Pluripotent stem cells as a model for embryonic patterning: From signaling dynamics to spatial organization in a dish

Myc Depletion Induces a Pluripotent Dormant State Mimicking Diapause

(2016) Roberta Scognamiglio et al.   CELL

Precision Tumor Recognition by T Cells With Combinatorial Antigen-Sensing Circuits

(2016) Kole T. Roybal et al.   CELL

Engineering Customized Cell Sensing and Response Behaviors Using Synthetic Notch Receptors

(2016) Leonardo Morsut et al.   CELL

Visualization of a short-range Wnt gradient in the intestinal stem-cell niche

(2016) Henner F. Farin et al.   NATURE

Self-organization of the in vitro attached human embryo

(2016) Alessia Deglincerti et al.   NATURE

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

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

Nac1 Coordinates a Sub-network of Pluripotency Factors to Regulate Embryonic Stem Cell Differentiation

(2016) Mohan Malleshaiah et al.   Cell Reports

Naive Pluripotent Stem Cells Derived Directly from Isolated Cells of the Human Inner Cell Mass

(2016) Ge Guo et al.   Stem Cell Reports

Organoids and the genetically encoded self-assembly of embryonic stem cells

(2015) David A. Turner et al.   BIOESSAYS

Development of the anterior-posterior axis is a self-organizing process in the absence of maternal cues in the mouse embryo

(2015) Ivan Bedzhov et al.   CELL RESEARCH

Stem Cell Therapies in Clinical Trials: Progress and Challenges

(2015) Alan Trounson et al.   Cell Stem Cell

Positional information and reaction-diffusion: two big ideas in developmental biology combine

(2015) J. B. A. Green et al.   DEVELOPMENT

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

(2015) P. Blakeley et al.   DEVELOPMENT

A Temporal Window for Signal Activation Dictates the Dimensions of a Nodal Signaling Domain

(2015) Antonius L. van Boxtel et al.   DEVELOPMENTAL CELL

An in vitro gastrulation model recapitulates the morphogenetic impact of pharmacological inhibitors of developmental signaling pathways

(2015) Aileen S. W. Li et al.   MOLECULAR REPRODUCTION AND DEVELOPMENT

Dpp spreading is required for medial but not for lateral wing disc growth

(2015) Stefan Harmansa et al.   NATURE

A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs

(2015) Jiho Choi et al.   NATURE BIOTECHNOLOGY

What if stem cells turn into embryos in a dish?

(2015) Martin F Pera et al.   NATURE METHODS

BMP gradients: A paradigm for morphogen-mediated developmental patterning

(2015) E. Bier et al.   SCIENCE

Emergent genetic oscillations in a synthetic microbial consortium

(2015) Y. Chen et al.   SCIENCE

Induced Pluripotency and Epigenetic Reprogramming

(2015) Konrad Hochedlinger et al.   Cold Spring Harbor Perspectives in Biology

Self-organizing human cardiac microchambers mediated by geometric confinement

(2015) Zhen Ma et al.   Nature Communications

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

(2015) Jiangwa Xing et al.   Scientific Reports

Cell-Cycle Control of Bivalent Epigenetic Domains Regulates the Exit from Pluripotency

(2015) Amar M. Singh et al.   Stem Cell Reports

“Mesenchymal” Stem Cells

(2014) Paolo Bianco   Annual Review of Cell and Developmental Biology

Generation of Functional Human Pancreatic β Cells In Vitro

(2014) Felicia W. Pagliuca et al.   CELL

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

(2014) Ivan Bedzhov et al.   CELL

Resetting Transcription Factor Control Circuitry toward Ground-State Pluripotency in Human

(2014) Yasuhiro Takashima et al.   CELL

NANOG and CDX2 Pattern Distinct Subtypes of Human Mesoderm during Exit from Pluripotency

(2014) Sasha Mendjan et al.   Cell Stem Cell

Systematic Identification of Culture Conditions for Induction and Maintenance of Naive Human Pluripotency

(2014) Thorold W. Theunissen et al.   Cell Stem Cell

An iCRISPR Platform for Rapid, Multiplexable, and Inducible Genome Editing in Human Pluripotent Stem Cells

(2014) Federico González et al.   Cell Stem Cell

Mouse and human blastocyst-derived stem cells: vive les differences

(2014) J. Rossant   DEVELOPMENT

Transcription factor heterogeneity in pluripotent stem cells: a stochastic advantage

(2014) M.-E. Torres-Padilla et al.   DEVELOPMENT

Bioengineering approaches to guide stem cell-based organogenesis

(2014) Nikolche Gjorevski et al.   DEVELOPMENT

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

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

Encoding of Temporal Signals by the TGF-β Pathway and Implications for Embryonic Patterning

(2014) Benoit Sorre et al.   DEVELOPMENTAL CELL

BMP4 regulation of human trophoblast development

(2014) Yingchun Li et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Dynamic Heterogeneity and DNA Methylation in Embryonic Stem Cells

(2014) Zakary S. Singer et al.   MOLECULAR CELL

Reversal of diabetes with insulin-producing cells derived in vitro from human pluripotent stem cells

(2014) Alireza Rezania et al.   NATURE BIOTECHNOLOGY

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

(2014) Aryeh Warmflash et al.   NATURE METHODS

Generation of organized germ layers from a single mouse embryonic stem cell

(2014) Yeh-Chuin Poh et al.   Nature Communications

Single-Cell Gene Expression Profiles Define Self-Renewing, Pluripotent, and Lineage Primed States of Human Pluripotent Stem Cells

(2014) Shelley R. Hough et al.   Stem Cell Reports

3D Reconstitution of the Patterned Neural Tube from Embryonic Stem Cells

(2014) Andrea Meinhardt et al.   Stem Cell Reports

The Cell-Cycle State of Stem Cells Determines Cell Fate Propensity

(2013) Siim Pauklin et al.   CELL

Specified Neural Progenitors Sort to Form Sharp Domains after Noisy Shh Signaling

(2013) Fengzhu Xiong et al.   CELL

Induction of Pluripotency in Mouse Somatic Cells with Lineage Specifiers

(2013) Jian Shu et al.   CELL

Morphogen interpretation: the transcriptional logic of neural tube patterning

(2013) Michael Cohen et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Porcn-dependent Wnt signaling is not required prior to mouse gastrulation

(2013) S. Biechele et al.   DEVELOPMENT

BMP4-directed trophoblast differentiation of human embryonic stem cells is mediated through a ΔNp63 + cytotrophoblast stem cell state

(2013) Yingchun Li et al.   DEVELOPMENT

Morphogen transport

(2013) P. Muller et al.   DEVELOPMENT

The T-box transcription factor Eomesodermin is essential for AVE induction in the mouse embryo

(2013) S. Nowotschin et al.   GENES & DEVELOPMENT

Specialized filopodia direct long-range transport of SHH during vertebrate tissue patterning

(2013) Timothy A. Sanders et al.   NATURE

Derivation of novel human ground state naive pluripotent stem cells

(2013) Ohad Gafni et al.   NATURE

Cerebral organoids model human brain development and microcephaly

(2013) Madeline A. Lancaster et al.   NATURE

ECM-Dependent HIF Induction Directs Trophoblast Stem Cell Fate via LIMK1-Mediated Cytoskeletal Rearrangement

(2013) Hwa J. Choi et al.   PLoS One

Growing Self-Organizing Mini-Guts from a Single Intestinal Stem Cell: Mechanism and Applications

(2013) T. Sato et al.   SCIENCE

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Cell-Cycle Control of Developmentally Regulated Transcription Factors Accounts for Heterogeneity in Human Pluripotent Cells

(2013) Amar M. Singh et al.   Stem Cell Reports

Probing Embryonic Stem Cell Autocrine and Paracrine Signaling Using Microfluidics

(2012) Laralynne Przybyla et al.   Annual Review of Analytical Chemistry

Gene Regulatory Logic for Reading the Sonic Hedgehog Signaling Gradient in the Vertebrate Neural Tube

(2012) Nikolaos Balaskas et al.   CELL

Signaling Network Crosstalk in Human Pluripotent Cells: A Smad2/3-Regulated Switch that Controls the Balance between Self-Renewal and Differentiation

(2012) Amar M. Singh et al.   Cell Stem Cell

Distinct Lineage Specification Roles for NANOG, OCT4, and SOX2 in Human Embryonic Stem Cells

(2012) Zheng Wang et al.   Cell Stem Cell

Self-Formation of Optic Cups and Storable Stratified Neural Retina from Human ESCs

(2012) Tokushige Nakano et al.   Cell Stem Cell

Analysis of human embryos from zygote to blastocyst reveals distinct gene expression patterns relative to the mouse

(2012) Kathy K. Niakan et al.   DEVELOPMENTAL BIOLOGY

The promise of induced pluripotent stem cells in research and therapy

(2012) Daisy A. Robinton et al.   NATURE

Dynamics of TGF-  signaling reveal adaptive and pulsatile behaviors reflected in the nuclear localization of transcription factor Smad4

(2012) A. Warmflash et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predictive microfluidic control of regulatory ligand trajectories in individual pluripotent cells

(2012) F. Moledina et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Geometry, epistasis, and developmental patterning

(2012) F. Corson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential Diffusivity of Nodal and Lefty Underlies a Reaction-Diffusion Patterning System

(2012) P. Muller et al.   SCIENCE

FGF Inhibition Directs BMP4-Mediated Differentiation of Human Embryonic Stem Cells to Syncytiotrophoblast

(2012) Smita Sudheer et al.   STEM CELLS AND DEVELOPMENT

The molecular circuitry underlying pluripotency in embryonic stem cells

(2012) Aryeh Warmflash et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Dynamics of anterior–posterior axis formation in the developing mouse embryo

(2012) Samantha A. Morris et al.   Nature Communications

Transport of Fibroblast Growth Factor 2 in the Pericellular Matrix Is Controlled by the Spatial Distribution of Its Binding Sites in Heparan Sulfate

(2012) Laurence Duchesne et al.   PLOS BIOLOGY

A sensitive and bright single-cell resolution live imaging reporter of Wnt/ß-catenin signaling in the mouse

(2011) Anna Ferrer-Vaquer et al.   BMC DEVELOPMENTAL BIOLOGY

Pluripotency Factors in Embryonic Stem Cells Regulate Differentiation into Germ Layers

(2011) Matt Thomson et al.   CELL

BRACHYURY and CDX2 Mediate BMP-Induced Differentiation of Human and Mouse Pluripotent Stem Cells into Embryonic and Extraembryonic Lineages

(2011) Andreia S. Bernardo et al.   Cell Stem Cell

FGF2 Sustains NANOG and Switches the Outcome of BMP4-Induced Human Embryonic Stem Cell Differentiation

(2011) Pengzhi Yu et al.   Cell Stem Cell

A Precarious Balance: Pluripotency Factors as Lineage Specifiers

(2011) Kyle M. Loh et al.   Cell Stem Cell

Anterior Visceral Endoderm Directs Ventral Morphogenesis and Placement of Head and Heart via BMP2 Expression

(2011) Mary Madabhushi et al.   DEVELOPMENTAL CELL

The microenvironment patterns the pluripotent mouse epiblast through paracrine Furin and Pace4 proteolytic activities

(2011) D. Mesnard et al.   GENES & DEVELOPMENT

Pluripotency factors regulate definitive endoderm specification through eomesodermin

(2011) A. K. K. Teo et al.   GENES & DEVELOPMENT

Spatially organized in vitro models instruct asymmetric stem cell differentiation

(2011) Yi-Chin Toh et al.   Integrative Biology

Self-organizing optic-cup morphogenesis in three-dimensional culture

(2011) Mototsugu Eiraku et al.   NATURE

Embryonic stem cells require Wnt proteins to prevent differentiation to epiblast stem cells

(2011) Derk ten Berge et al.   NATURE CELL BIOLOGY

Dynamics of Dpp Signaling and Proliferation Control

(2011) O. Wartlick et al.   SCIENCE

Development and cancer of the cerebellum

(2011) Mary E. Hatten et al.   TRENDS IN NEUROSCIENCES

Pluripotency and Cellular Reprogramming: Facts, Hypotheses, Unresolved Issues

(2010) Jacob H. Hanna et al.   CELL

Tracing the Derivation of Embryonic Stem Cells from the Inner Cell Mass by Single-Cell RNA-Seq Analysis

(2010) Fuchou Tang et al.   Cell Stem Cell

Oxygen in Stem Cell Biology: A Critical Component of the Stem Cell Niche

(2010) Ahmed Mohyeldin et al.   Cell Stem Cell

On the origin of amniotic stem cells: of mice and men

(2010) Mariya P. Dobreva et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Physiological levels of TNF  stimulation induce stochastic dynamics of NF- B responses in single living cells

(2010) D. A. Turner et al.   JOURNAL OF CELL SCIENCE

Variability in gene expression underlies incomplete penetrance

(2010) Arjun Raj et al.   NATURE

Single-cell NF-κB dynamics reveal digital activation and analogue information processing

(2010) Savaş Tay et al.   NATURE

Rac1-Dependent Collective Cell Migration Is Required for Specification of the Anterior-Posterior Body Axis of the Mouse

(2010) Isabelle Migeotte et al.   PLOS BIOLOGY

Aggregated P19 mouse embryonal carcinoma cells as a simple in vitro model to study the molecular regulations of mesoderm formation and axial elongation morphogenesis

(2009) Yusuke Marikawa et al.   GENESIS

Generation of functional hepatocytes from human embryonic stem cells under chemically defined conditions that recapitulate liver development

(2009) Thomas Touboul et al.   HEPATOLOGY

Simple and rapid process for single cell micro-patterning

(2009) Ammar Azioune et al.   LAB ON A CHIP

Fgf8 morphogen gradient forms by a source-sink mechanism with freely diffusing molecules

(2009) Shuizi Rachel Yu et al.   NATURE

Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling

(2009) Stuart M Chambers et al.   NATURE BIOTECHNOLOGY

Material properties of the cell dictate stress-induced spreading and differentiation in embryonic stem cells

(2009) Farhan Chowdhury et al.   NATURE MATERIALS

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

Visualisation and Quantification of Morphogen Gradient Formation in the Zebrafish

(2009) Steven A Harvey et al.   PLOS BIOLOGY

Wnt Signaling Mediates Self-Organization and Axis Formation in Embryoid Bodies

(2008) Derk ten Berge et al.   Cell Stem Cell

The Endoderm of the Mouse Embryo Arises by Dynamic Widespread Intercalation of Embryonic and Extraembryonic Lineages

(2008) Gloria S. Kwon et al.   DEVELOPMENTAL CELL

Real time monitoring of BMP Smads transcriptional activity during mouse development

(2008) Rui M. Monteiro et al.   GENESIS

The ground state of embryonic stem cell self-renewal

(2008) Qi-Long Ying et al.   NATURE

Micropatterning of human embryonic stem cells dissects the mesoderm and endoderm lineages

(2008) Lawrence Haoran Lee et al.   Stem Cell Research

Biomolecular gradients in cell culture systems

(2007) Thomas M. Keenan et al.   LAB ON A CHIP