Comparison of methods to detect differentially expressed genes between single-cell populations

The heterogeneity of human CD127+ innate lymphoid cells revealed by single-cell RNA sequencing

(2016) Åsa K Björklund et al.   NATURE IMMUNOLOGY

Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells

(2015) Monika S. Kowalczyk et al.   GENOME RESEARCH

Optimization of Statistical Methods Impact on Quantitative Proteomics Data

(2015) Anna Pursiheimo et al.   JOURNAL OF PROTEOME RESEARCH

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

ROTS: reproducible RNA-seq biomarker detector—prognostic markers for clear cell renal cell cancer

(2015) Fatemeh Seyednasrollah et al.   NUCLEIC ACIDS RESEARCH

De novo assembly of bacterial transcriptomes from RNA-seq data

(2015) Brian Tjaden   GENOME BIOLOGY

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Comparison of software packages for detecting differential expression in RNA-seq studies

(2013) F. Seyednasrollah et al.   BRIEFINGS IN BIOINFORMATICS

Entering the era of single-cell transcriptomics in biology and medicine

(2013) Rickard Sandberg   NATURE METHODS

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

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

(2013) Franck Rapaport et al.   GENOME BIOLOGY

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

(2011) S. Islam et al.   GENOME RESEARCH

A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies

(2011) Wenyu Zhang et al.   PLoS One

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

RNA-Seq gene expression estimation with read mapping uncertainty

(2009) Bo Li et al.   BIOINFORMATICS

Reproducibility-Optimized Test Statistic for Ranking Genes in Microarray Studies

(2008) L.L. Elo et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Mouse Embryonic Stem Cell-Derived Spheres with Distinct Neurogenic Potentials

(2008) Annalena Moliner et al.   STEM CELLS AND DEVELOPMENT