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Ecogenetics of antibiotic resistance in Listeria monocytogenes

Molecular microbiology, 2020-03, Vol.113 (3), p.570-579

2020

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Dissemination of cephalosporin resistance genes between Escherichia coli strains from farm animals and humans by specific plasmid lineages

PLoS genetics, 2014-12, Vol.10 (12), p.e1004776-e1004776

2014

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PLACNETw: a web-based tool for plasmid reconstruction from bacterial genomes

Bioinformatics (Oxford, England), 2017-12, Vol.33 (23), p.3796-3798

2017

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Plasmid flux in Escherichia coli ST131 sublineages, analyzed by plasmid constellation network (PLACNET), a new method for plasmid reconstruction from whole genome sequences

PLoS genetics, 2014-12, Vol.10 (12), p.e1004766-e1004766

2014

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Gene Transmission in the One Health Microbiosphere and the Channels of Antimicrobial Resistance

Frontiers in microbiology, 2019-12, Vol.10, p.2892

2019

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Microcins in Enterobacteriaceae: Peptide Antimicrobials in the Eco-Active Intestinal Chemosphere

Frontiers in microbiology, 2019-10, Vol.10, p.2261-2261

2019

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Fecal microbiota transplantation in HIV: A pilot placebo-controlled study

Nature communications, 2021-02, Vol.12 (1), p.1139-1139, Article 1139

2021

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Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era

Nature communications, 2021-03, Vol.12 (1), p.1523-1523, Article 1523

2021

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Phylogenomics of Globally Spread Clonal Groups 14 and 15 of Klebsiella pneumoniae

Microbiology spectrum, 2023-06, Vol.11 (3), p.e0339522-e0339522

2023

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AcCNET (Accessory Genome Constellation Network): comparative genomics software for accessory genome analysis using bipartite networks

Bioinformatics (Oxford, England), 2017-01, Vol.33 (2), p.283-285

2017

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Strain-specific predation of Bdellovibrio bacteriovorus on Pseudomonas aeruginosa with a higher range for cystic fibrosis than for bacteremia isolates

Scientific reports, 2022-06, Vol.12 (1), p.10523-10523, Article 10523

2022

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In-depth resistome analysis by targeted metagenomics

Microbiome, 2018-01, Vol.6 (1), p.11-14, Article 11

2018

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PipX, the coactivator of NtcA, is a global regulator in cyanobacteria

Proceedings of the National Academy of Sciences - PNAS, 2014-06, Vol.111 (23), p.E2423-E2430

2014

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The ICU environment contributes to the endemicity of the " Serratia marcescens complex" in the hospital setting

mBio, 2024-05, Vol.15 (5), p.e0305423-e0305423

2024

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Genomics of Serratia marcescens Isolates Causing Outbreaks in the Same Pediatric Unit 47 Years Apart: Position in an Updated Phylogeny of the Species

Frontiers in microbiology, 2020-03, Vol.11, p.451-451

2020

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Relationship of Diet to Gut Microbiota and Inflammatory Biomarkers in People with HIV

Nutrients, 2022-03, Vol.14 (6), p.1221

2022

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Co-diversification of Enterococcus faecium Core Genomes and PBP5: Evidences of pbp5 Horizontal Transfer

Frontiers in microbiology, 2016-10, Vol.7, p.1581-1581

2016

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High Genomic Diversity and Heterogenous Origins of Pathogenic and Antibiotic-Resistant Escherichia coli in Household Settings Represent a Challenge to Reducing Transmission in Low-Income Settings

mSphere, 2020-01, Vol.5 (1)

2020

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A 21-Year Survey of Escherichia coli from Bloodstream Infections (BSI) in a Tertiary Hospital Reveals How Community-Hospital Dynamics of B2 Phylogroup Clones Influence Local BSI Rates

mSphere, 2021-12, Vol.6 (6), p.e0086821-e0086821

2021

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Serum microRNAs are key predictors of long‐term heart failure and cardiovascular death after myocardial infarction

ESC Heart Failure, 2022-10, Vol.9 (5), p.3367-3379

2022

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Mge-cluster: a reference-free approach for typing bacterial plasmids

NAR genomics and bioinformatics, 2023-09, Vol.5 (3)

2023

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Detection of Minority Variants and Mixed Infections in Mycobacterium tuberculosis by Direct Whole-Genome Sequencing on Noncultured Specimens Using a Specific-DNA Capture Strategy

mSphere, 2021-12, Vol.6 (6), p.e0074421-e0074421

2021

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PATO: Pangenome Analysis Toolkit

Bioinformatics, 2021-12, Vol.37 (23), p.4564-4566

2021

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Fitness cost of vancomycin-resistant Enterococcus faecium plasmids associated with hospital infection outbreaks

Journal of antimicrobial chemotherapy, 2021-10, Vol.76 (11), p.2757-2764

2021

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Ecogenetics of antibiotic resistance in Listeria monocytogenes

Dissemination of cephalosporin resistance genes between Escherichia coli strains from farm animals and humans by specific plasmid lineages

PLACNETw: a web-based tool for plasmid reconstruction from bacterial genomes

Plasmid flux in Escherichia coli ST131 sublineages, analyzed by plasmid constellation network (PLACNET), a new method for plasmid reconstruction from whole genome sequences

Gene Transmission in the One Health Microbiosphere and the Channels of Antimicrobial Resistance

Microcins in Enterobacteriaceae: Peptide Antimicrobials in the Eco-Active Intestinal Chemosphere

Fecal microbiota transplantation in HIV: A pilot placebo-controlled study

Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era

Phylogenomics of Globally Spread Clonal Groups 14 and 15 of Klebsiella pneumoniae

AcCNET (Accessory Genome Constellation Network): comparative genomics software for accessory genome analysis using bipartite networks

Strain-specific predation of Bdellovibrio bacteriovorus on Pseudomonas aeruginosa with a higher range for cystic fibrosis than for bacteremia isolates

In-depth resistome analysis by targeted metagenomics

PipX, the coactivator of NtcA, is a global regulator in cyanobacteria

The ICU environment contributes to the endemicity of the " Serratia marcescens complex" in the hospital setting

Genomics of Serratia marcescens Isolates Causing Outbreaks in the Same Pediatric Unit 47 Years Apart: Position in an Updated Phylogeny of the Species

Relationship of Diet to Gut Microbiota and Inflammatory Biomarkers in People with HIV

Co-diversification of Enterococcus faecium Core Genomes and PBP5: Evidences of pbp5 Horizontal Transfer

High Genomic Diversity and Heterogenous Origins of Pathogenic and Antibiotic-Resistant Escherichia coli in Household Settings Represent a Challenge to Reducing Transmission in Low-Income Settings

A 21-Year Survey of Escherichia coli from Bloodstream Infections (BSI) in a Tertiary Hospital Reveals How Community-Hospital Dynamics of B2 Phylogroup Clones Influence Local BSI Rates

Serum microRNAs are key predictors of long‐term heart failure and cardiovascular death after myocardial infarction

Mge-cluster: a reference-free approach for typing bacterial plasmids

The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies [version 2; peer review: 2 approved]

Detection of Minority Variants and Mixed Infections in Mycobacterium tuberculosis by Direct Whole-Genome Sequencing on Noncultured Specimens Using a Specific-DNA Capture Strategy

PATO: Pangenome Analysis Toolkit

Fitness cost of vancomycin-resistant Enterococcus faecium plasmids associated with hospital infection outbreaks

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