Lineage specification of early embryos and embryonic stem cells at the dawn of enabling technologies

Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq

(2017) Jun Chen et al.   Nature Protocols

Building a lineage from single cells: genetic techniques for cell lineage tracking

(2017) Mollie B. Woodworth et al.   NATURE REVIEWS GENETICS

Transcriptional Control of Developmental Cell Behaviors

(2016) Yelena Bernadskaya et al.   Annual Review of Cell and Developmental Biology

Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos

(2016) Sophie Petropoulos et al.   CELL

Mapping the Pairwise Choices Leading from Pluripotency to Human Bone, Heart, and Other Mesoderm Cell Types

(2016) Kyle M. Loh et al.   CELL

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

(2016) Karthik Shekhar et al.   CELL

De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

(2016) Dominic Grün et al.   Cell Stem Cell

Dissecting stem cell differentiation using single cell expression profiling

(2016) Victoria Moignard et al.   CURRENT OPINION IN CELL BIOLOGY

Lineage specification in the mouse preimplantation embryo

(2016) Claire Chazaud et al.   DEVELOPMENT

Cycling through developmental decisions: how cell cycle dynamics control pluripotency, differentiation and reprogramming

(2016) Abdenour Soufi et al.   DEVELOPMENT

Single-Cell Resolution of Temporal Gene Expression during Heart Development

(2016) Daniel M. DeLaughter et al.   DEVELOPMENTAL CELL

Transcriptomic Profiling Maps Anatomically Patterned Subpopulations among Single Embryonic Cardiac Cells

(2016) Guang Li et al.   DEVELOPMENTAL CELL

Spatial Transcriptome for the Molecular Annotation of Lineage Fates and Cell Identity in Mid-gastrula Mouse Embryo

(2016) Guangdun Peng et al.   DEVELOPMENTAL CELL

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

(2016) Kotaro Sasaki et al.   DEVELOPMENTAL CELL

The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation

(2016) Makiko Iwafuchi-Doi et al.   MOLECULAR CELL

Mechanics drives cell differentiation

(2016) Berenika Plusa et al.   NATURE

Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos

(2016) Xiaoyu Liu et al.   NATURE

Allelic reprogramming of the histone modification H3K4me3 in early mammalian development

(2016) Bingjie Zhang et al.   NATURE

Single-cell analysis of mixed-lineage states leading to a binary cell fate choice

(2016) Andre Olsson et al.   NATURE

Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition

(2016) John Arne Dahl et al.   NATURE

Tracing haematopoietic stem cell formation at single-cell resolution

(2016) Fan Zhou et al.   NATURE

Asymmetric division of contractile domains couples cell positioning and fate specification

(2016) Jean-Léon Maître et al.   NATURE

The landscape of accessible chromatin in mammalian preimplantation embryos

(2016) Jingyi Wu et al.   NATURE

Self-organization of the in vitro attached human embryo

(2016) Alessia Deglincerti et al.   NATURE

Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma

(2016) Itay Tirosh et al.   NATURE

Resolving early mesoderm diversification through single-cell expression profiling

(2016) Antonio Scialdone et al.   NATURE

A developmental coordinate of pluripotency among mice, monkeys and humans

(2016) Tomonori Nakamura et al.   NATURE

Revealing the vectors of cellular identity with single-cell genomics

(2016) Allon Wagner et al.   NATURE BIOTECHNOLOGY

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

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

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

Transition states and cell fate decisions in epigenetic landscapes

(2016) Naomi Moris et al.   NATURE REVIEWS GENETICS

Molecular features of cellular reprogramming and development

(2016) Zachary D. Smith et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain

(2016) B. B. Lake et al.   SCIENCE

Past Roadblocks and New Opportunities in Transcription Factor Network Mapping

(2016) Michael R. Brent   TRENDS IN GENETICS

Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling

(2016) Susanne Nichterwitz et al.   Nature Communications

Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNA-Seq

(2016) Ozgun Gokce et al.   Cell Reports

Single-Cell Transcriptomics Reveals that Differentiation and Spatial Signatures Shape Epidermal and Hair Follicle Heterogeneity

(2016) Simon Joost et al.   Cell Systems

Design and Analysis of Single-Cell Sequencing Experiments

(2015) Dominic Grün et al.   CELL

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

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations

(2015) Nicola K. Wilson et al.   Cell Stem Cell

A developmental framework for induced pluripotency

(2015) Kazutoshi Takahashi et al.   DEVELOPMENT

Intrinsic regulations in neural fate commitment

(2015) Ke Tang et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Lineage-Specific Profiling Delineates the Emergence and Progression of Naive Pluripotency in Mammalian Embryogenesis

(2015) Thorsten Boroviak et al.   DEVELOPMENTAL CELL

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

The Technology and Biology of Single-Cell RNA Sequencing

(2015) Aleksandra A. Kolodziejczyk et al.   MOLECULAR CELL

How to catch rare cell types

(2015) Lu Wen et al.   NATURE

Pioneer factors govern super-enhancer dynamics in stem cell plasticity and lineage choice

(2015) Rene C. Adam et al.   NATURE

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

Hallmarks of pluripotency

(2015) Alejandro De Los Angeles et al.   NATURE

Putting cells in their place

(2015) Omid R Faridani et al.   NATURE BIOTECHNOLOGY

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

Decoding the regulatory network of early blood development from single-cell gene expression measurements

(2015) Victoria Moignard et al.   NATURE BIOTECHNOLOGY

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

(2015) Kaia Achim et al.   NATURE BIOTECHNOLOGY

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

Linking the Cell Cycle to Cell Fate Decisions

(2015) Stephen Dalton   TRENDS IN CELL BIOLOGY

Histone deacetylation promotes mouse neural induction by restricting Nodal-dependent mesendoderm fate

(2015) Pingyu Liu et al.   Nature Communications

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

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

Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes

(2014) Jill M. Dowen et al.   CELL

Molecular Control of Induced Pluripotency

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

Quantitative Single-Cell Approaches to Stem Cell Research

(2014) Martin Etzrodt et al.   Cell Stem Cell

Efficient Endoderm Induction from Human Pluripotent Stem Cells by Logically Directing Signals Controlling Lineage Bifurcations

(2014) Kyle M. Loh et al.   Cell Stem Cell

Single cell sequencing approaches for complex biological systems

(2014) Timour Baslan et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Modelling human development and disease in pluripotent stem-cell-derived gastric organoids

(2014) Kyle W. McCracken et al.   NATURE

Transcriptional landscape of the prenatal human brain

(2014) Jeremy A. Miller et al.   NATURE

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Spatially resolved transcriptomics and beyond

(2014) Nicola Crosetto et al.   NATURE REVIEWS GENETICS

CORTECON: A Temporal Transcriptome Analysis of In Vitro Human Cerebral Cortex Development from Human Embryonic Stem Cells

(2014) Joyce van de Leemput et al.   NEURON

Developmental plasticity, cell fate specification and morphogenesis in the early mouse embryo

(2014) I. Bedzhov et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Mapping the route from naive pluripotency to lineage specification

(2014) T. Kalkan et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Cancer by super-enhancer

(2014) A. Vaharautio et al.   SCIENCE

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

Timing of developmental events in the early mouse embryo

(2014) Yoji Kojima et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

The Dynamics of Morphogenesis in the Early Mouse Embryo

(2014) Jaime A. Rivera-Pérez et al.   Cold Spring Harbor Perspectives in Biology

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

(2013) Zhigang Xue et al.   NATURE

Quantitative assessment of single-cell RNA-sequencing methods

(2013) Angela R Wu et al.   NATURE METHODS

Computational solutions for omics data

(2013) Bonnie Berger et al.   NATURE REVIEWS GENETICS

Unravelling stem cell dynamics by lineage tracing

(2013) Cédric Blanpain et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

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

Lineage Tracing

(2012) Kai Kretzschmar et al.   CELL

Efficient Derivation of Purified Lung and Thyroid Progenitors from Embryonic Stem Cells

(2012) Tyler A. Longmire et al.   Cell Stem Cell

Self-Renewing Endodermal Progenitor Lines Generated from Human Pluripotent Stem Cells

(2012) Xin Cheng et al.   Cell Stem Cell

Patterning and shaping the endoderm in vivo and in culture

(2012) Marine RC Kraus et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Transcriptional regulatory networks in epiblast cells and during anterior neural plate development as modeled in epiblast stem cells

(2012) M. Iwafuchi-Doi et al.   DEVELOPMENT

Cell-Surface Proteomics Identifies Lineage-Specific Markers of Embryo-Derived Stem Cells

(2012) Peter J. Rugg-Gunn et al.   DEVELOPMENTAL CELL

Experimental approaches for gene regulatory network construction: The chick as a model system

(2012) Andrea Streit et al.   GENESIS

An anatomically comprehensive atlas of the adult human brain transcriptome

(2012) Michael J. Hawrylycz et al.   NATURE

Studying and modelling dynamic biological processes using time-series gene expression data

(2012) Ziv Bar-Joseph et al.   NATURE REVIEWS GENETICS

A Molecular Signature for Purified Definitive Endoderm Guides Differentiation and Isolation of Endoderm from Mouse and Human Embryonic Stem Cells

(2012) Pei Wang et al.   STEM CELLS AND DEVELOPMENT

Control of the Embryonic Stem Cell State

(2011) Richard A. Young   CELL

Intrinsic transition of embryonic stem-cell differentiation into neural progenitors

(2011) Daisuke Kamiya et al.   NATURE

Resolution of Cell Fate Decisions Revealed by Single-Cell Gene Expression Analysis from Zygote to Blastocyst

(2010) Guoji Guo et al.   DEVELOPMENTAL CELL

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Systems biology of stem cell fate and cellular reprogramming

(2009) Ben D. MacArthur et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

Epigenetic dynamics of stem cells and cell lineage commitment: digging Waddington's canal

(2009) Myriam Hemberger et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Stem Cells, the Molecular Circuitry of Pluripotency and Nuclear Reprogramming

(2008) Rudolf Jaenisch et al.   CELL

Modelling and analysis of gene regulatory networks

(2008) Guy Karlebach et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY