Combined single-cell and spatial transcriptomics reveal the molecular, cellular and spatial bone marrow niche organization

A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia

(2019) Ninib Baryawno et al.   CELL

The bone marrow microenvironment at single-cell resolution

(2019) Anastasia N. Tikhonova et al.   NATURE

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Visualizing structure and transitions in high-dimensional biological data

(2019) Kevin R. Moon et al.   NATURE BIOTECHNOLOGY

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

Lineage-Biased Hematopoietic Stem Cells Are Regulated by Distinct Niches

(2018) Sandra Pinho et al.   DEVELOPMENTAL CELL

Niches for Hematopoietic Stem Cells and Their Progeny

(2018) Qiaozhi Wei et al.   IMMUNITY

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

scmap: projection of single-cell RNA-seq data across data sets

(2018) Vladimir Yu Kiselev et al.   NATURE METHODS

Quantitative spatial analysis of haematopoiesis-regulating stromal cells in the bone marrow microenvironment by 3D microscopy

(2018) Alvaro Gomariz et al.   Nature Communications

Stem cell factor is selectively secreted by arterial endothelial cells in bone marrow

(2018) Chunliang Xu et al.   Nature Communications

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Population snapshots predict early haematopoietic and erythroid hierarchies

(2018) Betsabeh Khoramian Tusi et al.   NATURE

Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting

(2018) Merav Cohen et al.   CELL

The Majority of CD45– Ter119– CD31– Bone Marrow Cell Fraction Is of Hematopoietic Origin and Contains Erythroid and Lymphoid Progenitors

(2018) Philip E. Boulais et al.   IMMUNITY

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

(2018) Roser Vento-Tormo et al.   NATURE

Semisoft clustering of single-cell data

(2018) Lingxue Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multilineage communication regulates human liver bud development from pluripotency

(2017) J. Gray Camp et al.   NATURE

Three-dimensional map of nonhematopoietic bone and bone-marrow cells and molecules

(2017) Daniel L Coutu et al.   NATURE BIOTECHNOLOGY

Human haematopoietic stem cell lineage commitment is a continuous process

(2017) Lars Velten et al.   NATURE CELL BIOLOGY

Bone marrow adipocytes promote the regeneration of stem cells and haematopoiesis by secreting SCF

(2017) Bo O. Zhou et al.   NATURE CELL BIOLOGY

Differential cytokine contributions of perivascular haematopoietic stem cell niches

(2017) Noboru Asada et al.   NATURE CELL BIOLOGY

Vascular heterogeneity and specialization in development and disease

(2017) Michael Potente et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Spatial reconstruction of immune niches by combining photoactivatable reporters and scRNA-seq

(2017) Chiara Medaglia et al.   SCIENCE

Massively parallel digital transcriptional profiling of single cells

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

Large-Scale Low-Cost NGS Library Preparation Using a Robust Tn5 Purification and Tagmentation Protocol

(2017) Bianca P. Hennig et al.   G3-Genes Genomes Genetics

Regulation of Hematopoiesis and Osteogenesis by Blood Vessel–Derived Signals

(2016) Saravana K. Ramasamy et al.   Annual Review of Cell and Developmental Biology

Podoplanin-positive periarteriolar stromal cells promote megakaryocyte growth and proplatelet formation in mice by CLEC-2

(2016) S. Tamura et al.   BLOOD

A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation

(2016) S. Nestorowa et al.   BLOOD

Proximity-Based Differential Single-Cell Analysis of the Niche to Identify Stem/Progenitor Cell Regulators

(2016) Lev Silberstein et al.   Cell Stem Cell

Hematopoietic Stem Cell Niches Produce Lineage-Instructive Signals to Control Multipotent Progenitor Differentiation

(2016) Ana Cordeiro Gomes et al.   IMMUNITY

Distinct bone marrow blood vessels differentially regulate haematopoiesis

(2016) Tomer Itkin et al.   NATURE

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Physiological Bone Remodeling: Systemic Regulation and Growth Factor Involvement

(2016) Jawed A. Siddiqui et al.   PHYSIOLOGY

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

(2016) P. L. Stahl et al.   SCIENCE

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

(2016) Susanne Nichterwitz et al.   Nature Communications

A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure

(2016) Maayan Baron et al.   Cell Systems

Gremlin 1 Identifies a Skeletal Stem Cell with Bone, Cartilage, and Reticular Stromal Potential

(2015) Daniel L. Worthley et al.   CELL

Fixed single-cell transcriptomic characterization of human radial glial diversity

(2015) Elliot R Thomsen et al.   NATURE METHODS

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

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

(2014) S. Anders et al.   BIOINFORMATICS

The bone marrow niche for haematopoietic stem cells

(2014) Sean J. Morrison et al.   NATURE

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

CXCL12 in early mesenchymal progenitors is required for haematopoietic stem-cell maintenance

(2013) Adam Greenbaum et al.   NATURE

Haematopoietic stem cells and early lymphoid progenitors occupy distinct bone marrow niches

(2013) Lei Ding et al.   NATURE

Arteriolar niches maintain haematopoietic stem cell quiescence

(2013) Yuya Kunisaki et al.   NATURE

Immunological Genome Project and systems immunology

(2013) Tal Shay et al.   TRENDS IN IMMUNOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Endothelial and perivascular cells maintain haematopoietic stem cells

(2012) Lei Ding et al.   NATURE

The Essential Functions of Adipo-osteogenic Progenitors as the Hematopoietic Stem and Progenitor Cell Niche

(2010) Yoshiki Omatsu et al.   IMMUNITY

Mesenchymal and haematopoietic stem cells form a unique bone marrow niche

(2010) Simón Méndez-Ferrer et al.   NATURE