HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities

Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C

(2020) Alyssa G. Kent et al.   Nature Communications

Linking the resistome and plasmidome to the microbiome

(2019) Thibault Stalder et al.   ISME Journal

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

MetaTOR: A Computational Pipeline to Recover High-Quality Metagenomic Bins From Mammalian Gut Proximity-Ligation (meta3C) Libraries

(2019) Lyam Baudry et al.   Frontiers in Genetics

Microbiota Composition and Functional Profiling Throughout the Gastrointestinal Tract of Commercial Weaning Piglets

(2019) Gresse et al.   Microorganisms

Longitudinal Analysis of the Microbiota Composition and Enterotypes of Pigs from Post-Weaning to Finishing

(2019) Mathilde Le Sciellour et al.   Microorganisms

Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation

(2019) Eitan Yaffe et al.   Nature Microbiology

Comparative biogeography of the gut microbiome between Jinhua and Landrace pigs

(2018) Yingping Xiao et al.   Scientific Reports

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

(2018) Gherman V. Uritskiy et al.   Microbiome

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay

(2017) Martial Marbouty et al.   Science Advances

Antimicrobial usage and resistance in beef production

(2016) Andrew Cameron et al.   Journal of Animal Science and Biotechnology

Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps

(2014) Joshua N. Burton et al.   G3-Genes Genomes Genetics

Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms

(2014) Martial Marbouty et al.   eLife

Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products

(2014) Christopher W. Beitel et al.   PeerJ

Severe Sepsis Facilitates Intestinal Colonization by Extended-Spectrum-β-Lactamase-Producing Klebsiella pneumoniae and Transfer of the SHV-18 Resistance Gene to Escherichia coli during Antimicrobial Treatment

(2013) Jun Guan et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The role of horizontal gene transfer in the dissemination of extended-spectrum beta-lactamase–producing Escherichia coli and Klebsiella pneumoniae isolates in an endemic setting

(2012) Yohei Doi et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae

(2012) B. Stecher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In-feed antibiotic effects on the swine intestinal microbiome

(2012) T. Looft et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resistance Gene Transfer during Treatments for Experimental Avian Colibacillosis

(2011) Alexandra Dheilly et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Comparative fecal metagenomics unveils unique functional capacity of the swine gut

(2011) Regina Lamendella et al.   BMC MICROBIOLOGY

Antibiotics in Feed Induce Prophages in Swine Fecal Microbiomes

(2011) H. K. Allen et al.   mBio

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

(2010) Nynke L. van Berkum et al.   Jove-Journal of Visualized Experiments

Transfer of Plasmid-Mediated CTX-M-9 from Salmonella enterica Serotype Virchow to Enterobacteriaceae in Human Flora-Associated Rats Treated with Cefixime

(2009) S. Faure et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Development of a Bacterial Cell Enrichment Method and its Application to the Community Analysis in Soybean Stems

(2009) Seishi Ikeda et al.   MICROBIAL ECOLOGY