Reconstituting human somitogenesis in vitro

Paraxial mesoderm organoids model development of human somites

(2022) Christoph Budjan et al.   eLife

Periodic formation of epithelial somites from human pluripotent stem cells

(2022) Marina Sanaki-Matsumiya et al.   Nature Communications

Rostrocaudal patterning and neural crest differentiation of human pre-neural spinal cord progenitors in vitro

(2022) Fay Cooper et al.   Stem Cell Reports

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

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

Epigenetic regulator function through mouse gastrulation

(2020) Stefanie Grosswendt 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

Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue

(2020) Daniel Gyllborg et al.   NUCLEIC ACIDS RESEARCH

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

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

CUT&Tag for efficient epigenomic profiling of small samples and single cells

(2019) Hatice S. Kaya-Okur et al.   Nature Communications

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

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

ES cell-derived presomitic mesoderm-like tissues for analysis of synchronized oscillations in the segmentation clock

(2018) Marina Matsumiya et al.   DEVELOPMENT

Third-generationin situhybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust

(2018) Harry M. T. Choi et al.   DEVELOPMENT

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

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

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

ScaleS: an optical clearing palette for biological imaging

(2015) Hiroshi Hama et al.   NATURE NEUROSCIENCE

Deterministic HOX Patterning in Human Pluripotent Stem Cell-Derived Neuroectoderm

(2015) Ethan S. Lippmann et al.   Stem Cell Reports

Haematopoietic stem cell induction by somite-derived endothelial cells controlled by meox1

(2014) Phong Dang Nguyen et al.   NATURE

Regulation of mesenchymal-to-epithelial transition by PARAXIS during somitogenesis

(2013) Megan Rowton et al.   DEVELOPMENTAL DYNAMICS

Signaling by FGF4 and FGF8 is required for axial elongation of the mouse embryo

(2012) Anne M. Boulet et al.   DEVELOPMENTAL BIOLOGY

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Loss of FGF-Dependent Mesoderm Identity and Rise of Endogenous Retinoid Signalling Determine Cessation of Body Axis Elongation

(2012) Isabel Olivera-Martinez et al.   PLOS BIOLOGY

Ribosome-Mediated Specificity in Hox mRNA Translation and Vertebrate Tissue Patterning

(2011) Nadya Kondrashov et al.   CELL

A more efficient method to generate integration-free human iPS cells

(2011) Keisuke Okita et al.   NATURE METHODS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Emergence of traveling waves in the zebrafish segmentation clock

(2010) K. Ishimatsu et al.   DEVELOPMENT

The HUDSEN Atlas: a three-dimensional (3D) spatial framework for studying gene expression in the developing human brain

(2010) Janet Kerwin et al.   JOURNAL OF ANATOMY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Signaling Gradients during Paraxial Mesoderm Development

(2009) A. Aulehla et al.   Cold Spring Harbor Perspectives in Biology

Notch Mediates the Segmental Specification of Angioblasts in Somites and Their Directed Migration toward the Dorsal Aorta in Avian Embryos

(2008) Yuki Sato et al.   DEVELOPMENTAL CELL

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

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