Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities

Bacteriophages as Environmental Reservoirs of Antibiotic Resistance

(2019) William Calero-Cáceres et al.   TRENDS IN MICROBIOLOGY

Genetic transduction by phages and chromosomal islands: The new and noncanonical

(2019) Yin Ning Chiang et al.   PLoS Pathogens

Horizontal Gene Transfer and Acquired Antibiotic Resistance in Salmonella enterica Serovar Heidelberg following In Vitro Incubation in Broiler Ceca

(2019) Adelumola Oladeinde et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Packaging of Dinoroseobacter shibae DNA into Gene Transfer Agent Particles Is Not Random

(2018) Jürgen Tomasch et al.   Genome Biology and Evolution

Murine colitis reveals a disease-associated bacteriophage community

(2018) Breck A. Duerkop et al.   Nature Microbiology

Genome hypermobility by lateral transduction

(2018) John Chen et al.   SCIENCE

Large Preferred Region for Packaging of Bacterial DNA by phiC725A, a Novel Pseudomonas aeruginosa F116-Like Bacteriophage

(2017) Christine Pourcel et al.   PLoS One

Bacterial membrane vesicles transport their DNA cargo into host cells

(2017) Natalie J. Bitto et al.   Scientific Reports

PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data

(2017) Julian R. Garneau et al.   Scientific Reports

Phylogenomic networks reveal limited phylogenetic range of lateral gene transfer by transduction

(2016) Ovidiu Popa et al.   ISME Journal

Phage-inducible islands in the Gram-positive cocci

(2016) Roser Martínez-Rubio et al.   ISME Journal

Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses

(2016) François Enault et al.   ISME Journal

Bacterial viruses enable their host to acquire antibiotic resistance genes from neighbouring cells

(2016) Jakob Haaber et al.   Nature Communications

Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes

(2015) Manuel Kleiner et al.   BMC GENOMICS

Horizontal gene transfer: building the web of life

(2015) Shannon M. Soucy et al.   NATURE REVIEWS GENETICS

The type VI secretion system of Vibrio cholerae fosters horizontal gene transfer

(2015) S. Borgeaud et al.   SCIENCE

Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples

(2015) T. Korem et al.   SCIENCE

The Phage-Inducible Chromosomal Islands: A Family of Highly Evolved Molecular Parasites

(2015) José R. Penadés et al.   Annual Review of Virology

Gene Transfer Potential of Outer Membrane Vesicles of Acinetobacter baylyi and Effects of Stress on Vesiculation

(2014) Shweta Fulsundar et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle

(2014) Xuesong He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Developmentally-Regulated Excision of the SPβ Prophage Reconstitutes a Gene Required for Spore Envelope Maturation in Bacillus subtilis

(2014) Kimihiro Abe et al.   PLoS Genetics

Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome

(2013) Sheetal R. Modi et al.   NATURE

Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut

(2013) A. Reyes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enterococcus faecalis Prophage Dynamics and Contributions to Pathogenic Traits

(2013) Renata C. Matos et al.   PLoS Genetics

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Gene transfer agents: phage-like elements of genetic exchange

(2012) Andrew S. Lang et al.   NATURE REVIEWS MICROBIOLOGY

A composite bacteriophage alters colonization by an intestinal commensal bacterium

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

Pirates of the Caudovirales

(2012) Gail E. Christie et al.   VIROLOGY

Lateral gene transfer

(2011) Olga Zhaxybayeva et al.   CURRENT BIOLOGY

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

High-frequency phage-mediated gene transfer in freshwater environments determined at single-cell level

(2010) Takehiko Kenzaka et al.   ISME Journal

Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota

(2010) Jan-Hendrik Hehemann et al.   NATURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Laboratory procedures to generate viral metagenomes

(2009) Rebecca V Thurber et al.   Nature Protocols

Phage-Mediated Intergeneric Transfer of Toxin Genes

(2009) J. Chen et al.   SCIENCE

Listeria monocytogenes Internalin and E-cadherin: From Bench to Bedside

(2009) M. Bonazzi et al.   Cold Spring Harbor Perspectives in Biology