Axial elongation of caudalized human organoids mimics aspects of neural tube development

Understanding axial progenitor biology in vivo and in vitro

(2021) Filip J. Wymeersch et al.   DEVELOPMENT

Dynamic extrinsic pacing of the HOX clock in human axial progenitors controls motor neuron subtype specification

(2021) Vincent Mouilleau et al.   DEVELOPMENT

Cell intercalation driven by SMAD3 underlies secondary neural tube formation

(2021) Elena Gonzalez-Gobartt et al.   DEVELOPMENTAL CELL

Self-Organizing 3D Human Trunk Neuromuscular Organoids

(2020) Jorge-Miguel Faustino Martins et al.   Cell Stem Cell

Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids

(2020) Susanne C. van den Brink et al.   NATURE

Directed Differentiation of Notochord-like and Nucleus Pulposus-like Cells Using Human Pluripotent Stem Cells

(2020) Yuelin Zhang et al.   Cell Reports

Intracellular pH controls WNT downstream of glycolysis in amniote embryos

(2020) Masayuki Oginuma et al.   NATURE

An in vitro model of early anteroposterior organization during human development

(2020) Naomi Moris et al.   NATURE

Buckling of an Epithelium Growing under Spherical Confinement

(2020) Anastasiya Trushko et al.   DEVELOPMENTAL CELL

Diverse Routes toward Early Somites in the Mouse Embryo

(2020) Carolina Guibentif et al.   DEVELOPMENTAL CELL

Mechanical Tension Promotes Formation of Gastrulation-like Nodes and Patterns Mesoderm Specification in Human Embryonic Stem Cells

(2020) Jonathon M. Muncie et al.   DEVELOPMENTAL CELL

Mouse embryonic stem cells self-organize into trunk-like structures with neural tube and somites

(2020) Jesse V. Veenvliet et al.   SCIENCE

MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices

(2019) Christopher S. McGinnis et al.   NATURE METHODS

Prediction and control of symmetry breaking in embryoid bodies by environment and signal integration

(2019) Naor Sagy et al.   DEVELOPMENT

Exposure-based assessment of chemical teratogenicity using morphogenetic aggregates of human embryonic stem cells

(2019) Yusuke Marikawa et al.   REPRODUCTIVE TOXICOLOGY

Dorsal-ventral patterned neural cyst from human pluripotent stem cells in a neurogenic niche

(2019) Y. Zheng et al.   Science Advances

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Geometrical confinement controls the asymmetric patterning of brachyury in cultures of pluripotent cells

(2018) Guillaume Blin et al.   DEVELOPMENT

Nervous System Regionalization Entails Axial Allocation before Neural Differentiation

(2018) Vicki Metzis et al.   CELL

Multi-axial self-organization properties of mouse embryonic stem cells into gastruloids

(2018) Leonardo Beccari et al.   NATURE

Spatiotemporal mosaic self-patterning of pluripotent stem cells using CRISPR interference

(2018) Ashley RG Libby et al.   eLife

Differentiation of V2a interneurons from human pluripotent stem cells

(2017) Jessica C. Butts et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs

(2016) Mohammad A. Mandegar et al.   Cell Stem Cell

Species-specific contribution of volumetric growth and tissue convergence to posterior body elongation in vertebrates

(2016) Ben Steventon et al.   DEVELOPMENT

Aggregate formation and suspension culture of human pluripotent stem cells and differentiated progeny

(2016) Tracy A. Hookway et al.   METHODS

Culture and establishment of self-renewing human and mouse adult liver and pancreas 3D organoids and their genetic manipulation

(2016) Laura Broutier et al.   Nature Protocols

Cdx and T Brachyury Co-activate Growth Signaling in the Embryonic Axial Progenitor Niche

(2016) Shilu Amin et al.   Cell Reports

Rapid Induction of Cerebral Organoids From Human Induced Pluripotent Stem Cells Using a Chemically Defined Hydrogel and Defined Cell Culture Medium

(2016) Beth A. Lindborg et al.   Stem Cells Translational Medicine

Position-dependent plasticity of distinct progenitor types in the primitive streak

(2016) Filip J Wymeersch et al.   eLife

Thiazovivin, a Rho kinase inhibitor, improves stemness maintenance of embryo-derived stem-like cells under chemically defined culture conditions in cattle

(2015) Sangkyu Park et al.   ANIMAL REPRODUCTION SCIENCE

From Discrete to Continuum Models of Three-Dimensional Deformations in Epithelial Sheets

(2015) Nebojsa Murisic et al.   BIOPHYSICAL JOURNAL

Neuromesodermal progenitors and the making of the spinal cord

(2015) D. Henrique et al.   DEVELOPMENT

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Efficient genetic engineering of human intestinal organoids using electroporation

(2015) Masayuki Fujii et al.   Nature Protocols

Skilled reaching relies on a V2a propriospinal internal copy circuit

(2014) Eiman Azim et al.   NATURE

Isolation of single-base genome-edited human iPS cells without antibiotic selection

(2014) Yuichiro Miyaoka et al.   NATURE METHODS

Organogenesis in a dish: Modeling development and disease using organoid technologies

(2014) M. A. Lancaster et al.   SCIENCE

In Vitro Generation of Neuromesodermal Progenitors Reveals Distinct Roles for Wnt Signalling in the Specification of Spinal Cord and Paraxial Mesoderm Identity

(2014) Mina Gouti et al.   PLOS BIOLOGY

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

scikit-image: image processing in Python

(2014) Stéfan van der Walt et al.   PeerJ

3D Reconstitution of the Patterned Neural Tube from Embryonic Stem Cells

(2014) Andrea Meinhardt et al.   Stem Cell Reports

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

(2013) Y. Liao et al.   BIOINFORMATICS

Accelerated High-Yield Generation of Limb-Innervating Motor Neurons from Human Stem Cells

(2013) M. W. Amoroso et al.   JOURNAL OF NEUROSCIENCE

Cerebral organoids model human brain development and microcephaly

(2013) Madeline A. Lancaster et al.   NATURE

Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals

(2013) Esteban O Mazzoni et al.   NATURE NEUROSCIENCE

CRISPR interference (CRISPRi) for sequence-specific control of gene expression

(2013) Matthew H Larson et al.   Nature Protocols

In vivo knockdown of Brachyury results in skeletal defects and urorectal malformations resembling caudal regression syndrome

(2012) Tracie Pennimpede et al.   DEVELOPMENTAL BIOLOGY

Human cerebral cortex development from pluripotent stem cells to functional excitatory synapses

(2012) Yichen Shi et al.   NATURE NEUROSCIENCE

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

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

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

(2011) Tatsuya Takemoto et al.   NATURE

Self-organizing optic-cup morphogenesis in three-dimensional culture

(2011) Mototsugu Eiraku et al.   NATURE

Growth-induced buckling of an epithelial layer

(2010) M. R. Nelson et al.   Biomechanics and Modeling in Mechanobiology

The relationship between sonic Hedgehog signaling, cilia, and neural tube defects

(2010) Jennifer N. Murdoch et al.   BIRTH DEFECTS RESEARCH PART A-CLINICAL AND MOLECULAR TERATOLOGY

Electrophysiological Characterization of V2a Interneurons and Their Locomotor-Related Activity in the Neonatal Mouse Spinal Cord

(2010) G. Zhong et al.   JOURNAL OF NEUROSCIENCE

Stem cells, signals and vertebrate body axis extension

(2009) V. Wilson et al.   DEVELOPMENT

Actomyosin stiffens the vertebrate embryo during crucial stages of elongation and neural tube closure

(2009) J. Zhou et al.   DEVELOPMENT

Regulation of mouse embryonic stem cell neural differentiation by retinoic acid

(2009) Mijeong Kim et al.   DEVELOPMENTAL BIOLOGY

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

(2009) Stuart M Chambers et al.   NATURE BIOTECHNOLOGY

Genetic Ablation of V2a Ipsilateral Interneurons Disrupts Left-Right Locomotor Coordination in Mammalian Spinal Cord

(2008) Steven A. Crone et al.   NEURON