Yolk sac cell atlas reveals multiorgan functions during human early development

Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender

(2023) Stephen J. Fleming et al.   NATURE METHODS

A Python library for probabilistic analysis of single-cell omics data

(2022) Adam Gayoso et al.   NATURE BIOTECHNOLOGY

Erythropoietin directly remodels the clonal composition of murine hematopoietic multipotent progenitor cells

(2022) Almut S Eisele et al.   eLife

Three tissue resident macrophage subsets coexist across organs with conserved origins and life cycles

(2022) Sarah A. Dick et al.   Science Immunology

Mapping human haematopoietic stem cells from haemogenic endothelium to birth

(2022) Vincenzo Calvanese et al.   NATURE

Mapping the developing human immune system across organs

(2022) Chenqu Suo et al.   SCIENCE

Cross-tissue immune cell analysis reveals tissue-specific features in humans

(2022) C. Domínguez Conde et al.   SCIENCE

The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

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Normalizing and denoising protein expression data from droplet-based single cell profiling

(2022) Matthew P. Mulè et al.   Nature Communications

Robust temporal map of human in vitro myelopoiesis using single-cell genomics

(2022) Clara Alsinet et al.   Nature Communications

Single-cell roadmap of human gonadal development

(2022) Luz Garcia-Alonso et al.   NATURE

Vitronectin‐activated αvβ3 and αvβ5 integrin signalling specifies haematopoietic fate in human pluripotent stem cells

(2021) Jun Shen et al.   CELL PROLIFERATION

First blood: the endothelial origins of hematopoietic progenitors

(2021) Giovanni Canu et al.   ANGIOGENESIS

Single-cell atlas of early human brain development highlights heterogeneity of human neuroepithelial cells and early radial glia

(2021) Ugomma C. Eze et al.   NATURE NEUROSCIENCE

Mapping single-cell atlases throughout Metazoa unravels cell type evolution

(2021) Alexander J Tarashansky et al.   eLife

Capillary-associated microglia regulate vascular structure and function through PANX1-P2RY12 coupling in mice

(2021) Kanchan Bisht et al.   Nature Communications

The Hematopoietic Bone Marrow Niche Ecosystem

(2021) Julia Fröbel et al.   Frontiers in Cell and Developmental Biology

Blood and immune development in human fetal bone marrow and Down syndrome

(2021) Laura Jardine et al.   NATURE

Single-cell transcriptomic characterization of a gastrulating human embryo

(2021) Richard C. V. Tyser et al.   NATURE

Differential abundance testing on single-cell data using k-nearest neighbor graphs

(2021) Emma Dann et al.   NATURE BIOTECHNOLOGY

CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

(2020) Mirjana Efremova et al.   Nature Protocols

Deciphering human macrophage development at single-cell resolution

(2020) Zhilei Bian et al.   NATURE

Effects of NRP1 on angiogenesis and vascular maturity in�endothelial cells are dependent on the expression of SEMA4D

(2020) Zhi Lyu et al.   INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE

Origin and function of the yolk sac in primate embryogenesis

(2020) Connor Ross et al.   Nature Communications

Multi-layered Spatial Transcriptomics Identify Secretory Factors Promoting Human Hematopoietic Stem Cell Development

(2020) Edie I. Crosse et al.   Cell Stem Cell

Trem2 promotes anti-inflammatory responses in microglia and is suppressed under pro-inflammatory conditions

(2020) Wenfei Liu et al.   HUMAN MOLECULAR GENETICS

Decoding Human Megakaryocyte Development

(2020) Hongtao Wang et al.   Cell Stem Cell

Characterization and generation of human definitive multipotent hematopoietic stem/progenitor cells

(2020) Yanling Zhu et al.   Cell Discovery

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

Lipid-Associated Macrophages Control Metabolic Homeostasis in a Trem2-Dependent Manner

(2019) Diego Adhemar Jaitin et al.   CELL

The Neural Crest as the First Production Site of the Erythroid Growth Factor Erythropoietin

(2019) Ikuo Hirano et al.   Frontiers in Cell and Developmental Biology

Tracing the first hematopoietic stem cell generation in human embryo by single-cell RNA sequencing

(2019) Yang Zeng et al.   CELL RESEARCH

BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples

(2019) David Hörl et al.   NATURE METHODS

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

In vivo generation of haematopoietic stem/progenitor cells from bone marrow-derived haemogenic endothelium

(2019) Laurent Yvernogeau et al.   NATURE CELL BIOLOGY

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

(2019) Ilya Korsunsky et al.   NATURE METHODS

The physical microenvironment of hematopoietic stem cells and its emerging roles in engineering applications

(2019) Pan Zhang et al.   Stem Cell Research & Therapy

Deep generative modeling for single-cell transcriptomics

(2018) Romain Lopez et al.   NATURE METHODS

A test metric for assessing single-cell RNA-seq batch correction

(2018) Maren Büttner et al.   NATURE METHODS

RNA-seq reveals conservation of function among the yolk sacs of human, mouse, and chicken

(2017) Tereza Cindrova-Davies et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

(2017) Alexandra-Chloé Villani et al.   SCIENCE

Tissue-Resident Macrophage Ontogeny and Homeostasis

(2016) Florent Ginhoux et al.   IMMUNITY

TREM2 Lipid Sensing Sustains the Microglial Response in an Alzheimer’s Disease Model

(2015) Yaming Wang et al.   CELL

GFI1 proteins orchestrate the emergence of haematopoietic stem cells through recruitment of LSD1

(2015) Roshana Thambyrajah et al.   NATURE CELL BIOLOGY

Definitive Hematopoiesis in the Yolk Sac Emerges from Wnt-Responsive Hemogenic Endothelium Independently of Circulation and Arterial Identity

(2015) Jenna M. Frame et al.   STEM CELLS

Primitive and definitive erythropoiesis in mammals

(2014) James Palis   Frontiers in Physiology

The transcription factor Fli-1 regulates monocyte, macrophage and dendritic cell development in mice

(2013) Eiji Suzuki et al.   IMMUNOLOGY

Mouse Embryonic Head as a Site for Hematopoietic Stem Cell Development

(2012) Zhuan Li et al.   Cell Stem Cell

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

(2012) Johannes Schindelin et al.   NATURE METHODS

Highly potent human hematopoietic stem cells first emerge in the intraembryonic aorta-gonad-mesonephros region

(2011) Andrejs Ivanovs et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Primitive erythropoiesis in the mammalian embryo

(2010) James Palis et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Fetal liver hepatic progenitors are supportive stromal cells for hematopoietic stem cells

(2010) Song Chou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fate Mapping Analysis Reveals That Adult Microglia Derive from Primitive Macrophages

(2010) F. Ginhoux et al.   SCIENCE

Tissue factor in cancer progression and angiogenesis

(2010) Wolfram Ruf et al.   THROMBOSIS RESEARCH

Mef2C is a lineage-restricted target of Scl/Tal1 and regulates megakaryopoiesis and B-cell homeostasis

(2009) C. Gekas et al.   BLOOD

The Emergence of Hematopoietic Stem Cells Is Initiated in the Placental Vasculature in the Absence of Circulation

(2008) Katrin E. Rhodes et al.   Cell Stem Cell