Adjusting microbiome profiles for differences in microbial load by spike-in bacteria

Low urinary indoxyl sulfate levels early after transplantation reflect a disrupted microbiome and are associated with poor outcome

(2015) D. Weber et al.   BLOOD

Assay for estimating total bacterial load: relative qPCR normalisation of bacterial load with associated clinical implications

(2015) Ivan Brukner et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

Library preparation methodology can influence genomic and functional predictions in human microbiome research

(2015) Marcus B. Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenomic Analysis of the Stool Microbiome in Patients Receiving Allogeneic Stem Cell Transplantation: Loss of Diversity Is Associated with Use of Systemic Antibiotics and More Pronounced in Gastrointestinal Graft-versus-Host Disease

(2014) Ernst Holler et al.   BIOLOGY OF BLOOD AND MARROW TRANSPLANTATION

The Microbiome in Inflammatory Bowel Disease: Current Status and the Future Ahead

(2014) Aleksandar D. Kostic et al.   GASTROENTEROLOGY

Distinct signatures of host–microbial meta-metabolome and gut microbiome in two C57BL/6 strains under high-fat diet

(2014) Alesia Walker et al.   ISME Journal

Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature

(2014) Yael Haberman et al.   JOURNAL OF CLINICAL INVESTIGATION

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development

(2014) Steven F. Stoddard et al.   NUCLEIC ACIDS RESEARCH

Genomic analysis of Agrobacterium radiobacter DSM 30147T and emended description of A. radiobacter (Beijerinck and van Delden 1902) Conn 1942 (Approved Lists 1980) emend. Sawada et al. 1993

(2014) Linshuang Zhang et al.   Standards in Genomic Sciences

Altered Gut Microbiota Promotes Colitis-Associated Cancer in IL-1 Receptor–Associated Kinase M–Deficient Mice

(2013) Klara Klimesova et al.   INFLAMMATORY BOWEL DISEASES

Species Identification and Profiling of Complex Microbial Communities Using Shotgun Illumina Sequencing of 16S rRNA Amplicon Sequences

(2013) Swee Hoe Ong et al.   PLoS One

Commensal Bacteria Control Cancer Response to Therapy by Modulating the Tumor Microenvironment

(2013) N. Iida et al.   SCIENCE

A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets

(2013) Omry Koren et al.   PLoS Computational Biology

Gut Immune Maturation Depends on Colonization with a Host-Specific Microbiota

(2012) Hachung Chung et al.   CELL

Regulation of intestinal inflammation by microbiota following allogeneic bone marrow transplantation

(2012) Robert R. Jenq et al.   JOURNAL OF EXPERIMENTAL MEDICINE

The human microbiome: at the interface of health and disease

(2012) Ilseung Cho et al.   NATURE REVIEWS GENETICS

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

The Application of Ecological Theory Toward an Understanding of the Human Microbiome

(2012) E. K. Costello et al.   SCIENCE

Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics

(2011) Tamar Geiger et al.   Nature Protocols

The Human Gut Microbiome: Ecology and Recent Evolutionary Changes

(2010) Jens Walter et al.   Annual Review of Microbiology

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Quantifying microbial communities with 454 pyrosequencing: does read abundance count?

(2010) ANTHONY S. AMEND et al.   MOLECULAR ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

(2010) Marcus J. Claesson et al.   NUCLEIC ACIDS RESEARCH

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 Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

(2009) P. J. Turnbaugh et al.   Science Translational Medicine

Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing

(2008) Susan M. Huse et al.   PLoS Genetics