Microbial community dynamics during the early stages of plant polymer breakdown in paddy soil

STAMP: statistical analysis of taxonomic and functional profiles

(2014) Donovan H. Parks et al.   BIOINFORMATICS

Fungal lysis by a soil bacterium fermenting cellulose

(2014) Andrew C. Tolonen et al.   ENVIRONMENTAL MICROBIOLOGY

Description of Anaerobacterium chartisolvens gen. nov., sp. nov., an obligately anaerobic bacterium from Clostridium rRNA cluster III isolated from soil of a Japanese rice field, and reclassification of Bacteroides cellulosolvens Murray et al. 1984 as Pseudobacteroides cellulosolvens gen. nov., comb. nov.

(2014) H. Horino et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses

(2013) Steven J Blazewicz et al.   ISME Journal

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Comparative metatranscriptomics reveals widespread community responses during phenanthrene degradation in soil

(2012) Alexandre de Menezes et al.   ENVIRONMENTAL MICROBIOLOGY

Metatranscriptomics of the marine sponge Geodia barretti: tackling phylogeny and function of its microbial community

(2012) Regina Radax et al.   ENVIRONMENTAL MICROBIOLOGY

Organic carbon transformations in high-Arctic peat soils: key functions and microorganisms

(2012) Alexander Tveit et al.   ISME Journal

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Metatranscriptomics Reveals the Diversity of Genes Expressed by Eukaryotes in Forest Soils

(2012) Coralie Damon et al.   PLoS One

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Replication, lies and lesser-known truths regarding experimental design in environmental microbiology

(2011) Jay T. Lennon   ENVIRONMENTAL MICROBIOLOGY

Taxonomic classification of metagenomic shotgun sequences with CARMA3

(2011) Wolfgang Gerlach et al.   NUCLEIC ACIDS RESEARCH

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Metatranscriptomic Approach to Analyze the Functional Human Gut Microbiota

(2011) María José Gosalbes et al.   PLoS One

Intestinal Microbiota in Healthy Adults: Temporal Analysis Reveals Individual and Common Core and Relation to Intestinal Symptoms

(2011) Jonna Jalanka-Tuovinen et al.   PLoS One

Biological Consequences of Ancient Gene Acquisition and Duplication in the Large Genome of Candidatus Solibacter usitatus Ellin6076

(2011) Jean F. Challacombe et al.   PLoS One

Extraction of mRNA from Soil

(2010) C. Mettel et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Functional Gene Analysis Suggests Different Acetogen Populations in the Bovine Rumen and Tammar Wallaby Forestomach

(2010) E. J. Gagen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Methanocella arvoryzae sp. nov., a hydrogenotrophic methanogen isolated from rice field soil

(2010) S. Sakai et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus

(2010) Claudia Steglich et al.   GENOME BIOLOGY

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Methanocella paludicola gen. nov., sp. nov., a methane-producing archaeon, the first isolate of the lineage 'Rice Cluster I', and proposal of the new archaeal order Methanocellales ord. nov.

(2008) S. Sakai et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH