A roadmap for the Human Developmental Cell Atlas

The Organoid Cell Atlas

(2021) Christoph Bock et al.   NATURE BIOTECHNOLOGY

Developmental cell programs are co-opted in inflammatory skin disease

(2021) Gary Reynolds et al.   SCIENCE

Lab-grown structures mimic human embryo's earliest stage yet

(2021) Nidhi Subbaraman   NATURE

Modelling human blastocysts by reprogramming fibroblasts into iBlastoids

(2021) Xiaodong Liu et al.   NATURE

Blastocyst-like structures generated from human pluripotent stem cells

(2021) Leqian Yu et al.   NATURE

Cells of the human intestinal tract mapped across space and time

(2021) Rasa Elmentaite et al.   NATURE

Mapping the Fine-Scale Organization and Plasticity of the Brain Vasculature

(2020) Christoph Kirst et al.   CELL

Cellular and Molecular Probing of Intact Human Organs

(2020) Shan Zhao et al.   CELL

In vitro characterization of the human segmentation clock

(2020) Margarete Diaz-Cuadros et al.   NATURE

Cell stress in cortical organoids impairs molecular subtype specification

(2020) Aparna Bhaduri et al.   NATURE

Fast and efficient generation of knock-in human organoids using homology-independent CRISPR–Cas9 precision genome editing

(2020) Benedetta Artegiani et al.   NATURE CELL BIOLOGY

Regenerative lineages and immune-mediated pruning in lung cancer metastasis

(2020) Ashley M. Laughney et al.   NATURE MEDICINE

Tissue clearing and its applications in neuroscience

(2020) Hiroki R. Ueda et al.   NATURE REVIEWS NEUROSCIENCE

A cell atlas of human thymic development defines T cell repertoire formation

(2020) Jong-Eun Park et al.   SCIENCE

Early Fate Defines Microglia and Non-parenchymal Brain Macrophage Development

(2020) Sebastian G. Utz et al.   CELL

Single-Cell Analysis of Human Retina Identifies Evolutionarily Conserved and Species-Specific Mechanisms Controlling Development

(2020) Yufeng Lu et al.   DEVELOPMENTAL CELL

Recapitulating the human segmentation clock with pluripotent stem cells

(2020) Mitsuhiro Matsuda et al.   NATURE

Construction of a human cell landscape at single-cell level

(2020) Xiaoping Han et al.   NATURE

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects

(2020) Elisabetta Mereu et al.   NATURE BIOTECHNOLOGY

SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes

(2020) Waradon Sungnak et al.   NATURE MEDICINE

Machine learning analysis of whole mouse brain vasculature

(2020) Mihail Ivilinov Todorov et al.   NATURE METHODS

Intravital imaging of mouse embryos

(2020) Qiang Huang et al.   SCIENCE

Hair-bearing human skin generated entirely from pluripotent stem cells

(2020) Jiyoon Lee et al.   NATURE

An in vitro model of early anteroposterior organization during human development

(2020) Naomi Moris et al.   NATURE

Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling

(2020) Caleb A. Lareau et al.   NATURE BIOTECHNOLOGY

Huntington’s disease alters human neurodevelopment

(2020) Monia Barnat et al.   SCIENCE

Onco-fetal Reprogramming of Endothelial Cells Drives Immunosuppressive Macrophages in Hepatocellular Carcinoma

(2020) Ankur Sharma et al.   CELL

Species-specific segmentation clock periods are due to differential biochemical reaction speeds

(2020) Mitsuhiro Matsuda et al.   SCIENCE

Species-specific pace of development is associated with differences in protein stability

(2020) Teresa Rayon et al.   SCIENCE

Single cell transcriptomics comes of age

(2020) Sarah Aldridge et al.   Nature Communications

Mapping Development of the Human Intestinal Niche at Single-Cell Resolution

(2020) Emily M. Holloway et al.   Cell Stem Cell

Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn’s Disease

(2020) Rasa Elmentaite et al.   DEVELOPMENTAL CELL

Human blood vessel organoids as a model of diabetic vasculopathy

(2019) Reiner A. Wimmer et al.   NATURE

Preparing for first human trial of induced pluripotent stem cell-derived cells for Parkinson's disease: an interview with Jun Takahashi

(2019) Jun Takahasi   Regenerative Medicine

Single-Cell Transcriptome Analysis Maps the Developmental Track of the Human Heart

(2019) Yueli Cui et al.   Cell Reports

Single-cell RNA sequencing reveals midbrain dopamine neuron diversity emerging during mouse brain development

(2019) Katarína Tiklová et al.   Nature Communications

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 Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution

(2019) Deanne M. Taylor et al.   DEVELOPMENTAL CELL

Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics

(2019) Leif S. Ludwig et al.   CELL

Childhood cerebellar tumours mirror conserved fetal transcriptional programs

(2019) Maria C. Vladoiu et al.   NATURE

Single-cell genomics identifies cell type–specific molecular changes in autism

(2019) Dmitry Velmeshev et al.   SCIENCE

A 3D model of a human epiblast reveals BMP4-driven symmetry breaking

(2019) Mijo Simunovic et al.   NATURE CELL BIOLOGY

MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices

(2019) Christopher S. McGinnis et al.   NATURE METHODS

Hydraulic fracturing and active coarsening position the lumen of the mouse blastocyst

(2019) Julien G. Dumortier et al.   SCIENCE

Self-organization of stem cells into embryos: A window on early mammalian development

(2019) Marta N. Shahbazi et al.   SCIENCE

Mechanical impact of epithelial−mesenchymal transition on epithelial morphogenesis in Drosophila

(2019) Mélanie Gracia et al.   Nature Communications

Human inborn errors of immunity to infection affecting cells other than leukocytes: from the immune system to the whole organism

(2019) Shen-Ying Zhang et al.   CURRENT OPINION IN IMMUNOLOGY

Modelling human hepato-biliary-pancreatic organogenesis from the foregut–midgut boundary

(2019) Hiroyuki Koike et al.   NATURE

Spatiotemporal immune zonation of the human kidney

(2019) Benjamin J. Stewart et al.   SCIENCE

Decoding human fetal liver haematopoiesis

(2019) Dorin-Mirel Popescu et al.   NATURE

Stalled developmental programs at the root of pediatric brain tumors

(2019) Selin Jessa et al.   NATURE GENETICS

How many rare diseases are there?

(2019) Melissa Haendel et al.   NATURE REVIEWS DRUG DISCOVERY

Single cell transcriptome analysis of developing arcuate nucleus neurons uncovers their key developmental regulators

(2019) Christian Huisman et al.   Nature Communications

Toward a Common Coordinate Framework for the Human Body

(2019) Jennifer E. Rood et al.   CELL

A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart

(2019) Michaela Asp et al.   CELL

Multi-omics profiling of mouse gastrulation at single-cell resolution

(2019) Ricard Argelaguet et al.   NATURE

Organoid and Assembloid Technologies for Investigating Cellular Crosstalk in Human Brain Development and Disease

(2019) Rebecca M. Marton et al.   TRENDS IN CELL BIOLOGY

Mapping human development at single-cell resolution

(2018) Sam Behjati et al.   DEVELOPMENT

Defining the earliest step of cardiovascular lineage segregation by single-cell RNA-seq

(2018) Fabienne Lescroart et al.   SCIENCE

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

(2018) Xiao Wang et al.   SCIENCE

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding

(2018) Alexander B. Rosenberg et al.   SCIENCE

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

(2018) James A. Briggs et al.   SCIENCE

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

(2018) Daniel E. Wagner et al.   SCIENCE

Parental haplotype-specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells

(2018) Ábel Vértesy et al.   Nature Communications

A Single-Cell Transcriptional Atlas of the Developing Murine Cerebellum

(2018) Robert A. Carter et al.   CURRENT BIOLOGY

The cis-regulatory dynamics of embryonic development at single-cell resolution

(2018) Darren A. Cusanovich et al.   NATURE

Population dynamics of normal human blood inferred from somatic mutations

(2018) Henry Lee-Six et al.   NATURE

Single-cell genomics to guide human stem cell and tissue engineering

(2018) J. Gray Camp et al.   NATURE METHODS

Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors

(2018) Matthew D. Young et al.   SCIENCE

Modeling Human Digestive Diseases With CRISPR-Cas9–Modified Organoids

(2018) Masayuki Fujii et al.   GASTROENTEROLOGY

Single-cell reconstruction of the early maternal–fetal interface in humans

(2018) Roser Vento-Tormo et al.   NATURE

Somatic mosaicism and neurodevelopmental disease

(2018) Alissa M. D’Gama et al.   NATURE NEUROSCIENCE

Human sex reversal is caused by duplication or deletion of core enhancers upstream of SOX9

(2018) Brittany Croft et al.   Nature Communications

A single-cell survey of the human first-trimester placenta and decidua

(2018) Hemant Suryawanshi et al.   Science Advances

Cell diversity and network dynamics in photosensitive human brain organoids

(2017) Giorgia Quadrato et al.   NATURE

Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex

(2017) Tomasz J. Nowakowski et al.   SCIENCE

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

A pluripotent stem cell-based model for post-implantation human amniotic sac development

(2017) Yue Shao et al.   Nature Communications

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Multiplexed Intact-Tissue Transcriptional Analysis at Cellular Resolution

(2016) Emily Lauren Sylwestrak et al.   CELL

Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells

(2016) Gioele La Manno et al.   CELL

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

(2016) Sophie Petropoulos et al.   CELL

Development of the neurons controlling fertility in humans: new insights from 3D imaging and transparent fetal brains

(2016) Filippo Casoni et al.   DEVELOPMENT

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

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

(2016) P. L. Stahl et al.   SCIENCE

The FAIR Guiding Principles for scientific data management and stewardship

(2016) Mark D. Wilkinson et al.   Scientific Data

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

(2015) Paul Blakeley et al.   DEVELOPMENT

Enabling research with human embryonic and fetal tissue resources

(2015) D. Gerrelli et al.   DEVELOPMENT

Human cerebral organoids recapitulate gene expression programs of fetal neocortex development

(2015) J. Gray Camp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

De novo mutations in congenital heart disease with neurodevelopmental and other congenital anomalies

(2015) J. Homsy et al.   SCIENCE

Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing

(2014) Bin Yang et al.   CELL

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex

(2014) Alex A Pollen et al.   NATURE BIOTECHNOLOGY

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

(2014) Aryeh Warmflash et al.   NATURE METHODS

Spatial and Temporal Mapping of De Novo Mutations in Schizophrenia to a Fetal Prefrontal Cortical Network

(2013) Suleyman Gulsuner et al.   CELL

Cerebral organoids model human brain development and microcephaly

(2013) Madeline A. Lancaster et al.   NATURE

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

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

Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro

(2010) Jason R. Spence et al.   NATURE

Developmental Origins of Adult Disease

(2009) Rebecca A. Simmons   PEDIATRIC CLINICS OF NORTH AMERICA

DSCAM Is a Netrin Receptor that Collaborates with DCC in Mediating Turning Responses to Netrin-1

(2008) Alice Ly et al.   CELL