“Every Gene Is Everywhere but the Environment Selects”: Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis

Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms

(2015) Dominik Forster et al.   BMC BIOLOGY

The Gut of Geographically Disparate Ciona intestinalis Harbors a Core Microbiota

(2014) Larry J. Dishaw et al.   PLoS One

Occurrence of Chloramphenicol-Resistance Genes as Environmental Pollutants from Swine Feedlots

(2013) Juan Li et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

Pfam: the protein families database

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

Marine bacteria exhibit a bipolar distribution

(2013) W. J. Sul et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene similarity networks provide tools for understanding eukaryote origins and evolution

(2013) D. Alvarez-Ponce et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Beyond biogeographic patterns: processes shaping the microbial landscape

(2012) China A. Hanson et al.   NATURE REVIEWS MICROBIOLOGY

Identification and removal of ribosomal RNA sequences from metatranscriptomes

(2011) Robert Schmieder et al.   BIOINFORMATICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

The public goods hypothesis for the evolution of life on Earth

(2011) James O McInerney et al.   Biology Direct

RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles

(2011) Ozkan U Nalbantoglu et al.   BMC BIOINFORMATICS

The mosaicism of plasmids revealed by atypical genes detection and analysis

(2011) Emanuele Bosi et al.   BMC GENOMICS

Trends and barriers to lateral gene transfer in prokaryotes

(2011) Ovidiu Popa et al.   CURRENT OPINION IN MICROBIOLOGY

Large-Scale Analysis of Plasmid Relationships through Gene-Sharing Networks

(2011) M. Tamminen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data

(2011) J. Raes et al.   Molecular Systems Biology

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

(2011) Chris S. Smillie et al.   NATURE

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Plasmid Metagenome Reveals High Levels of Antibiotic Resistance Genes and Mobile Genetic Elements in Activated Sludge

(2011) Tong Zhang et al.   PLoS One

Phylogenomic networks

(2011) Tal Dagan   TRENDS IN MICROBIOLOGY

Local Mobile Gene Pools Rapidly Cross Species Boundaries To Create Endemicity within Global Vibrio cholerae Populations

(2011) Y. Boucher et al.   mBio

cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data

(2010) Fengfeng Zhou et al.   BIOINFORMATICS

The horizontal flow of the plasmid resistome: clues from inter-generic similarity networks

(2010) Marco Fondi et al.   ENVIRONMENTAL MICROBIOLOGY

Unprecedented levels of horizontal gene transfer among spatially co-occurring Shewanella bacteria from the Baltic Sea

(2010) Alejandro Caro-Quintero et al.   ISME Journal

Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource

(2010) S. Sun et al.   NUCLEIC ACIDS RESEARCH

Evaluation of Pathogen Removal in a Solar Sludge Drying Facility Using Microbial Indicators

(2010) Emily F. Shanahan et al.   International Journal of Environmental Research and Public Health

Microbial community structure and its functional implications

(2009) Jed A. Fuhrman   NATURE

Biogeography of the Sulfolobus islandicus pan-genome

(2009) M. L. Reno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network analyses structure genetic diversity in independent genetic worlds

(2009) S. Halary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial co-habitation and lateral gene transfer: what transposases can tell us

(2009) Sean D Hooper et al.   GENOME BIOLOGY

Antibiotics and antibiotic resistance in water environments

(2008) Fernando Baquero et al.   CURRENT OPINION IN BIOTECHNOLOGY

Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes

(2008) G. Lima-Mendez et al.   MOLECULAR BIOLOGY AND EVOLUTION

ARDB--Antibiotic Resistance Genes Database

(2008) B. Liu et al.   NUCLEIC ACIDS RESEARCH

The Airborne Metagenome in an Indoor Urban Environment

(2008) Susannah G. Tringe et al.   PLoS One

A Molecular Study of Microbe Transfer between Distant Environments

(2008) Sean D. Hooper et al.   PLoS One