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

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain

(2018) Kristofer Davie et al.   CELL

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

Comprehensive Identification and Spatial Mapping of Habenular Neuronal Types Using Single-Cell RNA-Seq

(2018) Shristi Pandey et al.   CURRENT BIOLOGY

Cell type discovery using single-cell transcriptomics: implications for ontological representation

(2018) Brian D Aevermann et al.   HUMAN MOLECULAR GENETICS

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

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

Identification of spatial expression trends in single-cell gene expression data

(2018) Daniel Edsgärd et al.   NATURE METHODS

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

(2018) Vladimir Yu Kiselev et al.   NATURE METHODS

CellAtlasSearch: a scalable search engine for single cells

(2018) Divyanshu Srivastava et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Megan Crow et al.   Nature Communications

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

(2018) Lindsey W. Plasschaert et al.   NATURE

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

(2018) Darren A. Cusanovich et al.   NATURE

A revised airway epithelial hierarchy includes CFTR-expressing ionocytes

(2018) Daniel T. Montoro et al.   NATURE

Author Correction: Bi-directional cell-pericellular matrix interactions direct stem cell fate

(2018) Silvia A. Ferreira et al.   Nature Communications

The Human Cell Atlas: from vision to reality

(2017) Orit Rozenblatt-Rosen et al.   NATURE

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Normalizing single-cell RNA sequencing data: challenges and opportunities

(2017) Catalina A Vallejos et al.   NATURE METHODS

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning

(2017) Bo Wang et al.   NATURE METHODS

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

Detecting Activated Cell Populations Using Single-Cell RNA-Seq

(2017) Ye Emily Wu et al.   NEURON

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

(2017) Alexandra-Chloé Villani et al.   SCIENCE

Single-Cell Multiomics: Multiple Measurements from Single Cells

(2017) Iain C. Macaulay et al.   TRENDS IN GENETICS

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

(2017) Ashraful Haque et al.   Genome Medicine

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

(2016) Yurong Xin et al.   Cell Metabolism

Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes

(2016) Åsa Segerstolpe et al.   Cell Metabolism

De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

(2016) Dominic Grün et al.   Cell Stem Cell

Single-Cell Transcriptomics of the Human Endocrine Pancreas

(2016) Yue J. Wang et al.   DIABETES

Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma

(2016) Itay Tirosh et al.   NATURE

Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis

(2016) Jean Fan et al.   NATURE METHODS

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

(2016) Bosiljka Tasic et al.   NATURE NEUROSCIENCE

In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus

(2016) Sheel Shah et al.   NEURON

Multi-Omics of Single Cells: Strategies and Applications

(2016) Christoph Bock et al.   TRENDS IN BIOTECHNOLOGY

A Single-Cell Transcriptome Atlas of the Human Pancreas

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

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

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

(2015) Chen Xu et al.   BIOINFORMATICS

destiny: diffusion maps for large-scale single-cell data in R

(2015) Philipp Angerer et al.   BIOINFORMATICS

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

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

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

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

Computational assignment of cell-cycle stage from single-cell transcriptome data

(2015) Antonio Scialdone et al.   METHODS

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

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

(2015) A. Zeisel et al.   SCIENCE

RNA-seq: impact of RNA degradation on transcript quantification

(2014) Irene Gallego Romero et al.   BMC BIOLOGY

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

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

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

(2014) Q. Deng et al.   SCIENCE

Overlapping community detection in networks

(2013) Jierui Xie et al.   ACM COMPUTING SURVEYS

Latent Enhancers Activated by Stimulation in Differentiated Cells

(2013) Renato Ostuni et al.   CELL

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

Soft clustering – Fuzzy and rough approaches and their extensions and derivatives

(2012) Georg Peters et al.   INTERNATIONAL JOURNAL OF APPROXIMATE REASONING

Logical Development of the Cell Ontology

(2011) Terrence F Meehan et al.   BMC BIOINFORMATICS

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

RNAscope

(2011) Fay Wang et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Data clustering: 50 years beyond K-means

(2009) Anil K. Jain   PATTERN RECOGNITION LETTERS

Community detection algorithms: A comparative analysis

(2009) Andrea Lancichinetti et al.   PHYSICAL REVIEW E

Fast unfolding of communities in large networks

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