Functional traits dominate the diversity-related selection of bacterial communities in the rhizosphere

Revisiting the Dilution Procedure Used To Manipulate Microbial Biodiversity in Terrestrial Systems

(2015) Yan Yan et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley

(2015) Davide Bulgarelli et al.   Cell Host & Microbe

Soil-Borne Microbiome: Linking Diversity to Function

(2015) Lucas W. Mendes et al.   MICROBIAL ECOLOGY

HMMER web server: 2015 update

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Taxonomical and functional microbial community selection in soybean rhizosphere

(2014) Lucas W Mendes et al.   ISME Journal

FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus

(2014) Emmanuel Prestat et al.   NUCLEIC ACIDS RESEARCH

Niche and host-associated functional signatures of the root surface microbiome

(2014) Maya Ofek-Lalzar et al.   Nature Communications

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Loss in microbial diversity affects nitrogen cycling in soil

(2013) Laurent Philippot et al.   ISME Journal

Microbial Diversity and Structure Are Drivers of the Biological Barrier Effect against Listeria monocytogenes in Soil

(2013) Anne-Laure Vivant et al.   PLoS One

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Stochastic and deterministic assembly processes in subsurface microbial communities

(2012) James C Stegen et al.   ISME Journal

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

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

The rhizosphere microbiome and plant health

(2012) Roeland L. Berendsen et al.   TRENDS IN PLANT SCIENCE

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Soil characteristics more strongly influence soil bacterial communities than land-use type

(2011) Eiko E. Kuramae et al.   FEMS MICROBIOLOGY ECOLOGY

Species sorting and neutral processes are both important during the initial assembly of bacterial communities

(2011) Silke Langenheder et al.   ISME Journal

Bacterial community assembly based on functional genes rather than species

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

Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria

(2011) R. Mendes et al.   SCIENCE

The under-recognized dominance of Verrucomicrobia in soil bacterial communities

(2011) Gaddy T. Bergmann et al.   SOIL BIOLOGY & BIOCHEMISTRY

Soil beneficial bacteria and their role in plant growth promotion: a review

(2010) Rifat Hayat et al.   ANNALS OF MICROBIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Reduction of rare soil microbes modifies plant-herbivore interactions

(2010) W. H. Gera Hol et al.   ECOLOGY LETTERS

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions

(2010) Jens Reeder et al.   NATURE METHODS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Global Biodiversity: Indicators of Recent Declines

(2010) S. H. M. Butchart et al.   SCIENCE

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Rhizosphere bacterial communities associated with disease suppressiveness stages of take-all decline in wheat monoculture

(2009) H. Sanguin et al.   NEW PHYTOLOGIST

Soil-borne microorganisms and soil-type affect pyrrolizidine alkaloids in Jacobaea vulgaris

(2009) Lotte Joosten et al.   PLANT AND SOIL

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH