

scientific article (publication date: 13 December 2011)

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

scientific article

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

scientific article

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

scientific article

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

scientific article

Metabolic diversity of the emerging pathogenic lineages of Klebsiella pneumoniae

scientific article

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

scientific article

Mobility of plasmids.

scientific article published on September 2010

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

scientific article published on 30 July 2020

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

scientific article

Natural selection for operons depends on genome size.

scientific article published on January 2013

Neutral theory, microbial practice: challenges in bacterial population genetics.

scientific article published on 19 April 2018

No evidence for elemental-based streamlining of prokaryotic genomes

article

Order and disorder in bacterial genomes

scientific article published in October 2004

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

scientific article published in January 2009

PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph

scientific article published on 19 March 2020

PanACoTA: a modular tool for massive microbial comparative genomics

scientific article published on 12 January 2021

Parallels between experimental and natural evolution of legume symbionts.

scientific article

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

scientific article published on 17 July 2020

Persistence drives gene clustering in bacterial genomes

scientific article

Pervasive domestication of defective prophages by bacteria

scientific article

Phage–host coevolution in natural populations

Phylogenetic background and habitat drive the genetic diversification of Escherichia coli

scientific article published on 12 June 2020

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

scientific article published in August 2006

Publisher Correction: The impact of genetic diversity on gene essentiality within the Escherichia coli species

correction of a scholarly article

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

scientific article

Real-time search of all bacterial and viral genomic data

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

scientific article published on 10 July 2007

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

scientific article

Regulation of genetic flux between bacteria by restriction-modification systems

scientific article published on 02 May 2016

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

article

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

scientific article published on 11 October 2006

Selfish, promiscuous and sometimes useful: how mobile genetic elements drive horizontal gene transfer in microbial populations

scientific article published in 2022

Similar compositional biases are caused by very different mutational effects.

scientific article

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

scientific article published in June 2000

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

scientific article

The DB case: pattern matching evidence is not significant. MicroCorrespondence

article

The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography

scientific article

The adaptation of temperate bacteriophages to their host genomes.

scientific article published on 12 December 2012

The chromosomal accommodation and domestication of mobile genetic elements.

scientific article

The chromosomal organization of horizontal gene transfer in bacteria

scientific article published on 10 October 2017

The complete genome sequence of the gram-positive bacterium Bacillus subtilis

scientific article

The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis

scientific article

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

scientific article

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

scientific article published in 2021

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

scientific article published on 26 March 2008

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

scientific article

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

scientific article published on 09 April 2020

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

scientific article

The organization of the bacterial genome.

scientific article published on January 2008

The quest for the universals of protein evolution.

scientific article published on 30 June 2006

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

scientific article

The replication-related organization of bacterial genomes.

scientific article published on June 2004

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

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

Ultrafast search of all deposited bacterial and viral genomic data

scientific article published on 04 February 2019

Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity

scientific article published in February 2016

Universal replication biases in bacteria

article

Unlinked rRNA genes are widespread among bacteria and archaea

scientific article published on 11 November 2019

Using Sex to Cure the Genome

scientific article

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

scientific article

With a Little Help from Prokaryotes

scientific article

Paulina is supported by:

About Paulina

Help