Single-cell RNA sequencing in cardiovascular development, disease and medicine

Computational methods for single-cell omics across modalities

(2020) Mirjana Efremova et al.   NATURE METHODS

Challenges in unsupervised clustering of single-cell RNA-seq data

(2019) Vladimir Yu Kiselev et al.   NATURE REVIEWS GENETICS

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

(2019) Yueli Cui et al.   Cell Reports

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

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

(2019) Leif S. Ludwig et al.   CELL

Generation of Endothelial Cells From Human Pluripotent Stem Cells

(2019) Ian M. Williams et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

Identifying the Transcriptome Signatures of Calcium Channel Blockers in Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes

(2019) Chi Keung Lam et al.   CIRCULATION RESEARCH

Single cell expression analysis reveals anatomical and cell cycle-dependent transcriptional shifts during heart development

(2019) Guang Li et al.   DEVELOPMENT

Mechanosensing by the Lamina Protects against Nuclear Rupture, DNA Damage, and Cell-Cycle Arrest

(2019) Sangkyun Cho et al.   DEVELOPMENTAL CELL

Single-Cell Transcriptional Profiling of Aortic Endothelium Identifies a Hierarchy from Endovascular Progenitors to Differentiated Cells

(2019) Samuel W. Lukowski et al.   Cell Reports

Single cell RNA-seq identifies the origins of heterogeneity in efficient cell transdifferentiation and reprogramming

(2019) Mirko Francesconi et al.   eLife

Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury

(2019) Nona Farbehi et al.   eLife

Single-cell lineage tracing by endogenous mutations enriched in transposase accessible mitochondrial DNA

(2019) Jin Xu et al.   eLife

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Single-Cell Analysis of the Normal Mouse Aorta Reveals Functionally Distinct Endothelial Cell Populations

(2019) Aditya S. Kalluri et al.   CIRCULATION

Single-cell transcriptome analyses reveal novel targets modulating cardiac neovascularization by resident endothelial cells following myocardial infarction

(2019) Ziwen Li et al.   EUROPEAN HEART JOURNAL

Single-cell analysis of cardiogenesis reveals basis for organ-level developmental defects

(2019) T. Yvanka de Soysa et al.   NATURE

Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility

(2019) Caleb A. Lareau et al.   NATURE BIOTECHNOLOGY

A single-cell transcriptional roadmap for cardiopharyngeal fate diversification

(2019) Wei Wang et al.   NATURE CELL BIOLOGY

Atheroprotective roles of smooth muscle cell phenotypic modulation and the TCF21 disease gene as revealed by single-cell analysis

(2019) Robert C. Wirka et al.   NATURE MEDICINE

Endothelial responses to shear stress in atherosclerosis: a novel role for developmental genes

(2019) Celine Souilhol et al.   Nature Reviews Cardiology

Vascular smooth muscle cells in atherosclerosis

(2019) Gemma L. Basatemur et al.   Nature Reviews Cardiology

Quantitative proteomics and single-nucleus transcriptomics of the sinus node elucidates the foundation of cardiac pacemaking

(2019) Nora Linscheid et al.   Nature Communications

Single-Cell Transcriptomics Reveals Chemotaxis-Mediated Intraorgan Crosstalk During Cardiogenesis

(2019) Haiqing Xiong et al.   CIRCULATION RESEARCH

Transcriptomic Profiling of the Developing Cardiac Conduction System at Single-Cell Resolution

(2019) William R. Goodyer et al.   CIRCULATION RESEARCH

Large Particle Fluorescence-Activated Cell Sorting Enables High-Quality Single-Cell RNA Sequencing and Functional Analysis of Adult Cardiomyocytes

(2019) Suraj Kannan et al.   CIRCULATION RESEARCH

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

(2019) Ansuman T. Satpathy et al.   NATURE BIOTECHNOLOGY

Atherosclerosis

(2019) Peter Libby et al.   Nature Reviews Disease Primers

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

(2019)   NATURE

Transcriptional and epigenetic regulation of macrophages in atherosclerosis

(2019) Tatyana Kuznetsova et al.   Nature Reviews Cardiology

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

(2019) Michaela Asp et al.   CELL

Arterial Sca1+ Vascular Stem Cells Generate De Novo Smooth Muscle for Artery Repair and Regeneration

(2019) Juan Tang et al.   Cell Stem Cell

Single-Cell Sequencing of Mouse Heart Immune Infiltrate in Pressure Overload–Driven Heart Failure Reveals Extent of Immune Activation

(2019) Elisa Martini et al.   CIRCULATION

Patient and Disease–Specific Induced Pluripotent Stem Cells for Discovery of Personalized Cardiovascular Drugs and Therapeutics

(2019) David T. Paik et al.   PHARMACOLOGICAL REVIEWS

Single-cell analysis uncovers that metabolic reprogramming by ErbB2 signaling is essential for cardiomyocyte proliferation in the regenerating heart

(2019) Hessel Honkoop et al.   eLife

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

Single-Cell Transcriptomics Meets Lineage Tracing

(2018) Lennart Kester et al.   Cell Stem Cell

Histone Variant H2A.Z is Required for the Maintenance of Smooth Muscle Cell Identity as Revealed by Single-Cell Transcriptomics

(2018) Fang Yao et al.   CIRCULATION

Single-Cell Sequencing of the Healthy and Diseased Heart Reveals Cytoskeleton-Associated Protein 4 as a New Modulator of Fibroblasts Activation

(2018) Monika M. Gladka et al.   CIRCULATION

Large-Scale Single-Cell RNA-Seq Reveals Molecular Signatures of Heterogeneous Populations of Human Induced Pluripotent Stem Cell-Derived Endothelial Cells

(2018) David T Paik et al.   CIRCULATION RESEARCH

Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine AtherosclerosisNovelty and Significance

(2018) Clément Cochain et al.   CIRCULATION RESEARCH

Atlas of the Immune Cell Repertoire in Mouse Atherosclerosis Defined by Single-Cell RNA-Sequencing and Mass CytometryNovelty and Significance

(2018) Holger Winkels et al.   CIRCULATION RESEARCH

Single-cell RNA-seq of human induced pluripotent stem cells reveals cellular heterogeneity and cell state transitions between subpopulations

(2018) Quan H. Nguyen et al.   GENOME RESEARCH

Identifying cell populations with scRNASeq

(2018) Tallulah S. Andrews et al.   MOLECULAR ASPECTS OF MEDICINE

A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex

(2018) Suijuan Zhong et al.   NATURE

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Tracing the temporal-spatial transcriptome landscapes of the human fetal digestive tract using single-cell RNA-sequencing

(2018) Shuai Gao et al.   NATURE CELL BIOLOGY

Transcript-indexed ATAC-seq for precision immune profiling

(2018) Ansuman T. Satpathy et al.   NATURE MEDICINE

Exponential scaling of single-cell RNA-seq in the past decade

(2018) Valentine Svensson et al.   Nature Protocols

Single-cell RNA sequencing for the study of development, physiology and disease

(2018) S. Steven Potter   Nature Reviews Nephrology

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

(2018) Fabienne Lescroart 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

Single-Cell DNA Methylation Profiling: Technologies and Biological Applications

(2018) Ino D. Karemaker et al.   TRENDS IN BIOTECHNOLOGY

Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor

(2018) Megan Crow et al.   Nature Communications

Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity

(2018) Emelie Berglund et al.   Nature Communications

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

(2018) Stephen J. Clark et al.   Nature Communications

Sensitive and powerful single-cell RNA sequencing using mcSCRB-seq

(2018) Johannes W. Bagnoli et al.   Nature Communications

Single-Cell Transcriptional Profiling Reveals Cellular Diversity and Intercommunication in the Mouse Heart

(2018) Daniel A. Skelly et al.   Cell Reports

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database

(2018) Luke Zappia et al.   PLoS Computational Biology

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

Endothelial Regeneration of Large Vessels Is a Biphasic Process Driven by Local Cells with Distinct Proliferative Capacities

(2018) Austin I. McDonald et al.   Cell Stem Cell

Single-nucleus transcriptomic survey of cell diversity and functional maturation in postnatal mammalian hearts

(2018) Peng Hu et al.   GENES & DEVELOPMENT

Single-cell analysis of early progenitor cells that build coronary arteries

(2018) Tianying Su et al.   NATURE

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

(2018) Darren A. Cusanovich et al.   NATURE

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

(2018) Junyue Cao et al.   SCIENCE

Dissecting the Global Dynamic Molecular Profiles of Human Fetal Kidney Development by Single-Cell RNA Sequencing

(2018) Ping Wang et al.   Cell Reports

Single-Cell Transcriptomic Analysis of Cardiac Differentiation from Human PSCs Reveals HOPX-Dependent Cardiomyocyte Maturation

(2018) Clayton E. Friedman et al.   Cell Stem Cell

Dissecting human disease with single-cell omics: application in model systems and in the clinic

(2018) Paulina M. Strzelecka et al.   Disease Models & Mechanisms

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures

(2018) Jagannath Swaminathan et al.   NATURE BIOTECHNOLOGY

Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections

(2018) Fredrik Salmén et al.   Nature Protocols

Following hearts, one cell at a time: recent applications of single-cell RNA sequencing to the understanding of heart disease

(2018) Matthew Ackers-Johnson et al.   Nature Communications

Cardiomyocyte gene programs encoding morphological and functional signatures in cardiac hypertrophy and failure

(2018) Seitaro Nomura et al.   Nature Communications

Defining human cardiac transcription factor hierarchies using integrated single-cell heterogeneity analysis

(2018) Jared M. Churko et al.   Nature Communications

Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement

(2018) Guangshuai Jia et al.   Nature Communications

Mechanosensing by the nucleus: From pathways to scaling relationships

(2017) Sangkyun Cho et al.   JOURNAL OF CELL BIOLOGY

Scaling single-cell genomics from phenomenology to mechanism

(2017) Amos Tanay et al.   NATURE

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

Single-cell analyses to tailor treatments

(2017) Alex K. Shalek et al.   Science Translational Medicine

Single cardiomyocyte nuclear transcriptomes reveal a lincRNA-regulated de-differentiation and cell cycle stress-response in vivo

(2017) Kelvin See et al.   Nature Communications

Massively parallel digital transcriptional profiling of single cells

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

Spatial detection of fetal marker genes expressed at low level in adult human heart tissue

(2017) Michaela Asp et al.   Scientific Reports

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells

(2017) Sebastian Pott   eLife

Maturation status of sarcomere structure and function in human iPSC-derived cardiac myocytes

(2016) Fikru B. Bedada et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

SCell: integrated analysis of single-cell RNA-seq data

(2016) Aaron Diaz et al.   BIOINFORMATICS

pcaReduce: hierarchical clustering of single cell transcriptional profiles

(2016) Justina žurauskienė et al.   BMC BIOINFORMATICS

Transcriptome Profiling of Patient-Specific Human iPSC-Cardiomyocytes Predicts Individual Drug Safety and Efficacy Responses In Vitro

(2016) Elena Matsa et al.   Cell Stem Cell

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

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

(2016) M Ryan Corces et al.   NATURE GENETICS

Single-cell multimodal profiling reveals cellular epigenetic heterogeneity

(2016) Lih Feng Cheow et al.   NATURE METHODS

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

(2016) Christof Angermueller et al.   NATURE METHODS

Induced pluripotent stem cell technology: a decade of progress

(2016) Yanhong Shi et al.   NATURE REVIEWS DRUG DISCOVERY

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

(2016) P. L. Stahl et al.   SCIENCE

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

A Single-Cell Transcriptome Atlas of the Human Pancreas

(2016) Mauro J. Muraro et al.   Cell Systems

What to Do When K-Means Clustering Fails: A Simple yet Principled Alternative Algorithm

(2016) Yordan P. Raykov et al.   PLoS One

Laminin-guided highly efficient endothelial commitment from human pluripotent stem cells

(2016) Ryo Ohta et al.   Scientific Reports

An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries

(2016) Anders Jemt et al.   Scientific Reports

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

(2015) Jacob H. Levine et al.   CELL

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

(2015) Evan Z. Macosko et al.   CELL

Wnt10b Gain-of-Function Improves Cardiac Repair by Arteriole Formation and Attenuation of FibrosisNovelty and Significance

(2015) David T. Paik et al.   CIRCULATION RESEARCH

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

A draft network of ligand–receptor-mediated multicellular signalling in human

(2015) Jordan A. Ramilowski et al.   Nature Communications

SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis

(2015) Minzhe Guo et al.   PLoS Computational Biology

Non-adherence to cardiovascular medications

(2014) K. Kolandaivelu et al.   EUROPEAN HEART JOURNAL

Mesenchymal–endothelial transition contributes to cardiac neovascularization

(2014) Eric Ubil 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

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

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

(2014) D. A. Jaitin et al.   SCIENCE

Early patterning and specification of cardiac progenitors in gastrulating mesoderm

(2014) W Patrick Devine et al.   eLife

Isolation and Functional Characterization of Human Ventricular Cardiomyocytes from Fresh Surgical Samples

(2014) Raffaele Coppini et al.   Jove-Journal of Visualized Experiments

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

RNA-SeQC: RNA-seq metrics for quality control and process optimization

(2012) David S. DeLuca et al.   BIOINFORMATICS

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

Experimental myocardial infarction triggers canonical Wnt signaling and endothelial-to-mesenchymal transition

(2011) O. Aisagbonhi et al.   Disease Models & Mechanisms

Coronary arteries form by developmental reprogramming of venous cells

(2010) Kristy Red-Horse et al.   NATURE