Controlling organoid symmetry breaking uncovers an excitable system underlying human axial elongation

Controlling human organoid symmetry breaking reveals signaling gradients drive segmentation clock waves

(2023) Yusuf Ilker Yaman et al.   CELL

Epha1 is a cell-surface marker for the neuromesodermal competent population

(2022) Luisa de Lemos et al.   DEVELOPMENT

Understanding axial progenitor biology in vivo and in vitro

(2021) Filip J. Wymeersch et al.   DEVELOPMENT

Bioengineering in vitro models of embryonic development

(2021) Ananya Gupta et al.   Stem Cell Reports

CellProfiler 4: improvements in speed, utility and usability

(2021) David R. Stirling et al.   BMC BIOINFORMATICS

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

3D gastruloids: a novel frontier in stem cell-based in vitro modeling of mammalian gastrulation

(2021) Susanne C. van den Brink et al.   TRENDS IN CELL BIOLOGY

Building consensus in neuromesodermal research: Current advances and future biomedical perspectives

(2021) Anahí Binagui-Casas et al.   CURRENT OPINION IN CELL BIOLOGY

ClusterMap for multi-scale clustering analysis of spatial gene expression

(2021) Yichun He et al.   Nature Communications

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

Discovering a sparse set of pairwise discriminating features in high dimensional data

(2020) Samuel Melton et al.   BIOINFORMATICS

An in vitro model of early anteroposterior organization during human development

(2020) Naomi Moris et al.   NATURE

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

(2020) Jesse V. Veenvliet et al.   SCIENCE

Rapid Prototyping of Soft Lithography Masters for Microfluidic Devices Using Dry Film Photoresist in a Non-Cleanroom Setting

(2019) Prithviraj Mukherjee et al.   Micromachines

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Sall4 regulates neuromesodermal progenitors and their descendants during body elongation in mouse embryos

(2019) Naoyuki Tahara et al.   DEVELOPMENT

Controlled modelling of human epiblast and amnion development using stem cells

(2019) Yi Zheng et al.   NATURE

ilastik: interactive machine learning for (bio)image analysis

(2019) Stuart Berg et al.   NATURE METHODS

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

(2018) Xiao Wang et al.   SCIENCE

Lineage tracing axial progenitors using Nkx1-2CreERT2 mice defines their trunk and tail contributions

(2018) Aida Rodrigo Albors et al.   DEVELOPMENT

A fluid-to-solid jamming transition underlies vertebrate body axis elongation

(2018) Alessandro Mongera et al.   NATURE

Temporal changes of Sall4 lineage contribution in developing embryos and the contribution of Sall4-lineages to postnatal germ cells in mice

(2018) Naoyuki Tahara et al.   Scientific Reports

Biomechanical coupling facilitates spinal neural tube closure in mouse embryos

(2017) Gabriel L. Galea 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

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

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

(2016) Shilu Amin et al.   Cell Reports

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

(2016) Filip J Wymeersch et al.   eLife

Neuromesodermal progenitors and the making of the spinal cord

(2015) D. Henrique et al.   DEVELOPMENT

Wnt8aandWnt3acooperate in the axial stem cell niche to promote mammalian body axis extension

(2015) Thomas J. Cunningham et al.   DEVELOPMENTAL DYNAMICS

Distinct Wnt-driven primitive streak-like populations reflect in vivo lineage precursors

(2014) A. Tsakiridis et al.   DEVELOPMENT

Wnt and FGF mediated epithelial-mesenchymal crosstalk during lung development

(2014) Thomas Volckaert et al.   DEVELOPMENTAL DYNAMICS

Generation of mouse models of myeloid malignancy with combinatorial genetic lesions using CRISPR-Cas9 genome editing

(2014) Dirk Heckl et al.   NATURE BIOTECHNOLOGY

Transcriptional Profiling of Wnt3a Mutants Identifies Sp Transcription Factors as Essential Effectors of the Wnt/β-catenin Pathway in Neuromesodermal Stem Cells

(2014) William C. Dunty et al.   PLoS One

Clustering by fast search and find of density peaks

(2014) A. Rodriguez et al.   SCIENCE

Characterization of a novel transgenic mouse line expressing Cre recombinase under the control of theCdx2neural specific enhancer

(2013) Baptiste Coutaud et al.   GENESIS

TCreERT2, a Transgenic Mouse Line for Temporal Control of Cre-Mediated Recombination in Lineages Emerging from the Primitive Streak or Tail Bud

(2013) Matthew J. Anderson et al.   PLoS One

Evolutionarily conserved requirement of Cdx for post-occipital tissue emergence

(2012) C. van Rooijen et al.   DEVELOPMENT

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

Birth defects associated with perturbations in preimplantation, gastrulation, and axis extension: from conjoined twinning to caudal dysgenesis

(2012) Anna Ferrer-Vaquer et al.   Wiley Interdisciplinary Reviews-Developmental Biology

Concerted involvement of Cdx / Hox genes and Wnt signaling in morphogenesis of the caudal neural tube and cloacal derivatives from the posterior growth zone

(2011) Cesca van de Ven et al.   DEVELOPMENT

A small molecule inhibitor of the Wnt antagonist secreted frizzled-related protein-1 stimulates bone formation

(2009) Peter V.N. Bodine et al.   BONE

Cdx2 regulation of posterior development through non-Hox targets

(2009) J. G. A. Savory et al.   DEVELOPMENT

Stem cells, signals and vertebrate body axis extension

(2009) V. Wilson et al.   DEVELOPMENT

Cdx and Hox Genes Differentially Regulate Posterior Axial Growth in Mammalian Embryos

(2009) Teddy Young et al.   DEVELOPMENTAL CELL

Wnt5a Knock-out Mouse as a New Model of Anorectal Malformation

(2009) Cindy C. Tai et al.   JOURNAL OF SURGICAL RESEARCH

Small molecule–mediated disruption of Wnt-dependent signaling in tissue regeneration and cancer

(2009) Baozhi Chen et al.   Nature Chemical Biology

Vertebrate limb bud development: moving towards integrative analysis of organogenesis

(2009) Rolf Zeller et al.   NATURE REVIEWS GENETICS

Regulation of Canonical Wnt Signaling by Brachyury Is Essential for Posterior Mesoderm Formation

(2008) Benjamin L. Martin et al.   DEVELOPMENTAL CELL