A transcribed enhancer dictates mesendoderm specification in pluripotency

Embryonic Stem Cell-Derived Neurons Grown on Multi-Electrode Arrays as a Novel In vitro Bioassay for the Detection of Clostridium botulinum Neurotoxins

(2017) Stephen P. Jenkinson et al.   Frontiers in Pharmacology

Super-enhancer lnc s to cardiovascular development and disease

(2016) Samir Ounzain et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   CELL

Stepwise Clearance of Repressive Roadblocks Drives Cardiac Induction in Human ESCs

(2016) Jyoti Rao et al.   Cell Stem Cell

Divergent lncRNAs Regulate Gene Expression and Lineage Differentiation in Pluripotent Cells

(2016) Sai Luo et al.   Cell Stem Cell

Rebuilding a broken heart: lessons from developmental and regenerative biology

(2016) Muge N. Kuyumcu-Martinez et al.   DEVELOPMENT

The functions of long noncoding RNAs in development and stem cells

(2016) Rotem Ben-Tov Perry et al.   DEVELOPMENT

Signaling Control of Differentiation of Embryonic Stem Cells toward Mesendoderm

(2016) Lu Wang et al.   JOURNAL OF MOLECULAR BIOLOGY

“Cat’s Cradling” the 3D Genome by the Act of LncRNA Transcription

(2016) Marta Melé et al.   MOLECULAR CELL

Transcription of the non-coding RNA upperhand controls Hand2 expression and heart development

(2016) Kelly M. Anderson et al.   NATURE

Local regulation of gene expression by lncRNA promoters, transcription and splicing

(2016) Jesse M. Engreitz et al.   NATURE

Generating high-purity cardiac and endothelial derivatives from patterned mesoderm using human pluripotent stem cells

(2016) Nathan J Palpant et al.   Nature Protocols

Enhancers as non-coding RNA transcription units: recent insights and future perspectives

(2016) Wenbo Li et al.   NATURE REVIEWS GENETICS

Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression

(2016) Jesse M. Engreitz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Breaking TADs: How Alterations of Chromatin Domains Result in Disease

(2016) Darío G. Lupiáñez et al.   TRENDS IN GENETICS

DIGIT Is a Conserved Long Noncoding RNA that Regulates GSC Expression to Control Definitive Endoderm Differentiation of Embryonic Stem Cells

(2016) Kaveh Daneshvar et al.   Cell Reports

Super-Enhancers at the Nanog Locus Differentially Regulate Neighboring Pluripotency-Associated Genes

(2016) Steven Blinka et al.   Cell Reports

Epigenetic Priming of Enhancers Predicts Developmental Competence of hESC-Derived Endodermal Lineage Intermediates

(2015) Allen Wang et al.   Cell Stem Cell

Opposing Roles for the lncRNA Haunt and Its Genomic Locus in Regulating HOXA Gene Activation during Embryonic Stem Cell Differentiation

(2015) Yafei Yin et al.   Cell Stem Cell

Investigating the Transcriptional Control of Cardiovascular Development

(2015) I. S. Kathiriya et al.   CIRCULATION RESEARCH

CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis

(2015) Samir Ounzain et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

Discovery and functional characterization of cardiovascular long noncoding RNAs

(2015) Samir Ounzain et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

(2015) Silvana Konermann et al.   NATURE

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

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

The promise of enhancer-associated long noncoding RNAs in cardiac regeneration

(2015) Samir Ounzain et al.   TRENDS IN CARDIOVASCULAR MEDICINE

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

(2014) S. Anders et al.   BIOINFORMATICS

Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus

(2014) Jian-Feng Xiang et al.   CELL RESEARCH

Genome-wide profiling of the cardiac transcriptome after myocardial infarction identifies novel heart-specific long non-coding RNAs

(2014) S. Ounzain et al.   EUROPEAN HEART JOURNAL

Functional importance of cardiac enhancer-associated noncoding RNAs in heart development and disease

(2014) Samir Ounzain et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

Chemically defined generation of human cardiomyocytes

(2014) Paul W Burridge et al.   NATURE METHODS

The rise of regulatory RNA

(2014) Kevin V. Morris et al.   NATURE REVIEWS GENETICS

Considerations when investigating lncRNA function in vivo

(2014) Andrew R Bassett et al.   eLife

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes

(2013) Andrew B. Stergachis et al.   CELL

eRNAs Promote Transcription by Establishing Chromatin Accessibility at Defined Genomic Loci

(2013) Kambiz Mousavi et al.   MOLECULAR CELL

Distal enhancers: new insights into heart development and disease

(2013) Joseph A. Wamstad et al.   TRENDS IN CELL BIOLOGY

Signaling and Transcriptional Networks in Heart Development and Regeneration

(2013) B. G. Bruneau   Cold Spring Harbor Perspectives in Biology

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage

(2012) Joseph A. Wamstad et al.   CELL

Human β Cell Transcriptome Analysis Uncovers lncRNAs That Are Tissue-Specific, Dynamically Regulated, and Abnormally Expressed in Type 2 Diabetes

(2012) Ignasi Morán et al.   Cell Metabolism

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Directed cardiomyocyte differentiation from human pluripotent stem cells by modulating Wnt/β-catenin signaling under fully defined conditions

(2012) Xiaojun Lian et al.   Nature Protocols

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Neural induction and early patterning in vertebrates

(2012) Mohammad Zeeshan Ozair et al.   Wiley Interdisciplinary Reviews-Developmental Biology

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

The T-box transcription factor Eomesodermin acts upstream of Mesp1 to specify cardiac mesoderm during mouse gastrulation

(2011) Ita Costello et al.   NATURE CELL BIOLOGY

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

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

Generation and analysis of a mouse line harboring GFP in the Eomes/Tbr2 locus

(2009) Sebastian J. Arnold et al.   GENESIS

Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells

(2008) Alexander Marson et al.   CELL