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

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

A checkpoint control orchestrates the replication of the two chromosomes of Vibrio cholerae

(2016) M.-E. Val et al.   Science Advances

Contact genomics: scaffolding and phasing (meta)genomes using chromosome 3D physical signatures

(2015) Jean-François Flot et al.   FEBS LETTERS

Condensin promotes the juxtaposition of DNA flanking its loading site inBacillus subtilis

(2015) Xindan Wang et al.   GENES & DEVELOPMENT

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Condensin- and Replication-Mediated Bacterial Chromosome Folding and Origin Condensation Revealed by Hi-C and Super-resolution Imaging

(2015) Martial Marbouty et al.   MOLECULAR CELL

A catalog of the mouse gut metagenome

(2015) Liang Xiao et al.   NATURE BIOTECHNOLOGY

Early life dynamics of the human gut virome and bacterial microbiome in infants

(2015) Efrem S Lim et al.   NATURE MEDICINE

Tara Oceans studies plankton at planetary scale

(2015) P. Bork et al.   SCIENCE

Metagenome Analysis Exploiting High-Throughput Chromosome Conformation Capture (3C) Data

(2015) Martial Marbouty et al.   TRENDS IN GENETICS

The human gut virome: a multifaceted majority

(2015) Lesley A. Ogilvie et al.   Frontiers in Microbiology

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Classification and quantification of bacteriophage taxa in human gut metagenomes

(2014) Alison S Waller et al.   ISME Journal

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

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

(2014) Julien Guglielmini et al.   NUCLEIC ACIDS RESEARCH

High-quality genome (re)assembly using chromosomal contact data

(2014) Hervé Marie-Nelly et al.   Nature Communications

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

(2014) Bas E. Dutilh et al.   Nature Communications

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

Evolutionary consequences of intra-patient phage predation on microbial populations

(2014) Kimberley D Seed et al.   eLife

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

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

(2014) Christopher W. Beitel et al.   PeerJ

Community-wide plasmid gene mobilization and selection

(2013) Vladimir Sentchilo et al.   ISME Journal

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

High-throughput genome scaffolding from in vivo DNA interaction frequency

(2013) Noam Kaplan et al.   NATURE BIOTECHNOLOGY

Going back to the roots: the microbial ecology of the rhizosphere

(2013) Laurent Philippot et al.   NATURE REVIEWS MICROBIOLOGY

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices

(2013) Jenna Morgan Lang et al.   PLoS One

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome

(2012) A. Stern et al.   GENOME RESEARCH

Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes

(2012) D. M. Kristensen et al.   JOURNAL OF BACTERIOLOGY

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

(2012) Nicholas A Bokulich et al.   NATURE METHODS

Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour

(2012) John F. Cryan et al.   NATURE REVIEWS NEUROSCIENCE

PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies

(2012) Sajia Akhter et al.   NUCLEIC ACIDS RESEARCH

Evolutionarily Conserved Orthologous Families in Phages Are Relatively Rare in Their Prokaryotic Hosts

(2011) D. M. Kristensen et al.   JOURNAL OF BACTERIOLOGY

Complete Genome Sequence of the Giant Virus OBP and Comparative Genome Analysis of the Diverse  KZ-Related Phages

(2011) A. Cornelissen et al.   JOURNAL OF VIROLOGY

The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation

(2011) Mark A. Umbarger et al.   MOLECULAR CELL

Human nutrition, the gut microbiome and the immune system

(2011) Andrew L. Kau et al.   NATURE

Statistical structure of host-phage interactions

(2011) C. O. Flores et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation

(2011) Julien Guglielmini et al.   PLoS Genetics

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

New dimensions of the virus world discovered through metagenomics

(2009) David M. Kristensen et al.   TRENDS IN MICROBIOLOGY

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Discovery and characterization of a new bacterial candidate division by an anaerobic sludge digester metagenomic approach

(2008) Sonda Guermazi et al.   ENVIRONMENTAL MICROBIOLOGY

Genetic diversity and composition of a plasmid metagenome from a wastewater treatment plant

(2008) Andreas Schlüter et al.   JOURNAL OF BIOTECHNOLOGY

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Rhizosphere bacteria help plants tolerate abiotic stress

(2008) Jungwook Yang et al.   TRENDS IN PLANT SCIENCE