Impact of the gut microbiota on the m6A epitranscriptome of mouse cecum and liver

A deep proteome and transcriptome abundance atlas of 29 healthy human tissues

(2019) Dongxue Wang et al.   Molecular Systems Biology

N6-methyladenosine modifications: interactions with novel RNA-binding proteins and roles in signal transduction

(2019) Jiaxin Chen et al.   RNA Biology

Regulation of Viral Infection by the RNA Modification N6-methyladenosine

(2019) Graham D. Williams et al.   Annual Review of Virology

Gut Microbiota Regulation of Tryptophan Metabolism in Health and Disease

(2018) Allison Agus et al.   Cell Host & Microbe

Dynamic transcriptomic m6A decoration: writers, erasers, readers and functions in RNA metabolism

(2018) Ying Yang et al.   CELL RESEARCH

Sphingolipids in host–microbial interactions

(2018) Stacey L Heaver et al.   CURRENT OPINION IN MICROBIOLOGY

Bile acids in glucose metabolism in health and disease

(2018) Hagit Shapiro et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Sink into the Epigenome: Histones as Repositories That Influence Cellular Metabolism

(2018) Cunqi Ye et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Transcriptome-wide reprogramming of N6-methyladenosine modification by the mouse microbiome

(2018) Xiaoyun Wang et al.   CELL RESEARCH

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Cap-specific terminal N6-methylation of RNA by an RNA polymerase II–associated methyltransferase

(2018) Shinichiro Akichika et al.   SCIENCE

Mouse Microbiota Models: Comparing Germ-Free Mice and Antibiotics Treatment as Tools for Modifying Gut Bacteria

(2018) Elizabeth A. Kennedy et al.   Frontiers in Physiology

Akkermansia muciniphila and its role in regulating host functions

(2017) Muriel Derrien et al.   MICROBIAL PATHOGENESIS

m6A mRNA methylation controls T cell homeostasis by targeting the IL-7/STAT5/SOCS pathways

(2017) Hua-Bing Li et al.   NATURE

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Human genetic variation and the gut microbiome in disease

(2017) Andrew Brantley Hall et al.   NATURE REVIEWS GENETICS

MeT-DB V2.0: elucidating context-specific functions of N6-methyl-adenosine methyltranscriptome

(2017) Hui Liu et al.   NUCLEIC ACIDS RESEARCH

N 6 -methyladenosine is required for the hypoxic stabilization of specific mRNAs

(2017) Nate J. Fry et al.   RNA

Metabolic programming of the epigenome: host and gut microbial metabolite interactions with host chromatin

(2017) Kimberly A. Krautkramer et al.   Translational Research

S -Adenosylmethionine Synthesis Is Regulated by Selective N 6 -Adenosine Methylation and mRNA Degradation Involving METTL16 and YTHDC1

(2017) Hiroki Shima et al.   Cell Reports

D-Alanylation of teichoic acids contributes to Lactobacillus plantarum-mediated Drosophila growth during chronic undernutrition

(2017) Renata C. Matos et al.   Nature Microbiology

Multi-omics Comparative Analysis Reveals Multiple Layers of Host Signaling Pathway Regulation by the Gut Microbiota

(2017) Nathan P. Manes et al.   mSystems

Know your neighbor: Microbiota and host epithelial cells interact locally to control intestinal function and physiology

(2016) Felix Sommer et al.   BIOESSAYS

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

DAPAR & ProStaR: software to perform statistical analyses in quantitative discovery proteomics

(2016) Samuel Wieczorek et al.   BIOINFORMATICS

From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites

(2016) Ara Koh et al.   CELL

Dynamics of Human and Viral RNA Methylation during Zika Virus Infection

(2016) Gianluigi Lichinchi et al.   Cell Host & Microbe

N6 -Methyladenosine in Flaviviridae Viral RNA Genomes Regulates Infection

(2016) Nandan S. Gokhale et al.   Cell Host & Microbe

Posttranscriptional m 6 A Editing of HIV-1 mRNAs Enhances Viral Gene Expression

(2016) Edward M. Kennedy et al.   Cell Host & Microbe

Metabolic control of methylation and acetylation

(2016) Xiaoyang Su et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Post-transcriptional modifications in development and stem cells

(2016) Michaela Frye et al.   DEVELOPMENT

Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease

(2016) Floris Imhann et al.   GUT

Nuclear m 6 A Reader YTHDC1 Regulates mRNA Splicing

(2016) Wen Xiao et al.   MOLECULAR CELL

m6A modulates neuronal functions and sex determination in Drosophila

(2016) Tina Lence et al.   NATURE

Reversible methylation of m6Am in the 5′ cap controls mRNA stability

(2016) Jan Mauer et al.   NATURE

Signals from the gut microbiota to distant organs in physiology and disease

(2016) Bjoern O Schroeder et al.   NATURE MEDICINE

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

Post-transcriptional gene regulation by mRNA modifications

(2016) Boxuan Simen Zhao et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Bacteriocin from epidemicListeriastrains alters the host intestinal microbiota to favor infection

(2016) Juan J. Quereda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Calibration plot for proteomics: A graphical tool to visually check the assumptions underlying FDR control in quantitative experiments

(2016) Quentin Giai Gianetto et al.   PROTEOMICS

Lactobacillus plantarum strain maintains growth of infant mice during chronic undernutrition

(2016) M. Schwarzer et al.   SCIENCE

N6-methyladenosine of HIV-1 RNA regulates viral infection and HIV-1 Gag protein expression

(2016) Nagaraja Tirumuru et al.   eLife

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Dynamics of the human and viral m6A RNA methylomes during HIV-1 infection of T cells

(2016) Gianluigi Lichinchi et al.   Nature Microbiology

Lactobacillus plantarumWCFS1 and its host interaction: a dozen years after the genome

(2016) Maurits van den Nieuwboer et al.   Microbial Biotechnology

Microbiota-Modulated Metabolites Shape the Intestinal Microenvironment by Regulating NLRP6 Inflammasome Signaling

(2015) Maayan Levy et al.   CELL

5′ UTR m6A Promotes Cap-Independent Translation

(2015) Kate D. Meyer et al.   CELL

HNRNPA2B1 Is a Mediator of m6A-Dependent Nuclear RNA Processing Events

(2015) Claudio R. Alarcón et al.   CELL

Creating reference gene annotation for the mouse C57BL6/J genome assembly

(2015) Jonathan M. Mudge et al.   MAMMALIAN GENOME

Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome

(2015) Bastian Linder et al.   NATURE METHODS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation

(2015) Shay Geula et al.   SCIENCE

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis

(2014) Xu Zhao et al.   CELL RESEARCH

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

Perturbation of m6A Writers Reveals Two Distinct Classes of mRNA Methylation at Internal and 5′ Sites

(2014) Schraga Schwartz et al.   Cell Reports

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

(2014) Charity W Law et al.   GENOME BIOLOGY

WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis

(2013) D. R. Zerbino et al.   BIOINFORMATICS

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

A comparison of methods for differential expression analysis of RNA-seq data

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

High-Resolution Mapping Reveals a Conserved, Widespread, Dynamic mRNA Methylation Program in Yeast Meiosis

(2013) Schraga Schwartz et al.   CELL

RNA-Methylation-Dependent RNA Processing Controls the Speed of the Circadian Clock

(2013) Jean-Michel Fustin et al.   CELL

AlienTrimmer: A tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads

(2013) Alexis Criscuolo et al.   GENOMICS

A METTL3–METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation

(2013) Jianzhao Liu et al.   Nature Chemical Biology

Transcriptome-wide mapping of N6-methyladenosine by m6A-seq based on immunocapturing and massively parallel sequencing

(2013) Dan Dominissini et al.   Nature Protocols

The gut microbiota — masters of host development and physiology

(2013) Felix Sommer et al.   NATURE REVIEWS MICROBIOLOGY

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons

(2012) Kate D. Meyer et al.   CELL

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

(2012) Dan Dominissini et al.   NATURE

Inferring direct DNA binding from ChIP-seq

(2012) Timothy L. Bailey 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

Host-Gut Microbiota Metabolic Interactions

(2012) J. K. Nicholson et al.   SCIENCE

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

Depletion of Murine Intestinal Microbiota: Effects on Gut Mucosa and Epithelial Gene Expression

(2011) Dag Henrik Reikvam et al.   PLoS One

Folate Production by Probiotic Bacteria

(2011) Maddalena Rossi et al.   Nutrients

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Inactivation of the Fto gene protects from obesity

(2009) Julia Fischer et al.   NATURE

A Mouse Model for the Metabolic Effects of the Human Fat Mass and Obesity Associated FTO Gene

(2009) Chris Church et al.   PLoS Genetics

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY