Lista de obras - Eduardo Rocha - Dominio Público Uruguay

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

artículo científico publicado en 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.

artículo científico publicado en 2009

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

artículo científico publicado en 2002

A novel heuristic for local multiple alignment of interspersed DNA repeats

artículo científico publicado en 2009

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

artículo científico publicado en 2019

A strand-specific model for chromosome segregation in bacteria.

artículo científico publicado en 2003

A widespread family of polymorphic toxins encoded by temperate phages.

artículo científico publicado en 2017

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

artículo científico publicado en 2017

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

artículo científico publicado en 2022

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

artículo científico publicado en 2009

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

artículo científico publicado en 2003

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

artículo científico publicado en 2003

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

artículo científico publicado en 2008

An integrative method for accurate comparative genome mapping

artículo científico publicado en 2006

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

artículo científico publicado en 2012

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

artículo científico publicado en 2024

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

artículo científico publicado en 2020

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

artículo científico publicado en 2018

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

artículo científico publicado en 2021

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

artículo científico publicado en 2018

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

artículo científico publicado en 2011

Bacteriophages benefit from generalized transduction ⬇️

scientific article published on 05 July 2019

Base composition bias might result from competition for metabolic resources.

artículo científico publicado en 2002

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

artículo científico publicado en 2011

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

artículo científico publicado en 2018

Causes of insertion sequences abundance in prokaryotic genomes

artículo científico publicado en 2007

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

artículo científico publicado en 2012

Coevolution of the Organization and Structure of Prokaryotic Genomes.

artículo científico

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

artículo científico publicado en 2020

Comparative and evolutionary analysis of the bacterial homologous recombination systems

artículo científico publicado en 2005

Comparative genomic analysis of Acinetobacter strains isolated from murine colonic crypts

artículo científico

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

artículo científico publicado en 2006

Complete genome sequence of the fish pathogen Flavobacterium branchiophilum

artículo científico publicado en 2011

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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 2017

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

artículo científico publicado en 2019

Erosion of interaction networks in reduced and degraded genomes.

artículo científico publicado en 2007

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

artículo científico publicado en 2003

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

artículo científico publicado en 2021

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

artículo científico publicado en 2017

Evolutionary patterns in prokaryotic genomes

artículo científico publicado en 2008

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

artículo científico publicado en 2001

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

artículo científico publicado en 2016

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

artículo científico publicado en 2007

Functional and evolutionary roles of long repeats in prokaryotes.

artículo científico publicado en 1999

Genesis, effects and fates of repeats in prokaryotic genomes.

artículo científico publicado en 2009

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

artículo científico publicado en 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

artículo científico publicado en 2009

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

artículo científico publicado en 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

artículo científico publicado en 2006

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

artículo científico publicado en 2009

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

artículo científico publicado en 2011

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?

artículo científico publicado en 2005

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

artículo científico publicado en 2021

Identification and analysis of integrons and cassette arrays in bacterial genomes

artículo científico publicado en 2016

Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder

artículo científico publicado en 2017

Identification of protein secretion systems in bacterial genomes

artículo científico publicado en 2016

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

artículo científico publicado en 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

artículo científico publicado en 2017

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

artículo científico publicado en 2017

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

artículo científico publicado en 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

artículo científico publicado en 2006

Investment in rapid growth shapes the evolutionary rates of essential proteins ⬇️

artículo científico publicado el 30 de noviembre de 2011

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

artículo científico publicado en 2002

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

artículo científico publicado en 2014

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

artículo científico publicado en 2014

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

artículo científico publicado en 2013

Metabolic diversity of the emerging pathogenic lineages of Klebsiella pneumoniae

artículo científico publicado en 2017

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

artículo científico publicado en 2017

Mobility of plasmids.

artículo científico publicado en 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?

artículo científico publicado en 2010

Natural selection for operons depends on genome size.

artículo científico publicado en 2013

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

artículo científico publicado en 2018

No evidence for elemental-based streamlining of prokaryotic genomes

article

Order and disorder in bacterial genomes

artículo científico publicado en 2004

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

artículo científico publicado en 2009

PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph

artículo científico publicado en 2020

PanACoTA: a modular tool for massive microbial comparative genomics

artículo científico publicado en 2021

Parallels between experimental and natural evolution of legume symbionts.

artículo científico publicado en 2018

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

artículo científico publicado en 2020

Persistence drives gene clustering in bacterial genomes

artículo científico publicado en 2008

Pervasive domestication of defective prophages by bacteria

artículo científico publicado en 2014

Phage–host coevolution in natural populations

Phylogenetic background and habitat drive the genetic diversification of Escherichia coli

artículo científico publicado en 2020

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

artículo científico publicado en 2006

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

artículo científico publicado en 2021

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

artículo científico publicado en 2012

Real-time search of all bacterial and viral genomic data

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

artículo científico publicado en 2007

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

artículo científico publicado en 2017

Regulation of genetic flux between bacteria by restriction-modification systems

artículo científico publicado en 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.

artículo científico publicado en 2006

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

artículo científico publicado en 2022

Similar compositional biases are caused by very different mutational effects.

artículo científico publicado en 2006

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

artículo científico publicado en 2000

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

artículo científico publicado en 2014

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

artículo científico publicado en 2016

The adaptation of temperate bacteriophages to their host genomes.

artículo científico publicado en 2012

The chromosomal accommodation and domestication of mobile genetic elements.

artículo científico publicado en 2014

The chromosomal organization of horizontal gene transfer in bacteria

artículo científico publicado en 2017

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

artículo científico publicado en 1997

The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis

artículo científico publicado en 2001

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

artículo científico publicado en 2014

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

artículo científico publicado en 2021

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

artículo científico publicado en 2008

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

artículo científico publicado en 2014

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

artículo científico publicado en 2020

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

artículo científico publicado en 2012

The organization of the bacterial genome.

artículo científico publicado en 2008

The quest for the universals of protein evolution

artículo científico publicado en 2006

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

artículo científico publicado en 2011

The replication-related organization of bacterial genomes.

artículo científico publicado en 2004

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

artículo científico publicado en 2010

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

artículo científico publicado en 2010

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

artículo científico publicado en 2008

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

artículo científico publicado en 2005

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

artículo científico publicado en 2014

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

artículo científico publicado en 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

artículo científico publicado en 2016

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

artículo científico publicado en 2010

With a Little Help from Prokaryotes

artículo científico publicado en 2013

Lista de obras de Eduardo Rocha

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

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.

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

A novel heuristic for local multiple alignment of interspersed DNA repeats

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

A strand-specific model for chromosome segregation in bacteria.

A widespread family of polymorphic toxins encoded by temperate phages.

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

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

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

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

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

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

An integrative method for accurate comparative genome mapping

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

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

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

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

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

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

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

Bacteriophages benefit from generalized transduction ⬇️

Base composition bias might result from competition for metabolic resources.

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

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

Causes of insertion sequences abundance in prokaryotic genomes

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

Coevolution of the Organization and Structure of Prokaryotic Genomes.

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

Comparative and evolutionary analysis of the bacterial homologous recombination systems

Comparative genomic analysis of Acinetobacter strains isolated from murine colonic crypts

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

Complete genome sequence of the fish pathogen Flavobacterium branchiophilum

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

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

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

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

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

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

Erosion of interaction networks in reduced and degraded genomes.

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

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

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

Evolutionary patterns in prokaryotic genomes

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

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

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

Functional and evolutionary roles of long repeats in prokaryotes.

Genesis, effects and fates of repeats in prokaryotic genomes.

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

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

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

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

Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages

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

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

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

How essential are nonessential genes?

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

Identification and analysis of integrons and cassette arrays in bacterial genomes

Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder

Identification of protein secretion systems in bacterial genomes

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

Inference and Analysis of the Relative Stability of Bacterial Chromosomes

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

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

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

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

Investment in rapid growth shapes the evolutionary rates of essential proteins ⬇️

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

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

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

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

Metabolic diversity of the emerging pathogenic lineages of Klebsiella pneumoniae

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

Mobility of plasmids.

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

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

Natural selection for operons depends on genome size.