Next Generation Sequencing to Define Prokaryotic and Fungal Diversity in the Bovine Rumen

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

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Composition and Similarity of Bovine Rumen Microbiota across Individual Animals

(2012) Elie Jami et al.   PLoS One

Microbiome analysis of dairy cows fed pasture or total mixed ration diets

(2011) Alexandre B. de Menezes et al.   FEMS MICROBIOLOGY ECOLOGY

Status of the phylogenetic diversity census of ruminal microbiomes

(2011) Minseok Kim et al.   FEMS MICROBIOLOGY ECOLOGY

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen

(2011) M. Hess et al.   SCIENCE

Clostridium perfringens bacteriophages ΦCP39O and ΦCP26F: genomic organization and proteomic analysis of the virions

(2010) Bruce S. Seal et al.   ARCHIVES OF VIROLOGY

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

Artificial and natural duplicates in pyrosequencing reads of metagenomic data

(2010) Beifang Niu et al.   BMC BIOINFORMATICS

Composition, spatial distribution, and diversity of the bacterial communities in the rumen of cows fed different forages

(2010) Yunhong Kong et al.   FEMS MICROBIOLOGY ECOLOGY

Assessment of the Microbial Ecology of Ruminal Methanogens in Cattle with Different Feed Efficiencies

(2009) M. Zhou et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

(2009) M. Hamady et al.   GENOME RESEARCH

Rumen Bacterial Diversity Dynamics Associated with Changing from Bermudagrass Hay to Grazed Winter Wheat Diets

(2009) Dipti W. Pitta et al.   MICROBIAL ECOLOGY

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases

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

Structure of the Archaeal Community of the Rumen

(2008) P. H. Janssen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

fdrtool: a versatile R package for estimating local and tail area-based false discovery rates

(2008) K. Strimmer   BIOINFORMATICS

A unified approach to false discovery rate estimation

(2008) Korbinian Strimmer   BMC BIOINFORMATICS

Linkage of microbial ecology to phenotype: correlation of rumen microbial ecology to cattle's feed efficiency

(2008) Le Luo Guan et al.   FEMS MICROBIOLOGY LETTERS

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

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