Eomes and Brachyury control pluripotency exit and germ-layer segregation by changing the chromatin state

Open Chromatin, Epigenetic Plasticity, and Nuclear Organization in Pluripotency

(2019) Sharon Schlesinger et al.   DEVELOPMENTAL CELL

A Linc1405/Eomes Complex Promotes Cardiac Mesoderm Specification and Cardiogenesis

(2018) Xudong Guo et al.   Cell Stem Cell

Defining the earliest step of cardiovascular lineage segregation by single-cell RNA-seq

(2018) Fabienne Lescroart et al.   SCIENCE

The interaction landscape between transcription factors and the nucleosome

(2018) Fangjie Zhu et al.   NATURE

Combinatorial Smad2/3 Activities Downstream of Nodal Signaling Maintain Embryonic/Extra-Embryonic Cell Identities during Lineage Priming

(2018) Anna D. Senft et al.   Cell Reports

Nervous System Regionalization Entails Axial Allocation before Neural Differentiation

(2018) Vicki Metzis et al.   CELL

Cell fate control by pioneer transcription factors

(2016) Makiko Iwafuchi-Doi et al.   DEVELOPMENT

The Cardiac TBX5 Interactome Reveals a Chromatin Remodeling Network Essential for Cardiac Septation

(2016) Lauren Waldron et al.   DEVELOPMENTAL CELL

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Intermediate Progenitor Cohorts Differentially Generate Cortical Layers and Require Tbr2 for Timely Acquisition of Neuronal Subtype Identity

(2016) Anca B. Mihalas et al.   Cell Reports

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

Neuromesodermal progenitors and the making of the spinal cord

(2015) D. Henrique et al.   DEVELOPMENT

Brachyury and SMAD signalling collaboratively orchestrate distinct mesoderm and endoderm gene regulatory networks in differentiating human embryonic stem cells

(2015) T. Faial et al.   DEVELOPMENT

Intrinsic regulations in neural fate commitment

(2015) Ke Tang et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap

(2015) Tauno Metsalu et al.   NUCLEIC ACIDS RESEARCH

Global identification of Smad2 and Eomesodermin targets in zebrafish identifies a conserved transcriptional network in mesendoderm and a novel role for Eomesodermin in repression of ectodermal gene expression

(2014) Andrew C Nelson et al.   BMC BIOLOGY

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

The transcription factor Pou3f1 promotes neural fate commitment via activation of neural lineage genes and inhibition of external signaling pathways

(2014) Qingqing Zhu et al.   eLife

The histone demethylase Jmjd3 sequentially associates with the transcription factors Tbx3 and Eomes to drive endoderm differentiation

(2013) Apriliana E R Kartikasari et al.   EMBO JOURNAL

The T-box transcription factor Eomesodermin is essential for AVE induction in the mouse embryo

(2013) S. Nowotschin et al.   GENES & DEVELOPMENT

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

In Vivo T-Box Transcription Factor Profiling Reveals Joint Regulation of Embryonic Neuromesodermal Bipotency

(2013) George E. Gentsch et al.   Cell Reports

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Transcriptional regulatory networks in epiblast cells and during anterior neural plate development as modeled in epiblast stem cells

(2012) M. Iwafuchi-Doi et al.   DEVELOPMENT

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Genomic Targets of Brachyury (T) in Differentiating Mouse Embryonic Stem Cells

(2012) Amanda L. Evans et al.   PLoS One

Activin induces cortical interneuron identity and differentiation in embryonic stem cell-derived telencephalic neural precursors

(2012) Serafí Cambray et al.   Nature Communications

Pluripotency factors regulate definitive endoderm specification through eomesodermin

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

Tbx6-dependent Sox2 regulation determines neural or mesodermal fate in axial stem cells

(2011) Tatsuya Takemoto 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

Epiblast Stem Cell Subpopulations Represent Mouse Embryos of Distinct Pregastrulation Stages

(2010) Dong Wook Han et al.   CELL

The T-box transcription factor Brachyury promotes epithelial-mesenchymal transition in human tumor cells

(2010) Romaine I. Fernando et al.   JOURNAL OF CLINICAL INVESTIGATION

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

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Naive and Primed Pluripotent States

(2009) Jennifer Nichols et al.   Cell Stem Cell

Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling

(2009) Stuart M Chambers et al.   NATURE BIOTECHNOLOGY

Making a commitment: cell lineage allocation and axis patterning in the early mouse embryo

(2009) Sebastian J. Arnold et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Pivotal roles for eomesodermin during axis formation, epithelium-to-mesenchyme transition and endoderm specification in the mouse

(2008) S. J. Arnold et al.   DEVELOPMENT

The T-box transcription factor Eomes/Tbr2 regulates neurogenesis in the cortical subventricular zone

(2008) S. J. Arnold et al.   GENES & DEVELOPMENT

Coordinated but physically separable interaction with H3K27-demethylase and H3K4-methyltransferase activities are required for T-box protein-mediated activation of developmental gene expression

(2008) S. A. Miller et al.   GENES & DEVELOPMENT

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY