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The organization of the bacterial genome

Annual review of genetics, 2008-01, Vol.42 (1), p.211-233

Rocha, Eduardo P C

2008

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

Microbial biotechnology, 2018-01, Vol.11 (1), p.3-17

2018

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Genesis, effects and fates of repeats in prokaryotic genomes

FEMS microbiology reviews, 2009-05, Vol.33 (3), p.539-571

2009

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Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation

Nucleic acids research, 2023-04, Vol.51 (7), p.3001-3016

2023

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Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity

Nature genetics, 2016-03, Vol.48 (3), p.308-313

2016

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Evolution of Plasmid Mobility: Origin and Fate of Conjugative and Nonconjugative Plasmids

Molecular biology and evolution, 2022-06, Vol.39 (6)

2022

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

PLoS genetics, 2011-01, Vol.7 (1), p.e1001284

2011

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

PLoS genetics, 2012-09, Vol.8 (9), p.e1002983-e1002983

2012

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

PLoS genetics, 2011-08, Vol.7 (8), p.e1002222-e1002222

2011

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

PLoS genetics, 2010-01, Vol.6 (1), p.e1000808

2010

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Chance Favors the Prepared Genomes: Horizontal Transfer Shapes the Emergence of Antibiotic Resistance Mutations in Core Genes

Molecular biology and evolution, 2023-10, Vol.40 (10)

2023

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The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis

Nucleic acids research, 2001-05, Vol.29 (10), p.2145-2153

2001

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Coevolution of the Organization and Structure of Prokaryotic Genomes

Cold Spring Harbor perspectives in biology, 2016-01, Vol.8 (1), p.a018168-a018168

2016

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

Genome research, 2004-11, Vol.14 (11), p.2279-2286

Rocha, Eduardo P C

2004

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

Genome research, 2012-04, Vol.22 (4), p.721-734

2012

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Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder

Methods in molecular biology (Clifton, N.J.), 2017, Vol.1615, p.1

2017

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Horizontal Gene Transfer of the Secretome Drives the Evolution of Bacterial Cooperation and Virulence

Current biology, 2009-11, Vol.19 (20), p.1683-1691

2009

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

Scientific reports, 2019-02, Vol.9 (1), p.3149, Article 3149

2019

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A PNPase dependent CRISPR System in Listeria

PLoS genetics, 2014-01, Vol.10 (1), p.e1004065-e1004065

2014

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

Environmental microbiology, 2017-12, Vol.19 (12), p.5010-5024

2017

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

PLoS genetics, 2010-09, Vol.6 (9), p.e1001104-e1001104

2010

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

PLoS biology, 2014-09, Vol.12 (9), p.e1001942

2014

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Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan

Methods in molecular biology (Clifton, N.J.), 2020, Vol.2075, p.265

2020

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

Molecular microbiology, 2006-03, Vol.59 (5), p.1506-1518

2006

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Base composition bias might result from competition for metabolic resources

Trends in genetics, 2002-06, Vol.18 (6), p.291-294

2002

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The organization of the bacterial genome

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

Genesis, effects and fates of repeats in prokaryotic genomes

Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation

Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity

Evolution of Plasmid Mobility: Origin and Fate of Conjugative and Nonconjugative Plasmids

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

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

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

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

Chance Favors the Prepared Genomes: Horizontal Transfer Shapes the Emergence of Antibiotic Resistance Mutations in Core Genes

The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis

Coevolution of the Organization and Structure of Prokaryotic Genomes

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

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

Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder

Horizontal Gene Transfer of the Secretome Drives the Evolution of Bacterial Cooperation and Virulence

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

A PNPase dependent CRISPR System in Listeria

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

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

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

Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan

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

Base composition bias might result from competition for metabolic resources

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