Proteobacteria explain significant functional variability in the human gut microbiome

A two-part mixed-effects model for analyzing longitudinal microbiome compositional data

(2016) Eric Z. Chen et al.   BIOINFORMATICS

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

(2016) Stephen Nayfach et al.   GENOME RESEARCH

Metagenome-wide association studies: fine-mining the microbiome

(2016) Jun Wang et al.   NATURE REVIEWS MICROBIOLOGY

Human symbionts inject and neutralize antibacterial toxins to persist in the gut

(2016) Aaron G. Wexler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacteroides fragilistype VI secretion systems use novel effector and immunity proteins to antagonize human gut Bacteroidales species

(2016) Maria Chatzidaki-Livanis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population-level analysis of gut microbiome variation

(2016) Gwen Falony et al.   SCIENCE

Type III Secretion: Building and Operating a Remarkable Nanomachine

(2016) Athina G. Portaliou et al.   TRENDS IN BIOCHEMICAL SCIENCES

Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species

(2015) Sharon Greenblum et al.   CELL

Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates

(2015) Doris Vandeputte et al.   GUT

Species-Specific Dynamic Responses of Gut Bacteria to a Mammalian Glycan

(2015) Varsha Raghavan et al.   JOURNAL OF BACTERIOLOGY

Iron and zinc exploitation during bacterial pathogenesis

(2015) Li Ma et al.   Metallomics

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Channel crossing: how are proteins shipped across the bacterial plasma membrane?

(2015) Ian Collinson et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Proteobacteria: microbial signature of dysbiosis in gut microbiota

(2015) Na-Ri Shin et al.   TRENDS IN BIOTECHNOLOGY

Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes

(2015) Stephen Nayfach et al.   PLoS Computational Biology

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data

(2015) Catalina A. Vallejos et al.   PLoS Computational Biology

MUSiCC: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome

(2015) Ohad Manor et al.   GENOME BIOLOGY

Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome

(2015) Stephen Nayfach et al.   GENOME BIOLOGY

Regression Models for Count Data inR

(2015) Achim Zeileis et al.   Journal of Statistical Software

Assessment and Selection of Competing Models for Zero-Inflated Microbiome Data

(2015) Lizhen Xu et al.   PLoS One

Biosynthesis and Export of Bacterial Lipopolysaccharides

(2014) Chris Whitfield et al.   Annual Review of Biochemistry

Characterization of Glycosaminoglycan (GAG) Sulfatases from the Human Gut SymbiontBacteroides thetaiotaomicronReveals the First GAG-specific Bacterial Endosulfatase

(2014) Jonathan E. Ulmer et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Biological Network Module-Based Model for the Analysis of Differential Expression in Shotgun Proteomics

(2014) Jia Xu et al.   JOURNAL OF PROTEOME RESEARCH

Determinants of expression variability

(2014) Elfalem Y. Alemu et al.   NUCLEIC ACIDS RESEARCH

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size

(2013) Danni Yu et al.   BIOINFORMATICS

Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing

(2013) H. Guo et al.   GENOME RESEARCH

Gut metagenome in European women with normal, impaired and diabetic glucose control

(2013) Fredrik H. Karlsson et al.   NATURE

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups

(2013) Dongying Wu et al.   PLoS One

Modulating the innate immune response by combinatorial engineering of endotoxin

(2013) Brittany D. Needham et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Type VI secretion system – a widespread and versatile cell targeting system

(2013) Sarah J. Coulthurst   RESEARCH IN MICROBIOLOGY

Predicting and Manipulating Cardiac Drug Inactivation by the Human Gut Bacterium Eggerthella lenta

(2013) H. J. Haiser et al.   SCIENCE

Transient Inability to Manage Proteobacteria Promotes Chronic Gut Inflammation in TLR5-Deficient Mice

(2012) Frederic A. Carvalho et al.   Cell Host & Microbe

A framework for human microbiome research

(2012)   NATURE

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

IBD—what role do Proteobacteria play?

(2012) Indrani Mukhopadhya et al.   Nature Reviews Gastroenterology & Hepatology

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

(2011) Y. Zhao et al.   BIOINFORMATICS

Sulfatases and a RadicalS-Adenosyl-l-methionine (AdoMet) Enzyme Are Key for Mucosal Foraging and Fitness of the Prominent Human Gut Symbiont,Bacteroides thetaiotaomicron

(2011) Alhosna Benjdia et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

The tRNA synthetase paralog PoxA modifies elongation factor-P with (R)-β-lysine

(2011) Hervé Roy et al.   Nature Chemical Biology

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

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

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

Microreview: Type IV secretion systems: versatility and diversity in function

(2010) Karin Wallden et al.   CELLULAR MICROBIOLOGY

The Lipid A Phosphate Position Determines Differential Host Toll-Like Receptor 4 Responses to Phylogenetically Related Symbiotic and Pathogenic Bacteria

(2010) Stephen R. Coats et al.   INFECTION AND IMMUNITY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P

(2010) Tatsuo Yanagisawa et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

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

Alleviating Cancer Drug Toxicity by Inhibiting a Bacterial Enzyme

(2010) B. D. Wallace et al.   SCIENCE

Reversible Microbial Colonization of Germ-Free Mice Reveals the Dynamics of IgA Immune Responses

(2010) S. Hapfelmeier et al.   SCIENCE

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

(2010) Y. Taniguchi et al.   SCIENCE

Induction of Colonic Regulatory T Cells by Indigenous Clostridium Species

(2010) K. Atarashi et al.   SCIENCE

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age

(2009) D Mariat et al.   BMC MICROBIOLOGY

High Prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae Detected in the Human Gut Using an Improved DNA Detection Protocol

(2009) Bédis Dridi et al.   PLoS One

Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites

(2009) W. R. Wikoff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lipopolysaccharide: Biosynthetic pathway and structure modification

(2009) Xiaoyuan Wang et al.   PROGRESS IN LIPID RESEARCH

Innate and Adaptive Immunity Cooperate Flexibly to Maintain Host-Microbiota Mutualism

(2009) E. Slack et al.   SCIENCE

A microbial symbiosis factor prevents intestinal inflammatory disease

(2008) Sarkis K. Mazmanian et al.   NATURE

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

A simple, fast, and accurate method of phylogenomic inference

(2008) Martin Wu et al.   GENOME BIOLOGY