Inducible Stem-Cell-Derived Embryos Capture Mouse Morphogenetic Events In Vitro

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Basement membrane remodelling regulates mouse embryogenesis

(2020) Christos Kyprianou et al.   NATURE

Implantation initiation of self-assembled embryo-like structures generated using three types of mouse blastocyst-derived stem cells

(2019) Shaopeng Zhang et al.   Nature Communications

A single-cell molecular map of mouse gastrulation and early organogenesis

(2019) Blanca Pijuan-Sala et al.   NATURE

Distinct mesoderm migration phenotypes in extra-embryonic and embryonic regions of the early mouse embryo

(2019) Bechara Saykali et al.   eLife

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

Engineering Stem Cell Self-organization to Build Better Organoids

(2019) Jonathan A. Brassard et al.   Cell Stem Cell

The endoderm: a divergent cell lineage with many commonalities

(2019) Sonja Nowotschin et al.   DEVELOPMENT

N-cadherin stabilises neural identity by dampening anti-neural signals

(2019) Karolina Punovuori et al.   DEVELOPMENT

Morphogenesis of extra-embryonic tissues directs the remodelling of the mouse embryo at implantation

(2019) Neophytos Christodoulou et al.   Nature Communications

Self-Organization of Mouse Stem Cells into an Extended Potential Blastoid

(2019) Berna Sozen et al.   DEVELOPMENTAL CELL

Eomes and Brachyury control pluripotency exit and germ-layer segregation by changing the chromatin state

(2019) Jelena Tosic et al.   NATURE CELL BIOLOGY

Self-assembly of embryonic and two extra-embryonic stem cell types into gastrulating embryo-like structures

(2018) Berna Sozen et al.   NATURE CELL BIOLOGY

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

(2018) James A. Briggs et al.   SCIENCE

Micropattern differentiation of mouse pluripotent stem cells recapitulates embryo regionalized cell fate patterning

(2018) Sophie M Morgani et al.   eLife

zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs

(2018) Swati Parekh et al.   GigaScience

Mouse ICM Organoids Reveal Three-Dimensional Cell Fate Clustering

(2018) Biena Mathew et al.   BIOPHYSICAL JOURNAL

Sequential formation and resolution of multiple rosettes drive embryo remodelling after implantation

(2018) Neophytos Christodoulou et al.   NATURE CELL BIOLOGY

Pluripotent state transitions coordinate morphogenesis in mouse and human embryos

(2017) Marta N. Shahbazi et al.   NATURE

Both Nodal signalling and stochasticity select for prospective distal visceral endoderm in mouse embryos

(2017) Katsuyoshi Takaoka et al.   Nature Communications

Lineage Reprogramming of Fibroblasts into Proliferative Induced Cardiac Progenitor Cells by Defined Factors

(2016) Pratik A. Lalit et al.   Cell Stem Cell

Crumbs2 promotes cell ingression during the epithelial-to-mesenchymal transition at gastrulation

(2016) Nitya Ramkumar et al.   NATURE CELL BIOLOGY

Single-cell barcoding and sequencing using droplet microfluidics

(2016) Rapolas Zilionis et al.   Nature Protocols

Tissue morphodynamics shaping the early mouse embryo

(2016) Ann E. Sutherland   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

FGF/MAPK signaling sets the switching threshold of a bistable circuit controlling cell fate decisions in embryonic stem cells

(2015) C. Schro ter et al.   DEVELOPMENT

AVE protein expression and visceral endoderm cell behavior during anterior–posterior axis formation in mouse embryos: Asymmetry in OTX2 and DKK1 expression

(2015) Hideharu Hoshino et al.   DEVELOPMENTAL BIOLOGY

Distinct EMT programs control normal mammary stem cells and tumour-initiating cells

(2015) Xin Ye et al.   NATURE

Self-Organizing Properties of Mouse Pluripotent Cells Initiate Morphogenesis upon Implantation

(2014) Ivan Bedzhov et al.   CELL

β-Pix directs collective migration of anterior visceral endoderm cells in the early mouse embryo

(2014) Tatiana Omelchenko et al.   GENES & DEVELOPMENT

The ability of inner-cell-mass cells to self-renew as embryonic stem cells is acquired following epiblast specification

(2014) Thorsten Boroviak et al.   NATURE CELL BIOLOGY

In vitro culture of mouse blastocysts beyond the implantation stages

(2014) Ivan Bedzhov et al.   Nature Protocols

Circulation-Independent Differentiation Pathway from Extraembryonic Mesoderm toward Hematopoietic Stem Cells via Hemogenic Angioblasts

(2014) Yosuke Tanaka et al.   Cell Reports

Extraembryonic Endoderm cells as a model of endoderm development

(2013) Asja T. Moerkamp et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

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

(2012) Johannes Schindelin et al.   NATURE METHODS

BMP signaling induces visceral endoderm differentiation of XEN cells and parietal endoderm

(2011) Agnieszka Paca et al.   DEVELOPMENTAL BIOLOGY

Bone morphogenetic protein 4 signaling regulates development of the anterior visceral endoderm in the mouse embryo

(2010) Miguel L. Soares et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Patch-Based Nonlocal Functional for Denoising Fluorescence Microscopy Image Sequences

(2009) J. Boulanger et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Making a commitment: cell lineage allocation and axis patterning in the early mouse embryo

(2009) Sebastian J. Arnold et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH