The emergent landscape of the mouse gut endoderm at single-cell resolution

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

(2019) Manu Setty et al.   NATURE BIOTECHNOLOGY

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

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

(2018) Elham Azizi et al.   CELL

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

(2018) Sophie M. Morgani et al.   DEVELOPMENTAL BIOLOGY

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

(2018) Ximena Ibarra-Soria et al.   NATURE CELL BIOLOGY

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

(2018) Jeffrey A. Farrell et al.   SCIENCE

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Lineage specification in the mouse preimplantation embryo

(2016) Claire Chazaud et al.   DEVELOPMENT

In vitropatterning of pluripotent stem cell-derived intestine recapitulatesin vivohuman development

(2016) Yu-Hwai Tsai et al.   DEVELOPMENT

Cell Competition and Its Role in the Regulation of Cell Fitness from Development to Cancer

(2016) Aida Di Gregorio et al.   DEVELOPMENTAL CELL

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

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

(2015) Jacob H. Levine et al.   CELL

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

(2014) Nadine Schrode et al.   DEVELOPMENTAL CELL

SOX17 links gut endoderm morphogenesis and germ layer segregation

(2014) Manuel Viotti et al.   NATURE CELL BIOLOGY

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

(2013) Ryuji Hiramatsu et al.   DEVELOPMENTAL CELL

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

(2013) Ying Yang et al.   MECHANISMS OF DEVELOPMENT

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

(2013) El-ad David Amir et al.   NATURE BIOTECHNOLOGY

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

(2013) Yusuke Ohnishi et al.   NATURE CELL BIOLOGY

Totipotent Embryonic Stem Cells Arise in Ground-State Culture Conditions

(2013) Sophie M. Morgani et al.   Cell Reports

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

(2012) M. Kang et al.   DEVELOPMENT

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

(2011) M. K.-d. Julio et al.   DEVELOPMENT

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

(2011) Agnieszka Paca et al.   DEVELOPMENTAL BIOLOGY

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

(2011) Jérôme Artus et al.   DEVELOPMENTAL BIOLOGY

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

(2011) Katsuyoshi Takaoka et al.   NATURE CELL BIOLOGY

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

(2010) Sonja Nowotschin et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

(2010) Jérôme Artus et al.   DEVELOPMENTAL BIOLOGY

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

(2010) Manuel Viotti et al.   GENESIS

Vertebrate Endoderm Development and Organ Formation

(2009) Aaron M. Zorn et al.   Annual Review of Cell and Developmental Biology

Nanog Is the Gateway to the Pluripotent Ground State

(2009) Jose Silva et al.   CELL

Transthyretinmouse transgenes direct RFP expression or Cre-mediated recombination throughout the visceral endoderm

(2009) Gloria S. Kwon et al.   GENESIS

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

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

(2008) B. Plusa et al.   DEVELOPMENT

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

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

Transcriptional dynamics of endodermal organ formation

(2008) Richard I. Sherwood et al.   DEVELOPMENTAL DYNAMICS