Single cell RNA‐sequencing: A powerful yet still challenging technology to study cellular heterogeneity

Single-cell analysis of gastric pre-cancerous and cancer lesions reveals cell lineage diversity and intratumoral heterogeneity

(2022) Jihyun Kim et al.   npj Precision Oncology

Astrogenesis in the murine dentate gyrus is a life‐long and dynamic process

(2022) Julia Schneider et al.   EMBO JOURNAL

Multi-omics single-cell data integration and regulatory inference with graph-linked embedding

(2022) Zhi-Jie Cao et al.   NATURE BIOTECHNOLOGY

Fast and highly sensitive full-length single-cell RNA sequencing using FLASH-seq

(2022) Vincent Hahaut et al.   NATURE BIOTECHNOLOGY

Single-cell RNA sequencing reveals evolution of immune landscape during glioblastoma progression

(2022) Alan T. Yeo et al.   NATURE IMMUNOLOGY

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

(2022) et al.   SCIENCE

Integrating spatial transcriptomics with single-cell transcriptomics reveals a spatiotemporal gene landscape of the human developing kidney

(2022) Hongwei Wu et al.   Cell and Bioscience

Mapping and Validation of scRNA-Seq-Derived Cell-Cell Communication Networks in the Tumor Microenvironment

(2022) Kate Bridges et al.   Frontiers in Immunology

The Organoid Cell Atlas

(2021) Christoph Bock et al.   NATURE BIOTECHNOLOGY

Single-cell RNA-seq reveals transcriptomic heterogeneity mediated by host-pathogen dynamics in lymphoblastoid cell lines

(2021) Elliott D SoRelle et al.   eLife

Fast and precise single-cell data analysis using a hierarchical autoencoder

(2021) Duc Tran et al.   Nature Communications

Inference and analysis of cell-cell communication using CellChat

(2021) Suoqin Jin et al.   Nature Communications

Direct Comparative Analyses of 10X Genomics Chromium and Smart-seq2

(2021) Xiliang Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Applicability of spatial transcriptional profiling to cancer research

(2021) Rania Bassiouni et al.   MOLECULAR CELL

A Comparison for Dimensionality Reduction Methods of Single-Cell RNA-seq Data

(2021) Ruizhi Xiang et al.   Frontiers in Genetics

CytoTalk: De novo construction of signal transduction networks using single-cell transcriptomic data

(2021) Yuxuan Hu et al.   Science Advances

Unveiling Cancer Metabolism through Spontaneous and Coherent Raman Spectroscopy and Stable Isotope Probing

(2021) Jiabao Xu et al.   Cancers

PsiNorm: a scalable normalization for single-cell RNA-seq data

(2021) Matteo Borella et al.   BIOINFORMATICS

From bench to bedside: Single-cell analysis for cancer immunotherapy

(2021) Emily F. Davis-Marcisak et al.   CANCER CELL

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Exploring tissue architecture using spatial transcriptomics

(2021) Anjali Rao et al.   NATURE

A single-cell and spatially resolved atlas of human breast cancers

(2021) Sunny Z. Wu et al.   NATURE GENETICS

The multiple myeloma microenvironment is defined by an inflammatory stromal cell landscape

(2021) Madelon M. E. de Jong et al.   NATURE IMMUNOLOGY

Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics

(2021) Sophia K. Longo et al.   NATURE REVIEWS GENETICS

Multi-omics integration in the age of million single-cell data

(2021) Zhen Miao et al.   Nature Reviews Nephrology

Single-cell analysis of ductal differentiation

(2021) Jason R. Pitarresi et al.   Nature Biomedical Engineering

Understanding the pathogenesis of infectious diseases by single-cell RNA sequencing

(2021) Wanqiu Huang et al.   Microbial Cell

Single-cell analyses reveal key immune cell subsets associated with response to PD-L1 blockade in triple-negative breast cancer

(2021) Yuanyuan Zhang et al.   CANCER CELL

The landscape of tumor cell states and ecosystems in diffuse large B cell lymphoma

(2021) Chloé B. Steen et al.   CANCER CELL

Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data

(2021) Duanchen Sun et al.   NATURE BIOTECHNOLOGY

Pan-cancer single-cell landscape of tumor-infiltrating T cells

(2021) Liangtao Zheng et al.   SCIENCE

A topology-preserving dimensionality reduction method for single-cell RNA-seq data using graph autoencoder

(2021) Zixiang Luo et al.   Scientific Reports

Predicting heterogeneity in clone-specific therapeutic vulnerabilities using single-cell transcriptomic signatures

(2021) Chayaporn Suphavilai et al.   Genome Medicine

Light Sheet Fluorescence Microscopy Illuminating Soft Matter

(2021) Ruilin You et al.   Frontiers in Physics

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

(2020) Mirjana Efremova et al.   Nature Protocols

Spatially Resolved Transcriptomes—Next Generation Tools for Tissue Exploration

(2020) Michaela Asp et al.   BIOESSAYS

Intratumor Heterogeneity: The Rosetta Stone of Therapy Resistance

(2020) Andriy Marusyk et al.   CANCER CELL

Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis

(2020) Katerina Rohlenova et al.   Cell Metabolism

Multiplex digital spatial profiling of proteins and RNA in fixed tissue

(2020) Christopher R. Merritt et al.   NATURE BIOTECHNOLOGY

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

(2020) Michal Slyper et al.   NATURE MEDICINE

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

(2020) David T. Paik et al.   Nature Reviews Cardiology

Single-cell resolution analysis of the human pancreatic ductal progenitor cell niche

(2020) Mirza Muhammad Fahd Qadir et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Cell RNA Sequencing Reveals a Dynamic Stromal Niche That Supports Tumor Growth

(2020) Sarah Davidson et al.   Cell Reports

The Comparison of two Single-cell Sequencing Platforms: BD Rhapsody and 10x Genomics Chrominum

(2020) Caixia Gao et al.   CURRENT GENOMICS

A single-cell Raman-based platform to identify developmental stages of human pluripotent stem cell-derived neurons

(2020) Chia-Chen Hsu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell multiomics: technologies and data analysis methods

(2020) Jeongwoo Lee et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and therapeutic mechanism of action

(2020) James M. McFarland et al.   Nature Communications

Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data

(2019) Tianyu Wang et al.   BMC BIOINFORMATICS

Bulk tissue cell type deconvolution with multi-subject single-cell expression reference

(2019) Xuran Wang et al.   Nature Communications

Modeling genotypes in their microenvironment to predict single- and multi-cellular behavior

(2019) Dimitrios Voukantsis et al.   GigaScience

Multimodal Single-Cell Analysis Reveals Physiological Maturation in the Developing Human Neocortex

(2019) Simone Mayer et al.   NEURON

Integrative single-cell analysis

(2019) Tim Stuart et al.   NATURE REVIEWS GENETICS

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia

(2019) Federico Gaiti et al.   NATURE

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Dissecting intratumoral myeloid cell plasticity by single cell RNA‐seq

(2019) Qianqian Song et al.   Cancer Medicine

An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma

(2019) Cyril Neftel et al.   CELL

Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression

(2019) Chenglong Xia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping human cell phenotypes to genotypes with single-cell genomics

(2019) J. Gray Camp et al.   SCIENCE

NicheNet: modeling intercellular communication by linking ligands to target genes

(2019) Robin Browaeys et al.   NATURE METHODS

DEsingle for detecting three types of differential expression in single-cell RNA-seq data

(2018) Zhun Miao et al.   BIOINFORMATICS

How to design a single-cell RNA-sequencing experiment: pitfalls, challenges and perspectives

(2018) Alessandra Dal Molin et al.   BRIEFINGS IN BIOINFORMATICS

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

(2018) Elham Azizi et al.   CELL

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Simultaneous lineage tracing and cell-type identification using CRISPR–Cas9-induced genetic scars

(2018) Bastiaan Spanjaard et al.   NATURE BIOTECHNOLOGY

Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis

(2018) Peter Savas et al.   NATURE MEDICINE

Phenotype molding of stromal cells in the lung tumor microenvironment

(2018) Diether Lambrechts et al.   NATURE MEDICINE

Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq

(2018) Mariella G. Filbin et al.   SCIENCE

Clustering trees: a visualisation for evaluating clusterings at multiple resolutions

(2018) Luke Zappia et al.   GigaScience

A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte

(2018) Lindsey W. Plasschaert et al.   NATURE

A revised airway epithelial hierarchy includes CFTR-expressing ionocytes

(2018) Daniel T. Montoro et al.   NATURE

Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq

(2018) Mihriban Karaayvaz et al.   Nature Communications

Tutorial: guidelines for the experimental design of single-cell RNA sequencing studies

(2018) Atefeh Lafzi et al.   Nature Protocols

Spatially and functionally distinct subclasses of breast cancer-associated fibroblasts revealed by single cell RNA sequencing

(2018) Michael Bartoschek et al.   Nature Communications

A Single-Cell Sequencing Guide for Immunologists

(2018) Peter See et al.   Frontiers in Immunology

Computational approaches for interpreting scRNA-seq data

(2017) Raghd Rostom et al.   FEBS LETTERS

Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia

(2017) Lili Wang et al.   GENOME RESEARCH

The Human Cell Atlas: from vision to reality

(2017) Orit Rozenblatt-Rosen et al.   NATURE

Multiplexed quantification of proteins and transcripts in single cells

(2017) Vanessa M Peterson et al.   NATURE BIOTECHNOLOGY

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

SCnorm: robust normalization of single-cell RNA-seq data

(2017) Rhonda Bacher et al.   NATURE METHODS

SC3: consensus clustering of single-cell RNA-seq data

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

Accounting for technical noise in differential expression analysis of single-cell RNA sequencing data

(2017) Cheng Jia et al.   NUCLEIC ACIDS RESEARCH

Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq

(2017) Andrew S. Venteicher et al.   SCIENCE

Nanogrid single-nucleus RNA sequencing reveals phenotypic diversity in breast cancer

(2017) Ruli Gao et al.   Nature Communications

Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer

(2017) Woosung Chung et al.   Nature Communications

Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma

(2017) Spyros Darmanis et al.   Cell Reports

A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications

(2017) Ashraful Haque et al.   Genome Medicine

densityCut: an efficient and versatile topological approach for automatic clustering of biological data

(2016) Jiarui Ding et al.   BIOINFORMATICS

RNA Sequencing of Single Human Islet Cells Reveals Type 2 Diabetes Genes

(2016) Yurong Xin et al.   Cell Metabolism

Single-cell barcoding and sequencing using droplet microfluidics

(2016) Rapolas Zilionis et al.   Nature Protocols

Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes

(2016) Mark-Anthony Bray et al.   Nature Protocols

EMDomics: a robust and powerful method for the identification of genes differentially expressed between heterogeneous classes

(2015) Sheida Nabavi et al.   BIOINFORMATICS

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

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

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

An assessment of computational methods for estimating purity and clonality using genomic data derived from heterogeneous tumor tissue samples

(2014) V. K. Yadav et al.   BRIEFINGS IN BIOINFORMATICS

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

Learning subgroup-specific regulatory interactions and regulator independence with PARADIGM

(2013) Andrew J. Sedgewick et al.   BIOINFORMATICS

Inferring tumour purity and stromal and immune cell admixture from expression data

(2013) Kosuke Yoshihara et al.   Nature Communications

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT