m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation

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

(2014) S. Anders et al.   BIOINFORMATICS

Resetting Transcription Factor Control Circuitry toward Ground-State Pluripotency in Human

(2014) Yasuhiro Takashima et al.   CELL

Epigenomic Comparison Reveals Activation of “Seed” Enhancers during Transition from Naive to Primed Pluripotency

(2014) Daniel C. Factor et al.   Cell Stem Cell

Regulatory Principles of Pluripotency: From the Ground State Up

(2014) Jamie A. Hackett et al.   Cell Stem Cell

Systematic Identification of Culture Conditions for Induction and Maintenance of Naive Human Pluripotency

(2014) Thorold W. Theunissen 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

N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells

(2014) Yang Wang et al.   NATURE CELL BIOLOGY

Derivation of naive human embryonic stem cells

(2014) C. B. Ware et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Defining an essential transcription factor program for naive pluripotency

(2014) S.- J. Dunn et al.   SCIENCE

A genome-wide map of hyper-edited RNA reveals numerous new sites

(2014) Hagit T. Porath et al.   Nature Communications

Mammalian conserved ADAR targets comprise only a small fragment of the human editosome

(2014) Yishay Pinto et al.   GENOME BIOLOGY

REDItools: high-throughput RNA editing detection made easy

(2013) Ernesto Picardi et al.   BIOINFORMATICS

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

(2013) Schraga Schwartz et al.   CELL

Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins

(2013) Mitchell Guttman et al.   CELL

MBNL proteins repress ES-cell-specific alternative splicing and reprogramming

(2013) Hong Han et al.   NATURE

Deterministic direct reprogramming of somatic cells to pluripotency

(2013) Yoach Rais et al.   NATURE

Derivation of novel human ground state naive pluripotent stem cells

(2013) Ohad Gafni et al.   NATURE

N6-methyladenosine-dependent regulation of messenger RNA stability

(2013) Xiao Wang et al.   NATURE

SON connects the splicing-regulatory network with pluripotency in human embryonic stem cells

(2013) Xinyi Lu et al.   NATURE CELL BIOLOGY

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

Naive pluripotency is associated with global DNA hypomethylation

(2013) Harry G Leitch et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Novel RNA regulatory mechanisms revealed in the epitranscriptome

(2013) Yogesh Saletore et al.   RNA Biology

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The Transcriptional and Epigenomic Foundations of Ground State Pluripotency

(2012) Hendrik Marks et al.   CELL

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

(2012) Kate D. Meyer et al.   CELL

Otx2 is an intrinsic determinant of the embryonic stem cell state and is required for transition to a stable epiblast stem cell condition

(2012) D. Acampora et al.   DEVELOPMENT

ALKBH5 Is a Mammalian RNA Demethylase that Impacts RNA Metabolism and Mouse Fertility

(2012) Guanqun Zheng et al.   MOLECULAR CELL

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

(2012) Dan Dominissini et al.   NATURE

A unique regulatory phase of DNA methylation in the early mammalian embryo

(2012) Zachary D. Smith et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

(2012) Nicholas T Ingolia et al.   Nature Protocols

MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data

(2012) Shihao Shen et al.   NUCLEIC ACIDS RESEARCH

Anoctamin 1 (Tmem16A) Ca2+-activated chloride channel stoichiometrically interacts with an ezrin-radixin-moesin network

(2012) P. Perez-Cornejo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Decoding Human Cytomegalovirus

(2012) N. Stern-Ginossar et al.   SCIENCE

The ADAR protein family

(2012) Yiannis A Savva et al.   GENOME BIOLOGY

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

(2012) Yogesh Saletore et al.   GENOME BIOLOGY

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

An Alternative Splicing Switch Regulates Embryonic Stem Cell Pluripotency and Reprogramming

(2011) Mathieu Gabut et al.   CELL

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

N6-Methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO

(2011) Guifang Jia et al.   Nature Chemical Biology

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

Metastable Pluripotent States in NOD-Mouse-Derived ESCs

(2009) Jacob Hanna et al.   Cell Stem Cell

Naive and Primed Pluripotent States

(2009) Jennifer Nichols et al.   Cell Stem Cell

Is REST required for ESC pluripotency?

(2009) Helle F. Jørgensen et al.   NATURE

Direct cell reprogramming is a stochastic process amenable to acceleration

(2009) Jacob Hanna et al.   NATURE

How to map billions of short reads onto genomes

(2009) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

A reprogrammable mouse strain from gene-targeted embryonic stem cells

(2009) Matthias Stadtfeld et al.   NATURE METHODS

Rapid creation and quantitative monitoring of high coverage shRNA libraries

(2009) Michael C Bassik et al.   NATURE METHODS

Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells

(2008) L. V. Sharova et al.   DNA RESEARCH

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY