Soil microbiome responses to the short-term effects of Amazonian deforestation

Soil-Borne Microbiome: Linking Diversity to Function

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

Soil Bacterial Communities Respond to Mowing and Nutrient Addition in a Steppe Ecosystem

(2014) Ximei Zhang et al.   PLoS One

Tropical agricultural land management influences on soil microbial communities through its effect on soil organic carbon

(2013) Woo Jun Sul et al.   SOIL BIOLOGY & BIOCHEMISTRY

Acidobacterial community responses to agricultural management of soybean in Amazon forest soils

(2012) Acácio A. Navarrete et al.   FEMS MICROBIOLOGY ECOLOGY

Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes

(2012) Kelly S. Ramirez et al.   GLOBAL CHANGE BIOLOGY

High-Quality Draft Genome Sequence of the Opitutaceae Bacterium Strain TAV1, a Symbiont of the Wood-Feeding Termite Reticulitermes flavipes

(2012) J. Isanapong et al.   JOURNAL OF BACTERIOLOGY

Distinct Soil Bacterial Communities Revealed under a Diversely Managed Agroecosystem

(2012) Raymon S. Shange et al.   PLoS One

Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities

(2012) J. L. M. Rodrigues et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Shifts in the phylogenetic structure and functional capacity of soil microbial communities follow alteration of native tussock grassland ecosystems

(2012) Steven A. Wakelin et al.   SOIL BIOLOGY & BIOCHEMISTRY

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients

(2011) Noah Fierer et al.   ISME Journal

Using network analysis to explore co-occurrence patterns in soil microbial communities

(2011) Albert Barberán et al.   ISME Journal

Studies on the ecology of actinomycetes in an agricultural soil amended with organic residues: I. identification of the dominant groups of Actinomycetales

(2011) Mokni-Tlili Sonia et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Identifying biologically relevant differences between metagenomic communities

(2010) Donovan H. Parks et al.   BIOINFORMATICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

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

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

(2009) C. L. Lauber et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data

(2009) Micah Hamady et al.   ISME Journal

Changes in land use alter the structure of bacterial communities in Western Amazon soils

(2009) Ederson da C Jesus et al.   ISME Journal

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

(2008) F Meyer et al.   BMC BIOINFORMATICS

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS