The SMAD2/3 interactome reveals that TGFβ controls m6A mRNA methylation in pluripotency

MeTDiff: A Novel Differential RNA Methylation Analysis for MeRIP-Seq Data

(2018) Xiaodong Cui et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

m 6 A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover

(2017) Shengdong Ke et al.   GENES & DEVELOPMENT

Epitranscriptome sequencing technologies: decoding RNA modifications

(2017) Xiaoyu Li et al.   NATURE METHODS

RCAS: an RNA centric annotation system for transcriptome-wide regions of interest

(2017) Bora Uyar et al.   NUCLEIC ACIDS RESEARCH

N6-methyladenosine demethylase FTO targets pre-mRNAs and regulates alternative splicing and 3′-end processing

(2017) Marek Bartosovic et al.   NUCLEIC ACIDS RESEARCH

Inducible and Deterministic Forward Programming of Human Pluripotent Stem Cells into Neurons, Skeletal Myocytes, and Oligodendrocytes

(2017) Matthias Pawlowski et al.   Stem Cell Reports

Optimized inducible shRNA and CRISPR/Cas9 platforms forin vitrostudies of human development using hPSCs

(2016) Alessandro Bertero et al.   DEVELOPMENT

An Adenine Code for DNA: A Second Life for N6-Methyladenine

(2015) Holger Heyn et al.   CELL

5′ UTR m6A Promotes Cap-Independent Translation

(2015) Kate D. Meyer et al.   CELL

A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulation

(2015) Shengdong Ke et al.   GENES & DEVELOPMENT

Activin/Nodal signaling and NANOG orchestrate human embryonic stem cell fate decisions by controlling the H3K4me3 chromatin mark

(2015) Alessandro Bertero et al.   GENES & DEVELOPMENT

A Quantitative Proteomics Tool To Identify DNA–Protein Interactions in Primary Cells or Blood

(2015) Nina C. Hubner et al.   JOURNAL OF PROTEOME RESEARCH

m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation

(2015) Shay Geula et al.   SCIENCE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

NANOG and CDX2 Pattern Distinct Subtypes of Human Mesoderm during Exit from Pluripotency

(2014) Sasha Mendjan et al.   Cell Stem Cell

m6A RNA Modification Controls Cell Fate Transition in Mammalian Embryonic Stem Cells

(2014) Pedro J. Batista et al.   Cell Stem Cell

TGF-β signaling to chromatin: How Smads regulate transcription during self-renewal and differentiation

(2014) Tessa Gaarenstroom et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

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

(2014) Schraga Schwartz et al.   Cell Reports

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

GAT: a simulation framework for testing the association of genomic intervals

(2013) A. Heger et al.   BIOINFORMATICS

Exome-based analysis for RNA epigenome sequencing data

(2013) Jia Meng et al.   BIOINFORMATICS

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

N6-methyladenosine-dependent regulation of messenger RNA stability

(2013) Xiao Wang et al.   NATURE

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

(2013) Dan Dominissini et al.   Nature Protocols

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

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

(2012) Kate D. Meyer et al.   CELL

The Harmonies Played by TGF-β in Stem Cell Biology

(2012) Naoki Oshimori et al.   Cell Stem Cell

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

(2012) Dan Dominissini et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The birth of the Epitranscriptome: deciphering the function of RNA modifications

(2012) Yogesh Saletore et al.   GENOME BIOLOGY

Dalliance: interactive genome viewing on the web

(2011) T. A. Down et al.   BIOINFORMATICS

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

Pluripotency factors regulate definitive endoderm specification through eomesodermin

(2011) A. K. K. Teo et al.   GENES & DEVELOPMENT

Targeted gene correction of α1-antitrypsin deficiency in induced pluripotent stem cells

(2011) Kosuke Yusa et al.   NATURE

Activin/Nodal Signaling Controls Divergent Transcriptional Networks in Human Embryonic Stem Cells and in Endoderm Progenitors

(2011) Stephanie Brown et al.   STEM CELLS

Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions

(2010) Nina C. Hubner et al.   JOURNAL OF CELL BIOLOGY

Extracting gene function from protein–protein interactions using Quantitative BAC InteraCtomics (QUBIC)

(2010) Nina C. Hubner et al.   METHODS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Activin/Nodal signalling maintains pluripotency by controlling Nanog expression

(2009) L. Vallier et al.   DEVELOPMENT

TGF-β Superfamily Signaling in Embryonic Development and Homeostasis

(2009) Mary Y. Wu et al.   DEVELOPMENTAL CELL

Generation of functional hepatocytes from human embryonic stem cells under chemically defined conditions that recapitulate liver development

(2009) Thomas Touboul et al.   HEPATOLOGY

Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics

(2009) Paul J Boersema et al.   Nature Protocols

Early Cell Fate Decisions of Human Embryonic Stem Cells and Mouse Epiblast Stem Cells Are Controlled by the Same Signalling Pathways

(2009) Ludovic Vallier et al.   PLoS One

Signaling Pathways Controlling Pluripotency and Early Cell Fate Decisions of Human Induced Pluripotent Stem Cells

(2009) Ludovic Vallier et al.   STEM CELLS

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

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

Inhibition of Activin/Nodal signaling promotes specification of human embryonic stem cells into neuroectoderm

(2007) Joseph R. Smith et al.   DEVELOPMENTAL BIOLOGY