Related references
Note: Only part of the references are listed.A deep proteome and transcriptome abundance atlas of 29 healthy human tissues
Dongxue Wang et al.
MOLECULAR SYSTEMS BIOLOGY (2019)
N6-methyladenosine modifications: interactions with novel RNA-binding proteins and roles in signal transduction
Jiaxin Chen et al.
RNA BIOLOGY (2019)
Regulation of Viral Infection by the RNA Modification N6-Methyladenosine
Graham D. Williams et al.
ANNUAL REVIEW OF VIROLOGY, VOL 6, 2019 (2019)
Transcriptome-wide reprogramming of N6-methyladenosine modification by the mouse microbiome
Xiaoyun Wang et al.
CELL RESEARCH (2019)
The PRIDE database and related tools and resources in 2019: improving support for quantification data
Yasset Perez-Riverol et al.
NUCLEIC ACIDS RESEARCH (2019)
Cap-specific terminal N6-methylation of RNA by an RNA polymerase II-associated methyltransferase
Shinichiro Akichika et al.
SCIENCE (2019)
A novel RT-QPCR-based assay for the relative quantification of residue specific m6A RNA methylation
Ainara Castellanos-Rubio et al.
SCIENTIFIC REPORTS (2019)
Metabolism of Dietary and Microbial Vitamin B Family in the Regulation of Host Immunity
Ken Yoshii et al.
FRONTIERS IN NUTRITION (2019)
Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease
Floris Imhann et al.
GUT (2018)
MeT-DB V2.0: elucidating context-specific functions of N-6-methyl-adenosine methyltranscriptome
Hui Liu et al.
NUCLEIC ACIDS RESEARCH (2018)
Gut Microbiota Regulation of Tryptophan Metabolism in Health and Disease
Allison Agus et al.
CELL HOST & MICROBE (2018)
Dynamic transcriptomic m6A decoration: writers, erasers, readers and functions in RNA metabolism
Ying Yang et al.
CELL RESEARCH (2018)
Sphingolipids in host-microbial interactions
Stacey L. Heaver et al.
CURRENT OPINION IN MICROBIOLOGY (2018)
Bile acids in glucose metabolism in health and disease
Hagit Shapiro et al.
JOURNAL OF EXPERIMENTAL MEDICINE (2018)
Sink into the Epigenome: Histones as Repositories That Influence Cellular Metabolism
Cunqi Ye et al.
TRENDS IN ENDOCRINOLOGY AND METABOLISM (2018)
Mouse Microbiota Models: Comparing Germ-Free Mice and Antibiotics Treatment as Tools for Modifying Gut Bacteria
Elizabeth A. Kennedy et al.
FRONTIERS IN PHYSIOLOGY (2018)
DAPAR & ProStaR: software to perform statistical analyses in quantitative discovery proteomics
Samuel Wieczorek et al.
BIOINFORMATICS (2017)
Reversible methylation of m6Am in the 5′ cap controls mRNA stability
Jan Mauer et al.
NATURE (2017)
Post-transcriptional gene regulation by mRNA modifications
Boxuan Simen Zhao et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2017)
Akkermansia muciniphila and its role in regulating host functions
Muriel Derrien et al.
MICROBIAL PATHOGENESIS (2017)
m6A mRNA methylation controls T cell homeostasis by targeting the IL-7/STAT5/SOCS pathways
Hua-Bing Li et al.
NATURE (2017)
Salmon provides fast and bias-aware quantification of transcript expression
Rob Patro et al.
NATURE METHODS (2017)
Human genetic variation and the gut microbiome in disease
Andrew Brantley Hall et al.
NATURE REVIEWS GENETICS (2017)
N6-methyladenosine is required for the hypoxic stabilization of specific mRNAs
Nate J. Fry et al.
RNA (2017)
Metabolic programming of the epigenome: host and gut microbial metabolite interactions with host chromatin
Kimberly A. Krautkramer et al.
TRANSLATIONAL RESEARCH (2017)
S-Adenosylmethionine Synthesis Is Regulated by Selective N6-Adenosine Methylation and mRNA Degradation Involving METTL16 and YTHDC1
Hiroki Shima et al.
CELL REPORTS (2017)
D-Alanylation of teichoic acids contributes to Lactobacillus plantarum-mediated Drosophila growth during chronic undernutrition
Renata C. Matos et al.
NATURE MICROBIOLOGY (2017)
Multi-omics Comparative Analysis Reveals Multiple Layers of Host Signaling Pathway Regulation by the Gut Microbiota
Nathan P. Manes et al.
MSYSTEMS (2017)
Epitranscriptomics: regulation of mRNA metabolism through modifications
Eyal Peer et al.
CURRENT OPINION IN CHEMICAL BIOLOGY (2017)
Temporal Control of Mammalian Cortical Neurogenesis by m6A Methylation
Ki-Jun Yoon et al.
CELL (2017)
Human METTL16 is a N6-methyladenosine (m6A) methyltransferase that targets pre-mRNAs and various non-coding RNAs
Ahmed S. Warda et al.
EMBO REPORTS (2017)
stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage
Koen Van den Berge et al.
GENOME BIOLOGY (2017)
Host-microbiota interactions: epigenomic regulation
Vivienne Woo et al.
CURRENT OPINION IN IMMUNOLOGY (2017)
The U6 snRNA m6A Methyltransferase METTL16 Regulates SAM Synthetase Intron Retention
Kathryn E. Pendleton et al.
CELL (2017)
Know your neighbor: Microbiota and host epithelial cells interact locally to control intestinal function and physiology
Felix Sommer et al.
BIOESSAYS (2016)
MultiQC: summarize analysis results for multiple tools and samples in a single report
Philip Ewels et al.
BIOINFORMATICS (2016)
From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites
Ara Koh et al.
CELL (2016)
Dynamics of Human and Viral RNA Methylation during Zika Virus Infection
Gianluigi Lichinchi et al.
CELL HOST & MICROBE (2016)
N6-Methyladenosine in Flaviviridae Viral RNA Genomes Regulates Infection
Nandan S. Gokhale et al.
CELL HOST & MICROBE (2016)
Posttranscriptional m6A Editing of HIV-1 mRNAs Enhances Viral Gene Expression
Edward M. Kennedy et al.
CELL HOST & MICROBE (2016)
Metabolic control of methylation and acetylation
Xiaoyang Su et al.
CURRENT OPINION IN CHEMICAL BIOLOGY (2016)
Post-transcriptional modifications in development and stem cells
Michaela Frye et al.
DEVELOPMENT (2016)
Nuclear m6A Reader YTHDC1 Regulates mRNA Splicing
Wen Xiao et al.
MOLECULAR CELL (2016)
m6A modulates neuronal functions and sex determination in Drosophila
Tina Lence et al.
NATURE (2016)
Signals from the gut microbiota to distant organs in physiology and disease
Bjoern Schroeder et al.
NATURE MEDICINE (2016)
The Perseus computational platform for comprehensive analysis of (prote)omics data
Stefka Tyanova et al.
NATURE METHODS (2016)
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
Maxim V. Kuleshov et al.
NUCLEIC ACIDS RESEARCH (2016)
Bacteriocin from epidemic Listeria strains alters the host intestinal microbiota to favor infection
Juan J. Quereda et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Calibration plot for proteomics: A graphical tool to visually check the assumptions underlying FDR control in quantitative experiments
Quentin Giai Gianetto et al.
PROTEOMICS (2016)
Lactobacillus plantarum strain maintains growth of infant mice during chronic undernutrition
Martin Schwarzer et al.
SCIENCE (2016)
N6-methyladenosine of HIV-1 RNA regulates viral infection and HIV-1 Gag protein expression
Nagaraja Tirumuru et al.
ELIFE (2016)
VSEARCH: a versatile open source tool for metagenomics
Torbjorn Rognes et al.
PEERJ (2016)
Dynamics of the human and viral m6A RNA methylomes during HIV-1 infection of T cells
Gianluigi Lichinchi et al.
NATURE MICROBIOLOGY (2016)
Lactobacillus plantarum WCFS1 and its host interaction: a dozen years after the genome
Maurits van den Nieuwboer et al.
MICROBIAL BIOTECHNOLOGY (2016)
Microbiota-Modulated Metabolites Shape the Intestinal Microenvironment by Regulating NLRP6 Inflammasome Signaling
Maayan Levy et al.
CELL (2015)
5′ UTR m6A Promotes Cap-Independent Translation
Kate D. Meyer et al.
CELL (2015)
HNRNPA2B1 Is a Mediator of m6A-Dependent Nuclear RNA Processing Events
Claudio R. Alarcon et al.
CELL (2015)
Creating reference gene annotation for the mouse C57BL6/J genome assembly
Jonathan M. Mudge et al.
MAMMALIAN GENOME (2015)
Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome
Bastian Linder et al.
NATURE METHODS (2015)
limma powers differential expression analyses for RNA-sequencing and microarray studies
Matthew E. Ritchie et al.
NUCLEIC ACIDS RESEARCH (2015)
m6A mRNA methylation facilitates resolution of naive pluripotency toward differentiation
Shay Geula et al.
SCIENCE (2015)
HTSeq-a Python framework to work with high-throughput sequencing data
Simon Anders et al.
BIOINFORMATICS (2015)
WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis
Daniel R. Zerbino et al.
BIOINFORMATICS (2014)
FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis
Xu Zhao et al.
CELL RESEARCH (2014)
A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation
Jianzhao Liu et al.
NATURE CHEMICAL BIOLOGY (2014)
Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences
Pablo Yarza et al.
NATURE REVIEWS MICROBIOLOGY (2014)
Perturbation of m6A Writers Reveals Two Distinct Classes of mRNA Methylation at Internal and 5′ Sites
Schraga Schwartz et al.
CELL REPORTS (2014)
voom: precision weights unlock linear model analysis tools for RNA-seq read counts
Charity W. Law et al.
GENOME BIOLOGY (2014)
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Michael I. Love et al.
GENOME BIOLOGY (2014)
STAR: ultrafast universal RNA-seq aligner
Alexander Dobin et al.
BIOINFORMATICS (2013)
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool
Edward Y. Chen et al.
BMC BIOINFORMATICS (2013)
A comparison of methods for differential expression analysis of RNA-seq data
Charlotte Soneson et al.
BMC BIOINFORMATICS (2013)
High-Resolution Mapping Reveals a Conserved, Widespread, Dynamic mRNA Methylation Program in Yeast Meiosis
Schraga Schwartz et al.
CELL (2013)
RNA-Methylation-Dependent RNA Processing Controls the Speed of the Circadian Clock
Jean-Michel Fustin et al.
CELL (2013)
ALIENTRIMMER: A tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads
Alexis Criscuolo et al.
GENOMICS (2013)
Transcriptome-wide mapping of N6-methyladenosine by m6A-seq based on immunocapturing and massively parallel sequencing
Dan Dominissini et al.
NATURE PROTOCOLS (2013)
The gut microbiota - masters of host development and physiology
Felix Sommer et al.
NATURE REVIEWS MICROBIOLOGY (2013)
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Christian Quast et al.
NUCLEIC ACIDS RESEARCH (2013)
Software for Computing and Annotating Genomic Ranges
Michael Lawrence et al.
PLOS COMPUTATIONAL BIOLOGY (2013)
Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons
Kate D. Meyer et al.
CELL (2012)
Detecting differential usage of exons from RNA-seq data
Simon Anders et al.
GENOME RESEARCH (2012)
Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq
Dan Dominissini et al.
NATURE (2012)
Inferring direct DNA binding from ChIP-seq
Timothy L. Bailey et al.
NUCLEIC ACIDS RESEARCH (2012)
Host-Gut Microbiota Metabolic Interactions
Jeremy K. Nicholson et al.
SCIENCE (2012)
DREME: motif discovery in transcription factor ChIP-seq data
Timothy L. Bailey
BIOINFORMATICS (2011)
MEME-ChIP: motif analysis of large DNA datasets
Philip Machanick et al.
BIOINFORMATICS (2011)
Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment
Juergen Cox et al.
JOURNAL OF PROTEOME RESEARCH (2011)
Depletion of Murine Intestinal Microbiota: Effects on Gut Mucosa and Epithelial Gene Expression
Dag Henrik Reikvam et al.
PLOS ONE (2011)
Folate Production by Probiotic Bacteria
Maddalena Rossi et al.
NUTRIENTS (2011)
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan et al.
BIOINFORMATICS (2010)
Tackling the widespread and critical impact of batch effects in high-throughput data
Jeffrey T. Leek et al.
NATURE REVIEWS GENETICS (2010)
A scaling normalization method for differential expression analysis of RNA-seq data
Mark D. Robinson et al.
GENOME BIOLOGY (2010)
The Sequence Alignment/Map format and SAMtools
Heng Li et al.
BIOINFORMATICS (2009)
Inactivation of the Fto gene protects from obesity
Julia Fischer et al.
NATURE (2009)
A Mouse Model for the Metabolic Effects of the Human Fat Mass and Obesity Associated FTO Gene
Chris Church et al.
PLOS GENETICS (2009)
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
Juergen Cox et al.
NATURE BIOTECHNOLOGY (2008)
Intestinal integrity and Akkermansia muciniphila, a mucin-degrading member of the intestinal microbiota present in infants, adults, and the elderly
M. Carmen Collado et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2007)
A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity
Timothy M. Frayling et al.
SCIENCE (2007)