Embryo model completes gastrulation to neurulation and organogenesis

Systematic reconstruction of cellular trajectories across mouse embryogenesis

(2022) Chengxiang Qiu et al.   NATURE GENETICS

DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update)

(2022) Brad T Sherman et al.   NUCLEIC ACIDS RESEARCH

¬Post-Gastrulation Synthetic Embryos Generated Ex Utero from Mouse Naïve ESCs

(2022) Shadi Tarazi et al.   CELL

Mouse embryo model derived exclusively from embryonic stem cells undergoes neurulation and heart development

(2022) Kasey Y.C. Lau et al.   Cell Stem Cell

Stem cell-derived synthetic embryos self-assemble by exploiting cadherin codes and cortical tension

(2022) Min Bao et al.   NATURE CELL BIOLOGY

Optimized single-nucleus transcriptional profiling by combinatorial indexing

(2022) Beth K. Martin et al.   Nature Protocols

Integrated spatial genomics reveals global architecture of single nuclei

(2021) Yodai Takei et al.   NATURE

Ex utero mouse embryogenesis from pre-gastrulation to late organogenesis

(2021) Alejandro Aguilera-Castrejon et al.   NATURE

Molecular architecture of the developing mouse brain

(2021) Gioele La Manno et al.   NATURE

Construction of a mammalian embryo model from stem cells organized by a morphogen signalling centre

(2021) Peng-Fei Xu et al.   Nature Communications

Induction of Rosette-to-Lumen stage embryoids using reprogramming paradigms in ESCs

(2021) Jan Langkabel et al.   Nature Communications

Neural tube development depends on notochord-derived sonic hedgehog released into the sclerotome

(2020) Nitza Kahane et al.   DEVELOPMENT

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

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

(2020) Gianluca Amadei et al.   DEVELOPMENTAL CELL

The Gene Ontology resource: enriching a GOld mine

(2020) et al.   NUCLEIC ACIDS RESEARCH

Mouse embryonic stem cells self-organize into trunk-like structures with neural tube and somites

(2020) Jesse V. Veenvliet et al.   SCIENCE

Nr2f-dependent allocation of ventricular cardiomyocyte and pharyngeal muscle progenitors

(2019) Tracy E. Dohn et al.   PLoS Genetics

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

(2019) Blanca Pijuan-Sala et al.   NATURE

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

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

(2019) Sonja Nowotschin et al.   NATURE

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

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

FOXG1 Dose in Brain Development

(2019) Nuwan C. Hettige et al.   Frontiers in Pediatrics

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

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

(2018) Swati Parekh et al.   GigaScience

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

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

(2018) Leonardo Beccari et al.   NATURE

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

(2018) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Identification of novel genetic markers for mouse yolk sac cells by using microarray analyses

(2017) Shinomi Yagi et al.   PLACENTA

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

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

(2017) Sarah Ellys Harrison et al.   SCIENCE

Specification of murine ground state pluripotent stem cells to regional neuronal populations

(2017) Walaa F. Alsanie et al.   Scientific Reports

From the stem of the placental tree: trophoblast stem cells and their progeny

(2016) Paulina Anna Latos et al.   DEVELOPMENT

Single-cell barcoding and sequencing using droplet microfluidics

(2016) Rapolas Zilionis et al.   Nature Protocols

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

(2015) Allon M. Klein et al.   CELL

Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord

(2015) Diana S. José-Edwards et al.   PLoS Genetics

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

deML: robust demultiplexing of Illumina sequences using a likelihood-based approach

(2014) Gabriel Renaud et al.   BIOINFORMATICS

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

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

In vitro culture of mouse blastocysts beyond the implantation stages

(2014) Ivan Bedzhov et al.   Nature Protocols

Pax3 and Hippo Signaling Coordinate Melanocyte Gene Expression in Neural Crest

(2014) Lauren J. Manderfield et al.   Cell Reports

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

(2014) Yosuke Tanaka et al.   Cell Reports

Notch signaling represses p63 expression in the developing surface ectoderm

(2013) A. M. B. Tadeu et al.   DEVELOPMENT

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

(2012) Johannes Schindelin et al.   NATURE METHODS

Periostin as a Biomarker of the Amniotic Membrane

(2012) Mariya P. Dobreva et al.   Stem Cells International

The role of the transcription factor Rbpj in the development of dorsal root ganglia

(2011) Ze-Lan Hu et al.   Neural Development

The transcription factors Nkx2.2 and Nkx2.9 play a novel role in floor plate development and commissural axon guidance

(2010) A. Holz et al.   DEVELOPMENT

Ets1 is required for proper migration and differentiation of the cardiac neural crest

(2010) Z. Gao et al.   DEVELOPMENT

Distinct Sonic Hedgehog signaling dynamics specify floor plate and ventral neuronal progenitors in the vertebrate neural tube

(2010) V. Ribes et al.   GENES & DEVELOPMENT

Redefining the Progression of Lineage Segregations during Mammalian Embryogenesis by Clonal Analysis

(2009) Elena Tzouanacou et al.   DEVELOPMENTAL CELL

Patch-Based Nonlocal Functional for Denoising Fluorescence Microscopy Image Sequences

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

Development and function of trophoblast giant cells in the rodent placenta

(2009) Dong Hu et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

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

(2009) Da Wei Huang et al.   Nature Protocols

The Level of the Transcription Factor Pax6 Is Essential for Controlling the Balance between Neural Stem Cell Self-Renewal and Neurogenesis

(2009) Stephen N. Sansom et al.   PLoS Genetics

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

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