Reactivation of the pluripotency program precedes formation of the cranial neural crest

Single-cell chromatin accessibility maps reveal regulatory programs driving early mouse organogenesis

(2020) Blanca Pijuan-Sala et al.   NATURE CELL BIOLOGY

The vertebrate-specific VENTX/NANOG gene empowers neural crest with ectomesenchyme potential

(2020) Pierluigi Scerbo et al.   Science Advances

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

An epiblast stem cell-derived multipotent progenitor population for axial extension

(2019) Shlomit Edri et al.   DEVELOPMENT

Spatiotemporal structure of cell fate decisions in murine neural crest

(2019) Ruslan Soldatov et al.   SCIENCE

ZIC3 Controls the Transition from Naive to Primed Pluripotency

(2019) Shen-Hsi Yang et al.   Cell Reports

Reconstruction of the Global Neural Crest Gene Regulatory Network In Vivo

(2019) Ruth M. Williams et al.   DEVELOPMENTAL CELL

Early chromatin shaping predetermines multipotent vagal neural crest into neural, neuronal and mesenchymal lineages

(2019) Irving T. C. Ling et al.   NATURE CELL BIOLOGY

Oct4 regulates the embryonic axis and coordinates exit from pluripotency and germ layer specification in the mouse embryo

(2018) Carla Mulas et al.   DEVELOPMENT

Cre-driver lines used for genetic fate mapping of neural crest cells in the mouse: An overview

(2018) Julien Debbache et al.   GENESIS

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution

(2018) James A. Briggs et al.   SCIENCE

CellProfiler 3.0: Next-generation image processing for biology

(2018) Claire McQuin et al.   PLOS BIOLOGY

Nervous System Regionalization Entails Axial Allocation before Neural Differentiation

(2018) Vicki Metzis et al.   CELL

Mll3 and Mll4 Facilitate Enhancer RNA Synthesis and Transcription from Promoters Independently of H3K4 Monomethylation

(2017) Kristel M. Dorighi et al.   MOLECULAR CELL

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Gene bivalency at Polycomb domains regulates cranial neural crest positional identity

(2017) Maryline Minoux et al.   SCIENCE

Identification of a neural crest stem cell niche by Spatial Genomic Analysis

(2017) Antti Lignell et al.   Nature Communications

Oct4 Is a Key Regulator of Vertebrate Trunk Length Diversity

(2016) Rita Aires et al.   DEVELOPMENTAL CELL

Polarized regulatory landscape and Wnt responsiveness underlie Hox activation in embryos

(2016) Roel Neijts et al.   GENES & DEVELOPMENT

OCT4 Acts as an Integrator of Pluripotency and Signal-Induced Differentiation

(2016) Zoltan Simandi et al.   MOLECULAR CELL

Production of hornless dairy cattle from genome-edited cell lines

(2016) Daniel F Carlson et al.   NATURE BIOTECHNOLOGY

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

(2016) M Ryan Corces et al.   NATURE GENETICS

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

(2015) Allen Wang et al.   Cell Stem Cell

Establishing neural crest identity: a gene regulatory recipe

(2015) M. Simoes-Costa et al.   DEVELOPMENT

Mef2c-F10N enhancer driven β-galactosidase (LacZ) and Cre recombinase mice facilitate analyses of gene function and lineage fate in neural crest cells

(2015) Kazushi Aoto et al.   DEVELOPMENTAL BIOLOGY

Shared regulatory programs suggest retention of blastula-stage potential in neural crest cells

(2015) E. Buitrago-Delgado et al.   SCIENCE

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

Reorganization of Enhancer Patterns in Transition from Naive to Primed Pluripotency

(2014) Christa Buecker et al.   Cell Stem Cell

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

The Transcriptional and Functional Properties of Mouse Epiblast Stem Cells Resemble the Anterior Primitive Streak

(2013) Yoji Kojima et al.   Cell Stem Cell

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

Oct4 Is Required ∼E7.5 for Proliferation in the Primitive Streak

(2013) Brian DeVeale et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Neural crest migration: interplay between chemorepellents, chemoattractants, contact inhibition, epithelial-mesenchymal transition, and collective cell migration

(2012) Eric Theveneau et al.   Wiley Interdisciplinary Reviews-Developmental Biology

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Wnt1 expression temporally allocates upper rhombic lip progenitors and defines their terminal cell fate in the cerebellum

(2011) Nellwyn Hagan et al.   MOLECULAR AND CELLULAR NEUROSCIENCE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Regulation of pre-otic brain development by the cephalic neural crest

(2009) S. E. Creuzet   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic localization of oct-3/4 to the gastrulating mouse conceptus suggests manifold roles in mammalian development

(2008) Karen M. Downs   DEVELOPMENTAL DYNAMICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY