Power analysis of single-cell RNA-sequencing experiments

Stan: A Probabilistic Programming Language

(2017) Bob Carpenter et al.   Journal of Statistical Software

RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes

(2016) Avi Srivastava et al.   BIOINFORMATICS

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development

(2016) Nick D.L. Owens et al.   Cell Reports

The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells

(2015) Fan Guo et al.   CELL

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

(2015) Allon M. Klein et al.   CELL

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

(2015) Franziska Paul et al.   CELL

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

(2015) Evan Z. Macosko et al.   CELL

Single-Cell Transcriptomics Reveals a Population of Dormant Neural Stem Cells that Become Activated upon Brain Injury

(2015) Enric Llorens-Bobadilla et al.   Cell Stem Cell

Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations

(2015) Nicola K. Wilson et al.   Cell Stem Cell

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

(2015) Antonio Scialdone et al.   METHODS

Single Mammalian Cells Compensate for Differences in Cellular Volume and DNA Copy Number through Independent Global Transcriptional Mechanisms

(2015) Olivia Padovan-Merhar et al.   MOLECULAR CELL

Single-cell polyadenylation site mapping reveals 3' isoform choice variability

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

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

Single-cell transcriptome analysis reveals coordinated ectopic gene-expression patterns in medullary thymic epithelial cells

(2015) Philip Brennecke et al.   NATURE IMMUNOLOGY

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

(2015) Iain C Macaulay et al.   NATURE METHODS

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

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

(2015) A. Zeisel 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

Population and single-cell genomics reveal theAiredependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia

(2014) Stephen N. Sansom 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

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

(2014)   NATURE BIOTECHNOLOGY

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

Silencing of Odorant Receptor Genes by G Protein βγ Signaling Ensures the Expression of One Odorant Receptor per Olfactory Sensory Neuron

(2014) Todd Ferreira et al.   NEURON

Microfluidic single-cell whole-transcriptome sequencing

(2014) A. M. Streets et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) D. A. Jaitin et al.   SCIENCE

Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures

(2014) Sarah A. Munro et al.   Nature Communications

Single-Cell RNA Sequencing Reveals T Helper Cells Synthesizing Steroids De Novo to Contribute to Immune Homeostasis

(2014) Bidesh Mahata et al.   Cell Reports

Single Cell Genomics: Advances and Future Perspectives

(2014) Iain C. Macaulay et al.   PLoS Genetics

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

Quantitative assessment of single-cell RNA-sequencing methods

(2013) Angela R Wu et al.   NATURE METHODS

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

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

(2012) Tamar Hashimshony et al.   Cell Reports

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

Incorporation of non-natural nucleotides into template-switching oligonucleotides reduces background and improves cDNA synthesis from very small RNA samples

(2010) Jeremy Kapteyn et al.   BMC GENOMICS

Understanding Equivalence and Noninferiority Testing

(2010) Esteban Walker et al.   JOURNAL OF GENERAL INTERNAL MEDICINE

Molecular dissection of mRNA poly(A) tail length control in yeast

(2008) Nicolas Viphakone et al.   NUCLEIC ACIDS RESEARCH