Metagenomic biomarker discovery and explanation

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

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

Survival of Campylobacter jejuni under Conditions of Atmospheric Oxygen Tension with the Support of Pseudomonas spp.

(2010) F. Hilbert et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

METAREP: JCVI metagenomics reports—an open source tool for high-performance comparative metagenomics

(2010) Johannes Goll et al.   BIOINFORMATICS

Identifying biologically relevant differences between metagenomic communities

(2010) Donovan H. Parks et al.   BIOINFORMATICS

Environmental distribution of prokaryotic taxa

(2010) Javier Tamames et al.   BMC MICROBIOLOGY

Enterobacteriaceae Act in Concert with the Gut Microbiota to Induce Spontaneous and Maternally Transmitted Colitis

(2010) Wendy S. Garrett et al.   Cell Host & Microbe

Reshaping the gut microbiome with bacterial transplantation and antibiotic intake

(2010) C. Manichanh et al.   GENOME RESEARCH

Comparison of multiple metagenomes using phylogenetic networks based on ecological indices

(2010) Suparna Mitra et al.   ISME Journal

Multivariate Cutoff Level Analysis (MultiCoLA) of large community data sets

(2010) Angélique Gobet et al.   NUCLEIC ACIDS RESEARCH

Specified Species in Gingival Crevicular Fluid Predict Bacterial Diversity

(2010) Sirkka Asikainen et al.   PLoS One

Exploring the within- and between-class correlation distributions for tumor classification

(2010) X. Wei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bifidobacterium animalis subsp. lactis fermented milk product reduces inflammation by altering a niche for colitogenic microbes

(2010) P. Veiga et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

(2010) C. De Filippo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Primer on Metagenomics

(2010) John C. Wooley et al.   PLoS Computational Biology

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

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Exploring the Diversity of the Bifidobacterial Population in the Human Intestinal Tract

(2009) F. Turroni 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

Over-optimism in bioinformatics research

(2009) A.-L. Boulesteix   BIOINFORMATICS

Visual and statistical comparison of metagenomes

(2009) Suparna Mitra et al.   BIOINFORMATICS

ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes

(2009) Erik Kristiansson et al.   BIOINFORMATICS

Targeting the Human Microbiome With Antibiotics, Probiotics, and Prebiotics: Gastroenterology Enters the Metagenomics Era

(2009) Geoffrey A. Preidis et al.   GASTROENTEROLOGY

Salivary Transcriptomic Biomarkers for Detection of Resectable Pancreatic Cancer

(2009) Lei Zhang et al.   GASTROENTEROLOGY

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

(2009) M. Hamady et al.   GENOME RESEARCH

Low counts of Faecalibacterium prausnitzii in colitis microbiota

(2009) H. Sokol et al.   INFLAMMATORY BOWEL DISEASES

The 'rare biosphere': a reality check

(2009) Jens Reeder et al.   NATURE METHODS

The clinical value of salivary biomarkers for periodontal disease

(2009) Lei Zhang et al.   PERIODONTOLOGY 2000

A High-Throughput DNA Sequence Aligner for Microbial Ecology Studies

(2009) Patrick D. Schloss   PLoS One

Bacterial Community Variation in Human Body Habitats Across Space and Time

(2009) E. K. Costello et al.   SCIENCE

Probiotics and gastrointestinal disease: successes, problems and future prospects

(2009) Eamonn P Culligan et al.   Gut Pathogens

Using prior knowledge and genome-wide association to identify pathways involved in multiple sclerosis

(2009) Marylyn D Ritchie   Genome Medicine

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

(2009) James Robert White et al.   PLoS Computational Biology

Diversity of Human Vaginal Bacterial Communities and Associations with Clinically Defined Bacterial Vaginosis

(2008) B. B. Oakley et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2008) F Meyer et al.   BMC BIOINFORMATICS

Metagenomic Approaches for Defining the Pathogenesis of Inflammatory Bowel Diseases

(2008) Daniel A. Peterson et al.   Cell Host & Microbe

Diet-Induced Obesity Is Linked to Marked but Reversible Alterations in the Mouse Distal Gut Microbiome

(2008) Peter J. Turnbaugh et al.   Cell Host & Microbe

Novel Molecular Subtypes of Serous and Endometrioid Ovarian Cancer Linked to Clinical Outcome

(2008) R. W. Tothill et al.   CLINICAL CANCER RESEARCH

Functional metagenomic profiling of nine biomes

(2008) Elizabeth A. Dinsdale et al.   NATURE

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

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

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

Substantial Alterations of the Cutaneous Bacterial Biota in Psoriatic Lesions

(2008) Zhan Gao et al.   PLoS One