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Charting the emergent organotypic landscape of the mammalian gut endoderm at single-cell resolution

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/dvdy.20843openalex-snapshot

Tg(Afp‐GFP) expression marks primitive and definitive endoderm lineages during mouse development

inferredcites →https://doi.org/10.1002/dvdy.21810openalex-snapshot

Transcriptional dynamics of endodermal organ formation

inferredcites →https://doi.org/10.1002/dvg.20695openalex-snapshot

Afp::mCherry, a red fluorescent transgenic reporter of the mouse visceral endoderm

inferredcites →https://doi.org/10.1002/wdev.319openalex-snapshot

Making lineage decisions with biological noise: Lessons from the early mouse embryo

inferredcites →https://doi.org/10.1016/0378-1119(94)90450-2openalex-snapshot

Sequence and expression of murine cDNAs encoding Xlr3a and Xlr3b, defining a new X-linked lymphocyte-regulated Xlr gene subfamily

inferredcites →https://doi.org/10.1016/b978-0-12-381280-3.00001-4openalex-snapshot

Formation of the Murine Endoderm

inferredcites →https://doi.org/10.1016/bs.ctdb.2017.11.003openalex-snapshot

The Head's Tale: Anterior-Posterior Axis Formation in the Mouse Embryo

inferredcites →https://doi.org/10.1016/j.cell.2009.07.039openalex-snapshot

Nanog Is the Gateway to the Pluripotent Ground State

inferredcites →https://doi.org/10.1016/j.cell.2014.04.005openalex-snapshot

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

inferredcites →https://doi.org/10.1016/j.cell.2015.05.047openalex-snapshot

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

inferredcites →https://doi.org/10.1016/j.cell.2018.05.060openalex-snapshot

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

inferredcites →https://doi.org/10.1016/j.cell.2018.05.061openalex-snapshot

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

inferredcites →https://doi.org/10.1016/j.celrep.2017.07.009openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.cub.2005.11.071openalex-snapshot

Comparison of Gene Expression in Male and Female Mouse Blastocysts Revealed Imprinting of the X-Linked Gene, Rhox5/Pem, at Preimplantation Stages

inferredcites →https://doi.org/10.1016/j.devcel.2006.02.020openalex-snapshot

Early Lineage Segregation between Epiblast and Primitive Endoderm in Mouse Blastocysts through the Grb2-MAPK Pathway

inferredcites →https://doi.org/10.1016/j.devcel.2008.07.017openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.devcel.2011.10.019openalex-snapshot

Primitive Endoderm Differentiates via a Three-Step Mechanism Involving Nanog and RTK Signaling

inferredcites →https://doi.org/10.1016/j.devcel.2013.06.012openalex-snapshot

Competitive Interactions Eliminate Unfit Embryonic Stem Cells at the Onset of Differentiation

inferredcites →https://doi.org/10.1016/j.devcel.2013.09.026openalex-snapshot

External Mechanical Cues Trigger the Establishment of the Anterior-Posterior Axis in Early Mouse Embryos

inferredcites →https://doi.org/10.1016/j.devcel.2014.04.011openalex-snapshot

GATA6 Levels Modulate Primitive Endoderm Cell Fate Choice and Timing in the Mouse Blastocyst

inferredcites →https://doi.org/10.1016/j.devcel.2017.05.003openalex-snapshot

Lineage Establishment and Progression within the Inner Cell Mass of the Mouse Blastocyst Requires FGFR1 and FGFR2

inferredcites →https://doi.org/10.1016/j.devcel.2017.05.004openalex-snapshot

Distinct Requirements for FGFR1 and FGFR2 in Primitive Endoderm Development and Exit from Pluripotency

inferredcites →https://doi.org/10.1016/j.devcel.2017.08.011openalex-snapshot

Pluripotency Surveillance by Myc-Driven Competitive Elimination of Differentiating Cells

inferredcites →https://doi.org/10.1016/j.gde.2010.05.008openalex-snapshot

Cellular dynamics in the early mouse embryo: from axis formation to gastrulation

inferredcites →https://doi.org/10.1016/j.mod.2013.08.002openalex-snapshot

Stage specific reprogramming of mouse embryo liver cells to a beta cell-like phenotype

inferredcites →https://doi.org/10.1016/j.ydbio.2010.04.020openalex-snapshot

Nanog is required for primitive endoderm formation through a non-cell autonomous mechanism

inferredcites →https://doi.org/10.1016/j.ydbio.2010.12.007openalex-snapshot

The primitive endoderm lineage of the mouse blastocyst: Sequential transcription factor activation and regulation of differentiation by Sox17

inferredcites →https://doi.org/10.1016/j.ydbio.2011.10.013openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.ydbio.2011.10.015openalex-snapshot

BMP4 signaling directs primitive endoderm-derived XEN cells to an extraembryonic visceral endoderm identity

inferredcites →https://doi.org/10.1016/j.ydbio.2013.09.023openalex-snapshot

FGF4 is a limiting factor controlling the proportions of primitive endoderm and epiblast in the ICM of the mouse blastocyst

inferredcites →https://doi.org/10.1016/j.ydbio.2018.06.017openalex-snapshot

A Sprouty4 reporter to monitor FGF/ERK signaling activity in ESCs and mice

inferredcites →https://doi.org/10.1016/s0074-7696(06)59002-3openalex-snapshot

Molecular Basis of Vertebrate Endoderm Development

inferredcites →https://doi.org/10.1016/s0092-8674(03)00393-3openalex-snapshot

The Homeoprotein Nanog Is Required for Maintenance of Pluripotency in Mouse Epiblast and ES Cells

inferredcites →https://doi.org/10.1016/s0925-4773(01)00412-9openalex-snapshot

Irx1 and Irx2 expression in early lung development

inferredcites →https://doi.org/10.1016/s0925-4773(97)00125-1openalex-snapshot

Cerberus-like is a secreted factor with neuralizing activity expressed in the anterior primitive endoderm of the mouse gastrula

inferredcites →https://doi.org/10.1016/s1097-2765(00)80331-7openalex-snapshot

Mouse Lefty2 and Zebrafish Antivin Are Feedback Inhibitors of Nodal Signaling during Vertebrate Gastrulation

inferredcites →https://doi.org/10.1038/35082103openalex-snapshot

Nodal signalling in the epiblast patterns the early mouse embryo

inferredcites →https://doi.org/10.1038/nature12389openalex-snapshot

Myc-driven endogenous cell competition in the early mammalian embryo

inferredcites →https://doi.org/10.1038/nature24489openalex-snapshot

A single-cell survey of the small intestinal epithelium

inferredcites →https://doi.org/10.1038/nature25999openalex-snapshot

Developmental diversification of cortical inhibitory interneurons

inferredcites →https://doi.org/10.1038/nbt.2594openalex-snapshot

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

inferredcites →https://doi.org/10.1038/nbt.3569openalex-snapshot

Wishbone identifies bifurcating developmental trajectories from single-cell data

inferredcites →https://doi.org/10.1038/nbt.4091openalex-snapshot

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

inferredcites →https://doi.org/10.1038/ncb2251openalex-snapshot

Origin and role of distal visceral endoderm, a group of cells that determines anterior–posterior polarity of the mouse embryo

inferredcites →https://doi.org/10.1038/ncb2881openalex-snapshot

Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages

inferredcites →https://doi.org/10.1038/ncb3070openalex-snapshot

SOX17 links gut endoderm morphogenesis and germ layer segregation

inferredcites →https://doi.org/10.1038/ncomms13463openalex-snapshot

Asynchronous fate decisions by single cells collectively ensure consistent lineage composition in the mouse blastocyst

inferredcites →https://doi.org/10.1038/nmeth.3971openalex-snapshot

Diffusion pseudotime robustly reconstructs lineage branching

inferredcites →https://doi.org/10.1038/nrm2618openalex-snapshot

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

inferredcites →https://doi.org/10.1038/s41467-018-04167-yopenalex-snapshot

P53 and mTOR signalling determine fitness selection through cell competition during early mouse embryonic development

inferredcites →https://doi.org/10.1038/s41556-017-0013-zopenalex-snapshot

Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation

inferredcites →https://doi.org/10.1038/s41587-019-0068-4openalex-snapshot

Characterization of cell fate probabilities in single-cell data with Palantir

inferredcites →https://doi.org/10.1073/pnas.0500334102openalex-snapshot

Geometric diffusions as a tool for harmonic analysis and structure definition of data: Diffusion maps

inferredcites →https://doi.org/10.1093/bioinformatics/btx792openalex-snapshot

SPRING: a kinetic interface for visualizing high dimensional single-cell expression data

inferredcites →https://doi.org/10.1101/191056openalex-snapshot

Reconstruction of developmental landscapes by optimal-transport analysis of single-cell gene expression sheds light on cellular reprogramming

inferredcites →https://doi.org/10.1101/cshperspect.a015867openalex-snapshot

The Dynamics of Morphogenesis in the Early Mouse Embryo

inferredcites →https://doi.org/10.1101/gad.303123.117openalex-snapshot

Embryonic timing, axial stem cells, chromatin dynamics, and the Hox clock

inferredcites →https://doi.org/10.1126/science.aaq1723openalex-snapshot

Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics

inferredcites →https://doi.org/10.1126/science.aar3131openalex-snapshot

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

inferredcites →https://doi.org/10.1126/science.aar4362openalex-snapshot

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo

inferredcites →https://doi.org/10.1126/science.aar5780openalex-snapshot

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

inferredcites →https://doi.org/10.1146/annurev.cellbio.042308.113344openalex-snapshot

Vertebrate Endoderm Development and Organ Formation

inferredcites →https://doi.org/10.1186/1471-213x-7-92openalex-snapshot

A systematic screen for genes expressed in definitive endoderm by Serial Analysis of Gene Expression (SAGE)

inferredcites →https://doi.org/10.1186/s12861-017-0150-4openalex-snapshot

The many faces of Pluripotency: in vitro adaptations of a continuum of in vivo states

inferredcites →https://doi.org/10.1242/dev.01897openalex-snapshot

Developmental regulation of the Hox genes during axial morphogenesis in the mouse

inferredcites →https://doi.org/10.1242/dev.021519openalex-snapshot

Distinct sequential cell behaviours direct primitive endoderm formation in the mouse blastocyst

inferredcites →https://doi.org/10.1242/dev.065656openalex-snapshot

Regulation of extra-embryonic endoderm stem cell differentiation by Nodal and Cripto signaling

inferredcites →https://doi.org/10.1242/dev.084996openalex-snapshot

FGF4 is required for lineage restriction and salt-and-pepper distribution of primitive endoderm factors but not their initial expression in the mouse

inferredcites →https://doi.org/10.1242/dev.109678openalex-snapshot

Gata6, Nanog and Erk signaling control cell fate in the inner cell mass through a tristable regulatory network

inferredcites →https://doi.org/10.1242/dev.122.3.983openalex-snapshot

PDX-1 is required for pancreatic outgrowth and differentiation of the rostral duodenum

inferredcites →https://doi.org/10.1242/dev.125.1.85openalex-snapshot

Hex: a homeobox gene revealing peri-implantation asymmetry in the mouse embryo and an early transient marker of endothelial cell precursors

inferredcites →https://doi.org/10.1242/dev.128314openalex-snapshot

Lineage specification in the mouse preimplantation embryo

inferredcites →https://doi.org/10.1242/dev.138453openalex-snapshot

In vitro patterning of pluripotent stem cell-derived intestine recapitulates in vivo human development

inferredcites →https://doi.org/10.1242/dev.150193openalex-snapshot

Pluripotent stem cell differentiation reveals distinct developmental pathways regulating lung versus thyroid lineage specification

inferredcites →https://doi.org/10.1242/dev.165852openalex-snapshot

ROSA26 reporter mouse lines and image analyses reveal distinct region-specific cell behaviors in the visceral endoderm

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.devcel.2019.02.024openalex-snapshot

Understanding the Mechanobiology of Early Mammalian Development through Bioengineered Models

inferred← citeshttps://doi.org/10.1016/j.devcel.2026.06.004openalex-snapshot

AXIN1 and AXIN2 regulate the WNT-signaling landscape to promote distinct mesoderm programs

inferred← citeshttps://doi.org/10.1016/j.stemcr.2023.12.002openalex-snapshot

Transcription factor co-expression mediates lineage priming for embryonic and extra-embryonic differentiation

inferred← citeshttps://doi.org/10.1038/s41586-021-04158-yopenalex-snapshot

Single-cell transcriptomic characterization of a gastrulating human embryo

inferred← citeshttps://doi.org/10.1073/pnas.2000238117openalex-snapshot

Lineage reconstruction from clonal correlations

inferred← citeshttps://doi.org/10.1242/dev.170506openalex-snapshot

Concepts and limitations for learning developmental trajectories from single cell genomics

inferred← citeshttps://doi.org/10.1242/dev.179564openalex-snapshot

Mapping cell migrations and fates in a gastruloid model to the human primitive streak

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