Discrete distributional differential expression (D3E) - a tool for gene expression analysis of single-cell RNA-seq data

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

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

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

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

(2014) Davide Risso 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

SnapShot-Seq: A Method for Extracting Genome-Wide, In Vivo mRNA Dynamics from a Single Total RNA Sample

(2014) Jesse M. Gray et al.   PLoS One

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

(2014) Q. Deng et al.   SCIENCE

Single-cell gene expression analysis reveals genetic associations masked in whole-tissue experiments

(2013) Quin F Wills et al.   NATURE BIOTECHNOLOGY

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

(2013) Philip Brennecke et al.   NATURE METHODS

Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data

(2013) Jong Kim et al.   GENOME BIOLOGY

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

(2013) Franck Rapaport et al.   GENOME BIOLOGY

Modeling RNA degradation for RNA-Seq with applications

(2012) L. Wan et al.   BIOSTATISTICS

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

On the spontaneous stochastic dynamics of a single gene: complexity of the molecular interplay at the promoter

(2010) Antoine Coulon et al.   BMC Systems Biology

Digital nature of the immediate-early transcriptional response

(2010) M. Stevense et al.   DEVELOPMENT

Variability in gene expression underlies incomplete penetrance

(2010) Arjun Raj et al.   NATURE

Single-allele analysis of transcription kinetics in living mammalian cells

(2010) Sharon Yunger et al.   NATURE METHODS

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

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

Quantification of mRNA in single cells and modelling of RT-qPCR induced noise

(2008) Martin Bengtsson et al.   BMC MOLECULAR BIOLOGY

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

(2008) Arjun Raj et al.   CELL

Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells

(2008) L. V. Sharova et al.   DNA RESEARCH