Opening the black box: Stem cell–based modeling of human post-implantation development

Spatial transcriptomic survey of human embryonic cerebral cortex by single-cell RNA-seq analysis

(2018) Xiaoying Fan et al.   CELL RESEARCH

Amniotic ectoderm expansion in mouse occurs via distinct modes and requires SMAD5-mediated signalling

(2018) Mariya P. Dobreva et al.   DEVELOPMENT

Pluripotency Deconstructed

(2018) Masaki Kinoshita et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex

(2018) Suijuan Zhong et al.   NATURE

Tracing the temporal-spatial transcriptome landscapes of the human fetal digestive tract using single-cell RNA-sequencing

(2018) Shuai Gao et al.   NATURE CELL BIOLOGY

Single-cell multi-omics sequencing of human early embryos

(2018) Lin Li 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

Deconstructing and reconstructing the mouse and human early embryo

(2018) Marta N. Shahbazi et al.   NATURE CELL BIOLOGY

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

(2018) Sarah Ellys Harrison et al.   Nature Protocols

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

(2018) Sophie M Morgani et al.   eLife

Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney

(2018) Rajasree Menon et al.   DEVELOPMENT

Self-organization of a human organizer by combined Wnt and Nodal signalling

(2018) I. Martyn et al.   NATURE

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Self-Renewing Trophoblast Organoids Recapitulate the Developmental Program of the Early Human Placenta

(2018) Sandra Haider et al.   Stem Cell Reports

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

(2018) Leonardo Beccari et al.   NATURE

An apicosome initiates self-organizing morphogenesis of human pluripotent stem cells

(2017) Kenichiro Taniguchi et al.   JOURNAL OF CELL BIOLOGY

Pluripotent state transitions coordinate morphogenesis in mouse and human embryos

(2017) Marta N. Shahbazi et al.   NATURE

Revisiting the Warnock rule

(2017) J Benjamin Hurlbut et al.   NATURE BIOTECHNOLOGY

Single-cell DNA methylome sequencing of human preimplantation embryos

(2017) Ping Zhu et al.   NATURE GENETICS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Assembly of embryonic and extraembryonic stem cells to mimic embryogenesis in vitro

(2017) Sarah Ellys Harrison et al.   SCIENCE

A pluripotent stem cell-based model for post-implantation human amniotic sac development

(2017) Yue Shao et al.   Nature Communications

Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation

(2017) Hisham Mohammed et al.   Cell Reports

Gene-free methodology for cell fate dynamics during development

(2017) Francis Corson et al.   eLife

Single-cell transcriptome of early embryos and cultured embryonic stem cells of cynomolgus monkeys

(2017) Tomonori Nakamura et al.   Scientific Data

Engineering Customized Cell Sensing and Response Behaviors Using Synthetic Notch Receptors

(2016) Leonardo Morsut et al.   CELL

A Balance between Secreted Inhibitors and Edge Sensing Controls Gastruloid Self-Organization

(2016) Fred Etoc et al.   DEVELOPMENTAL CELL

The Germ Cell Fate of Cynomolgus Monkeys Is Specified in the Nascent Amnion

(2016) Kotaro Sasaki et al.   DEVELOPMENTAL CELL

Regulation of podocalyxin trafficking by Rab small GTPases in 2D and 3D epithelial cell cultures

(2016) Paulina S. Mrozowska et al.   JOURNAL OF CELL BIOLOGY

Embryology policy: Revisit the 14-day rule

(2016) Insoo Hyun et al.   NATURE

Self-organization of the in vitro attached human embryo

(2016) Alessia Deglincerti et al.   NATURE

Resolving early mesoderm diversification through single-cell expression profiling

(2016) Antonio Scialdone et al.   NATURE

Self-organization of the human embryo in the absence of maternal tissues

(2016) Marta N. Shahbazi et al.   NATURE CELL BIOLOGY

Self-organized amniogenesis by human pluripotent stem cells in a biomimetic implantation-like niche

(2016) Yue Shao et al.   NATURE MATERIALS

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Cingulin and actin mediate midbody-dependent apical lumen formation during polarization of epithelial cells

(2016) Anthony J. Mangan et al.   Nature Communications

Rab35 GTPase couples cell division with initiation of epithelial apico-basal polarity and lumen opening

(2016) Kerstin Klinkert et al.   Nature Communications

Setting Global Standards for Stem Cell Research and Clinical Translation: The 2016 ISSCR Guidelines

(2016) George Q. Daley et al.   Stem Cell Reports

The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells

(2015) Fan Guo et al.   CELL

Defining the three cell lineages of the human blastocyst by single-cell RNA-seq

(2015) P. Blakeley et al.   DEVELOPMENT

Cell signaling and transcription factors regulating cell fate during formation of the mouse blastocyst

(2015) Tristan Frum et al.   TRENDS IN GENETICS

A method for human teratogen detection by geometrically confined cell differentiation and migration

(2015) Jiangwa Xing et al.   Scientific Reports

Edges of human embryonic stem cell colonies display distinct mechanical properties and differentiation potential

(2015) Kathryn A. Rosowski et al.   Scientific Reports

DNA Methylation Landscapes of Human Fetal Development

(2015) Roderick C. Slieker et al.   PLoS Genetics

KeyGenes, a Tool to Probe Tissue Differentiation Using a Human Fetal Transcriptional Atlas

(2015) Matthias S. Roost et al.   Stem Cell Reports

Lumen Formation Is an Intrinsic Property of Isolated Human Pluripotent Stem Cells

(2015) Kenichiro Taniguchi et al.   Stem Cell Reports

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

(2014) Ivan Bedzhov 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

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

A method to recapitulate early embryonic spatial patterning in human embryonic stem cells

(2014) Aryeh Warmflash et al.   NATURE METHODS

Organization and execution of the epithelial polarity programme

(2014) Enrique Rodriguez-Boulan et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Dose-dependent Nodal/Smad signals pattern the early mouse embryo

(2014) Elizabeth J. Robertson   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Derivation of human embryonic stem cells using a post–inner cell mass intermediate

(2013) Thomas O'Leary et al.   Nature Protocols

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Tracking the progression of the human inner cell mass during embryonic stem cell derivation

(2012) Thomas O'Leary et al.   NATURE BIOTECHNOLOGY

Boolean modeling in systems biology: an overview of methodology and applications

(2012) Rui-Sheng Wang et al.   PHYSICAL BIOLOGY

Amnion formation in the mouse embryo: the single amniochorionic fold model

(2011) Paulo NG Pereira et al.   BMC DEVELOPMENTAL BIOLOGY

Morphogenesis in sea urchin embryos: linking cellular events to gene regulatory network states

(2011) Deirdre C. Lyons et al.   Wiley Interdisciplinary Reviews-Developmental Biology

A molecular network for de novo generation of the apical surface and lumen

(2010) David M. Bryant et al.   NATURE CELL BIOLOGY

Control of Stem Cell Fate by Physical Interactions with the Extracellular Matrix

(2009) Farshid Guilak et al.   Cell Stem Cell

Trafficking of Crumbs3 during Cytokinesis Is Crucial for Lumen Formation

(2009) Marc A. Schlüter et al.   MOLECULAR BIOLOGY OF THE CELL

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