Single-cell RNA-seq clustering: datasets, models, and algorithms

A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications

(2019) He Peng et al.   PLoS Computational Biology

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

(2019) Katarína Tiklová et al.   Nature Communications

Fast interpolation-based t-SNE for improved visualization of single-cell RNA-seq data

(2019) George C. Linderman et al.   NATURE METHODS

Resolving Cell Fate Decisions during Somatic Cell Reprogramming by Single-Cell RNA-Seq

(2019) Lin Guo et al.   MOLECULAR CELL

Identification of Breast Cancer Stem Cell Related Genes Using Functional Cellular Assays Combined With Single-Cell RNA Sequencing in MDA-MB-231 Cells

(2019) Emma Jonasson et al.   Frontiers in Genetics

A computational method to aid the design and analysis of single cell RNA-seq experiments for cell type identification

(2019) Douglas Abrams et al.   BMC BIOINFORMATICS

Joint analysis of heterogeneous single-cell RNA-seq dataset collections

(2019) Nikolas Barkas et al.   NATURE METHODS

Stem cell differentiation trajectories in Hydra resolved at single-cell resolution

(2019) Stefan Siebert et al.   SCIENCE

Random forest based similarity learning for single cell RNA sequencing data

(2018) Maziyar Baran Pouyan et al.   BIOINFORMATICS

An interpretable framework for clustering single-cell RNA-Seq datasets

(2018) Jesse M. Zhang et al.   BMC BIOINFORMATICS

Mapping gene regulatory networks from single-cell omics data

(2018) Mark W E J Fiers et al.   Briefings in Functional Genomics

Single-Cell Transcriptomics Meets Lineage Tracing

(2018) Lennart Kester et al.   Cell Stem Cell

Single-cell analysis reveals cancer stem cell heterogeneity in hepatocellular carcinoma

(2018) Hongping Zheng et al.   HEPATOLOGY

Control of cell fraction and population recovery during tissue regeneration in stem cell lineages

(2018) Marissa Renardy et al.   JOURNAL OF THEORETICAL BIOLOGY

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain

(2018) Bushra Raj et al.   NATURE BIOTECHNOLOGY

Phenotype molding of stromal cells in the lung tumor microenvironment

(2018) Diether Lambrechts et al.   NATURE MEDICINE

SIMLR: A Tool for Large-Scale Genomic Analyses by Multi-Kernel Learning

(2018) Bo Wang et al.   PROTEOMICS

Single-Cell Multi-omics: An Engine for New Quantitative Models of Gene Regulation

(2018) Jonathan Packer et al.   TRENDS IN GENETICS

An accurate and robust imputation method scImpute for single-cell RNA-seq data

(2018) Wei Vivian Li et al.   Nature Communications

Profiling human breast epithelial cells using single cell RNA sequencing identifies cell diversity

(2018) Quy H. Nguyen et al.   Nature Communications

A general and flexible method for signal extraction from single-cell RNA-seq data

(2018) Davide Risso et al.   Nature Communications

A multitask clustering approach for single-cell RNA-seq analysis in Recessive Dystrophic Epidermolysis Bullosa

(2018) Huanan Zhang et al.   PLoS Computational Biology

Power in Numbers: Single-Cell RNA-Seq Strategies to Dissect Complex Tissues

(2018) Kenneth D. Birnbaum   Annual Review of Genetics

CellBIC: bimodality-based top-down clustering of single-cell RNA sequencing data reveals hierarchical structure of the cell type

(2018) Junil Kim et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Mihriban Karaayvaz et al.   Nature Communications

Single-cell RNA-Seq of lymphoma cancers reveals malignant B cell types and co-expression of T cell immune checkpoints

(2018) Noemi Andor et al.   BLOOD

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Developmental Heterogeneity of Microglia and Brain Myeloid Cells Revealed by Deep Single-Cell RNA Sequencing

(2018) Qingyun Li et al.   NEURON

Deconstructing Retinal Organoids: Single Cell RNA-Seq Reveals the Cellular Components of Human Pluripotent Stem Cell-Derived Retina

(2018) Joseph Collin et al.   STEM CELLS

Single cell RNA analysis identifies cellular heterogeneity and adaptive responses of the lung at birth

(2018) Minzhe Guo et al.   Nature Communications

Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations

(2018) Sonya A. MacParland et al.   Nature Communications

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

(2018) Michael Bartoschek 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

Analysis of Single-Cell RNA-Seq Identifies Cell-Cell Communication Associated with Tumor Characteristics

(2018) Manu P. Kumar et al.   Cell Reports

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

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

A molecular census of arcuate hypothalamus and median eminence cell types

(2017) John N Campbell et al.   NATURE NEUROSCIENCE

A sparse differential clustering algorithm for tracing cell type changes via single-cell RNA-sequencing data

(2017) Martin Barron et al.   NUCLEIC ACIDS RESEARCH

Using neural networks for reducing the dimensions of single-cell RNA-Seq data

(2017) Chieh Lin et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Alexandra-Chloé Villani et al.   SCIENCE

Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists

(2017) Xun Zhu et al.   Genome Medicine

pcaReduce: hierarchical clustering of single cell transcriptional profiles

(2016) Justina žurauskienė et al.   BMC BIOINFORMATICS

FastProject: a tool for low-dimensional analysis of single-cell RNA-Seq data

(2016) David DeTomaso et al.   BMC BIOINFORMATICS

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

(2016) Sophie Petropoulos et al.   CELL

Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos

(2016) Mubeen Goolam et al.   CELL

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

(2016) Karthik Shekhar et al.   CELL

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

(2016) Zhicheng Ji et al.   NUCLEIC ACIDS RESEARCH

Identification of cell types from single-cell transcriptomes using a novel clustering method

(2015) Chen Xu et al.   BIOINFORMATICS

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

(2015) Aleksandra A. Kolodziejczyk et al.   Cell Stem Cell

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

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

(2015) Minzhe Guo et al.   PLoS Computational Biology

Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos

(2015) Xiaoying Fan et al.   GENOME BIOLOGY

Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA sequencing

(2014) Fernando H. Biase et al.   GENOME RESEARCH

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein et al.   NATURE

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

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing

(2014) Dmitry Usoskin et al.   NATURE NEUROSCIENCE

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells

(2014) Q. Deng et al.   SCIENCE

Single-Cell RNA Sequencing Identifies Extracellular Matrix Gene Expression by Pancreatic Circulating Tumor Cells

(2014) David T. Ting et al.   Cell Reports

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

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