Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance

Isolation of oxygenase genes for indigo-forming activity from an artificially polluted soil metagenome by functional screening using Pseudomonas putida strains as hosts

(2015) Hirofumi Nagayama et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Metagenomic analysis reveals microbial functional redundancies and specificities in a soil under different tillage and crop-management regimes

(2015) Renata Carolini Souza et al.   APPLIED SOIL ECOLOGY

Deciphering microbial community robustness through synthetic ecology and molecular systems synecology

(2015) Ben Stenuit et al.   CURRENT OPINION IN BIOTECHNOLOGY

The Earth Microbiome project: successes and aspirations

(2014) Jack A Gilbert et al.   BMC BIOLOGY

Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage

(2014) Emilie E. L. Muller et al.   Nature Communications

Soil Microbial Community Responses to a Decade of Warming as Revealed by Comparative Metagenomics

(2013) Chengwei Luo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Ethyl tert-butyl ether (ETBE) biodegradation by a syntrophic association of Rhodococcus sp. IFP 2042 and Bradyrhizobium sp. IFP 2049 isolated from a polluted aquifer

(2013) Yoann Le Digabel et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Design and Experimental Application of a Novel Non-Degenerate Universal Primer Set that Amplifies Prokaryotic 16S rRNA Genes with a Low Possibility to Amplify Eukaryotic rRNA Genes

(2013) H. Mori et al.   DNA RESEARCH

Resistance and resilience of the forest soil microbiome to logging-associated compaction

(2013) Martin Hartmann et al.   ISME Journal

Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States

(2013) N. Fierer et al.   SCIENCE

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

(2012) Y. Peng et al.   BIOINFORMATICS

Analysis of the microbial gene landscape and transcriptome for aromatic pollutants and alkane degradation using a novel internally calibrated microarray system

(2012) Ramiro Vilchez-Vargas et al.   ENVIRONMENTAL MICROBIOLOGY

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

(2012) I. Sharon et al.   GENOME RESEARCH

Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation

(2012) María-Eugenia Guazzaroni et al.   ISME Journal

Structure, fluctuation and magnitude of a natural grassland soil metagenome

(2012) Tom O Delmont et al.   ISME Journal

Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes

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

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Metagenomic Analysis of the Bioremediation of Diesel-Contaminated Canadian High Arctic Soils

(2012) Etienne Yergeau et al.   PLoS One

Fundamentals of Microbial Community Resistance and Resilience

(2012) Ashley Shade et al.   Frontiers in Microbiology

Metagenomic Insights into the Evolution, Function, and Complexity of the Planktonic Microbial Community of Lake Lanier, a Temperate Freshwater Ecosystem

(2011) Seungdae Oh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Genomic analysis of the potential for aromatic compounds biodegradation in Burkholderiales

(2011) Danilo Pérez-Pantoja et al.   ENVIRONMENTAL MICROBIOLOGY

Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw

(2011) Rachel Mackelprang et al.   NATURE

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

PHAST: A Fast Phage Search Tool

(2011) Y. Zhou et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Viral and microbial community dynamics in four aquatic environments

(2010) Beltran Rodriguez-Brito et al.   ISME Journal

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

Succession of microbial consortia in the developing infant gut microbiome

(2010) J. E. Koenig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ACLAME: A CLAssification of Mobile genetic Elements, update 2010

(2009) Raphaël Leplae et al.   NUCLEIC ACIDS RESEARCH

Resistance, resilience, and redundancy in microbial communities

(2008) S. D. Allison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA