Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools

ICEberg 2.0: an updated database of bacterial integrative and conjugative elements

(2018) Meng Liu et al.   NUCLEIC ACIDS RESEARCH

Integrative and conjugative elements and their hosts: composition, distribution and organization

(2017) Jean Cury et al.   NUCLEIC ACIDS RESEARCH

Proteobacteria: A Common Factor in Human Diseases

(2017) G. Rizzatti et al.   Biomed Research International

Detecting horizontal gene transfer by mapping sequencing reads across species boundaries

(2016) Kathrin Trappe et al.   BIOINFORMATICS

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

(2016) Stephen Nayfach et al.   GENOME RESEARCH

A mobile genetic element profoundly increases heat resistance of bacterial spores

(2016) Erwin M Berendsen et al.   ISME Journal

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

(2016) François Enault et al.   ISME Journal

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation

(2016) Hilary P. Browne et al.   NATURE

Mobile genes in the human microbiome are structured from global to individual scales

(2016) I. L. Brito et al.   NATURE

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

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

Identification of protein secretion systems in bacterial genomes

(2016) Sophie S. Abby et al.   Scientific Reports

Integrative and Conjugative Elements (ICEs): What They Do and How They Work

(2015) Christopher M. Johnson et al.   Annual Review of Genetics

Current progress of targetron technology: Development, improvement and application in metabolic engineering

(2015) Ya-Jun Liu et al.   Biotechnology Journal

CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers

(2015) Rachid Ounit et al.   BMC GENOMICS

Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species

(2015) Sharon Greenblum et al.   CELL

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

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

ConStrains identifies microbial strains in metagenomic datasets

(2015) Chengwei Luo et al.   NATURE BIOTECHNOLOGY

A biosynthetic pathway for a prominent class of microbiota-derived bile acids

(2015) A Sloan Devlin et al.   Nature Chemical Biology

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Horizontal gene transfer: building the web of life

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

Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides

(2015) M. Wu et al.   SCIENCE

The outer mucus layer hosts a distinct intestinal microbial niche

(2015) Hai Li et al.   Nature Communications

Inferring Horizontal Gene Transfer

(2015) Matt Ravenhall et al.   PLoS Computational Biology

Current progress of targetron technology: Development, improvement and application in metabolic engineering

(2015) Ya-Jun Liu et al.   Biotechnology Journal

A call for benchmarking transposable element annotation methods

(2015) Douglas R. Hoen et al.   Mobile DNA

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Programming a Human Commensal Bacterium, Bacteroides thetaiotaomicron, to Sense and Respond to Stimuli in the Murine Gut Microbiota

(2015) Mark Mimee et al.   Cell Systems

Mucin glycan foraging in the human gut microbiome

(2015) Louise E. Tailford et al.   Frontiers in Genetics

Modeling the Infection Dynamics of Bacteriophages in Enteric Escherichia coli: Estimating the Contribution of Transduction to Antimicrobial Gene Spread

(2014) Victoriya V. Volkova et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance

(2014) Tae-Hyuk Ahn et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Correlation Between Intraluminal Oxygen Gradient and Radial Partitioning of Intestinal Microbiota

(2014) Lindsey Albenberg et al.   GASTROENTEROLOGY

Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology

(2014) Molly K Gibson et al.   ISME Journal

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

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Horizontal gene transfer in the human gastrointestinal tract: potential spread of antibiotic resistance genes

(2014) Jennifer R Huddleston   Infection and Drug Resistance

Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks

(2013) Dmitry A Ravcheev et al.   BMC GENOMICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Evolution of Conjugation and Type IV Secretion Systems

(2012) Julien Guglielmini et al.   MOLECULAR BIOLOGY AND EVOLUTION

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

How glycan metabolism shapes the human gut microbiota

(2012) Nicole M. Koropatkin et al.   NATURE REVIEWS MICROBIOLOGY

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Towards a more accurate annotation of tyrosine-based site-specific recombinases in bacterial genomes

(2012) Rob Van Houdt et al.   Mobile DNA

Longitudinal Analysis of the Prevalence, Maintenance, and IgA Response to Species of the Order Bacteroidales in the Human Gut

(2011) Naamah Levy Zitomersky et al.   INFECTION AND IMMUNITY

Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere

(2011) M. Krupovic et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

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

(2011) Chris S. Smillie et al.   NATURE

ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria

(2011) Dexi Bi et al.   NUCLEIC ACIDS RESEARCH

Mining Virulence Genes Using Metagenomics

(2011) Pedro Belda-Ferre et al.   PLoS One

Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes

(2011) Todd J. Treangen et al.   PLoS Genetics

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Hidden Markov model speed heuristic and iterative HMM search procedure

(2010) L Steven Johnson et al.   BMC BIOINFORMATICS

Oral biofilms: a reservoir of transferable, bacterial, antimicrobial resistance

(2010) Adam P Roberts et al.   Expert Review of Anti-Infective Therapy

What traits are carried on mobile genetic elements and why?

(2010) D J Rankin et al.   HEREDITY

Dichotomy in the evolution of pathogenicity island and bacteriophage encoded integrases from pathogenic Escherichia coli strains

(2010) Michael G. Napolitano et al.   INFECTION GENETICS AND EVOLUTION

Twenty-eight divergent polysaccharide loci specifying within- and amongst-strain capsule diversity in three strains of Bacteroides fragilis

(2010) S. Patrick et al.   MICROBIOLOGY-SGM

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

(2010) Jan-Hendrik Hehemann et al.   NATURE

Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow

(2010) Rachel A. F. Wozniak et al.   NATURE REVIEWS MICROBIOLOGY

The two mucus layers of colon are organized by the MUC2 mucin, whereas the outer layer is a legislator of host-microbial interactions

(2010) M. E. V. Johansson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Group II Introns: Mobile Ribozymes that Invade DNA

(2010) A. M. Lambowitz et al.   Cold Spring Harbor Perspectives in Biology

The human microbiome harbors a diverse reservoir of antibiotic resistance genes

(2010) Morten O.A. Sommer et al.   Virulence

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

ACLAME: A CLAssification of Mobile genetic Elements, update 2010

(2009) Raphaël Leplae et al.   NUCLEIC ACIDS RESEARCH

Role of glycan synthesis in colonization of the mammalian gut by the bacterial symbiont Bacteroides fragilis

(2008) M. J. Coyne et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome

(2008) B. V. Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria

(2008) M. E. V. Johansson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA