Periodic formation of epithelial somites from human pluripotent stem cells

Paraxial mesoderm organoids model development of human somites

(2022) Christoph Budjan et al.   eLife

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

MOrgAna: accessible quantitative analysis of organoids with machine learning

(2021) Nicola Gritti et al.   DEVELOPMENT

Sculpting with stem cells: how models of embryo development take shape

(2021) Jesse V. Veenvliet et al.   DEVELOPMENT

In vitro characterization of the human segmentation clock

(2020) Margarete Diaz-Cuadros et al.   NATURE

Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids

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

Recapitulating the human segmentation clock with pluripotent stem cells

(2020) Mitsuhiro Matsuda et al.   NATURE

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

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Species-specific segmentation clock periods are due to differential biochemical reaction speeds

(2020) Mitsuhiro Matsuda et al.   SCIENCE

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

(2020) Jesse V. Veenvliet et al.   SCIENCE

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

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

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

An In Vitro Human Segmentation Clock Model Derived from Embryonic Stem Cells

(2019) Li-Fang Chu et al.   Cell Reports

Modulation of Phase Shift between Wnt and Notch Signaling Oscillations Controls Mesoderm Segmentation

(2018) Katharina F. Sonnen et al.   CELL

Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos

(2018) Vikas Trivedi et al.   DEVELOPMENT

What does time mean in development?

(2018) Miki Ebisuya et al.   DEVELOPMENT

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

In vitro generation of mouse polarized embryo-like structures from embryonic and trophoblast stem cells

(2018) Sarah Ellys Harrison et al.   Nature Protocols

Modeling human somite development and fibrodysplasia ossificans progressiva with induced pluripotent stem cells

(2018) Taiki Nakajima et al.   DEVELOPMENT

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

4D imaging reveals stage dependent random and directed cell motion during somite morphogenesis

(2018) James McColl et al.   Scientific Reports

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

(2018) Leonardo Beccari et al.   NATURE

Optogenetic perturbation and bioluminescence imaging to analyze cell-to-cell transfer of oscillatory information

(2017) Akihiro Isomura et al.   GENES & DEVELOPMENT

Guided self-organization and cortical plate formation in human brain organoids

(2017) Madeline A Lancaster et al.   NATURE BIOTECHNOLOGY

In Vivo Human Somitogenesis Guides Somite Development from hPSCs

(2017) Haibin Xi et al.   Cell Reports

Mapping the Pairwise Choices Leading from Pluripotency to Human Bone, Heart, and Other Mesoderm Cell Types

(2016) Kyle M. Loh et al.   CELL

Symmetry breaking, germ layer specification and axial organisation in aggregates of mouse embryonic stem cells

(2014) S. C. van den Brink et al.   DEVELOPMENT

Signalling dynamics in vertebrate segmentation

(2014) Alexis Hubaud et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Somites Without a Clock

(2014) A. S. Dias et al.   SCIENCE

Cytosystems dynamics in self-organization of tissue architecture

(2013) Yoshiki Sasai   NATURE

The T-box transcription factor Brachyury regulates epithelial–mesenchymal transition in association with cancer stem-like cells in adenoid cystic carcinoma cells

(2012) Miyuki Shimoda et al.   BMC CANCER

A Mechanism for Gene-Environment Interaction in the Etiology of Congenital Scoliosis

(2012) Duncan B. Sparrow et al.   CELL

Scaling of embryonic patterning based on phase-gradient encoding

(2012) Volker M. Lauschke et al.   NATURE

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

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

FGF4 and FGF8 comprise the wavefront activity that controls somitogenesis

(2011) L. A. Naiche et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Matrigel: A complex protein mixture required for optimal growth of cell culture

(2010) Chris S. Hughes et al.   PROTEOMICS

Redefining the Progression of Lineage Segregations during Mammalian Embryogenesis by Clonal Analysis

(2009) Elena Tzouanacou et al.   DEVELOPMENTAL CELL

piggyBac transposition reprograms fibroblasts to induced pluripotent stem cells

(2009) Knut Woltjen et al.   NATURE

Dynamic 3D Cell Rearrangements Guided by a Fibronectin Matrix Underlie Somitogenesis

(2009) Gabriel G. Martins et al.   PLoS One

Notch Is a Critical Component of the Mouse Somitogenesis Oscillator and Is Essential for the Formation of the Somites

(2009) Zoltan Ferjentsik et al.   PLoS Genetics

Mutation of HAIRY-AND-ENHANCER-OF-SPLIT-7 in humans causes spondylocostal dysostosis

(2008) D. B. Sparrow et al.   HUMAN MOLECULAR GENETICS