scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets

From a common progenitor to distinct liver epithelial phenotypes

(2018) Anne Müsch   CURRENT OPINION IN CELL BIOLOGY

Integrated analysis of single-cell embryo data yields a unified transcriptome signature for the human pre-implantation epiblast

(2018) Giuliano G. Stirparo et al.   DEVELOPMENT

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

RLE plots: Visualizing unwanted variation in high dimensional data

(2018) Luke C. Gandolfo et al.   PLoS One

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

Impact of similarity metrics on single-cell RNA-seq data clustering

(2018) Taiyun Kim et al.   BRIEFINGS IN BIOINFORMATICS

A single-cell transcriptomic analysis reveals precise pathways and regulatory mechanisms underlying hepatoblast differentiation

(2017) Li Yang et al.   HEPATOLOGY

Multilineage communication regulates human liver bud development from pluripotency

(2017) J. Gray Camp et al.   NATURE

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

(2017) Rhonda Bacher et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Integrated single cell data analysis reveals cell specific networks and novel coactivation markers

(2016) Shila Ghazanfar et al.   BMC Systems Biology

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

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

Single-Cell Transcriptomics of the Human Endocrine Pancreas

(2016) Yue J. Wang et al.   DIABETES

Single-cell transcriptomes identify human islet cell signatures and reveal cell-type–specific expression changes in type 2 diabetes

(2016) Nathan Lawlor et al.   GENOME RESEARCH

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

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

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

Defining the three cell lineages of the human blastocyst by single-cell RNA-seq

(2015) Paul Blakeley et al.   DEVELOPMENT

Olfactory sensory neurons transiently express multiple olfactory receptors during development

(2015) L. Tan et al.   Molecular Systems Biology

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis

(2015) N. K. Hanchate et al.   SCIENCE

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

(2015) Xiaoying Fan et al.   GENOME BIOLOGY

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

(2014) S. Anders et al.   BIOINFORMATICS

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

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

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

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

(2014) D. A. Jaitin et al.   SCIENCE

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

(2013) Zhigang Xue et al.   NATURE

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

(2013) Philip Brennecke et al.   NATURE METHODS

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

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

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Using control genes to correct for unwanted variation in microarray data

(2011) J. A. Gagnon-Bartsch et al.   BIOSTATISTICS

Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics

(2011) D. M. Suter et al.   SCIENCE

Finding Structure with Randomness: Probabilistic Algorithms for Constructing Approximate Matrix Decompositions

(2011) N. Halko et al.   SIAM REVIEW

Making the blastocyst: lessons from the mouse

(2010) Katie Cockburn et al.   JOURNAL OF CLINICAL INVESTIGATION

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS