MetaDiff: differential isoform expression analysis using random-effects meta-regression

SMYD Proteins: Key Regulators in Skeletal and Cardiac Muscle Development and Function

(2014) Shao Jun Du et al.   Anatomical Record-Advances in Integrative Anatomy and Evolutionary Biology

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

(2014) Q. Deng et al.   SCIENCE

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments

(2013) Ning Leng et al.   BIOINFORMATICS

Flexible analysis of RNA-seq data using mixed effects models

(2013) Ernest Turro et al.   BIOINFORMATICS

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution

(2013) Yu Hu et al.   NUCLEIC ACIDS RESEARCH

Gene expression changes with age in skin, adipose tissue, blood and brain

(2013) Daniel Glass et al.   GENOME BIOLOGY

Identifying differentially expressed transcripts from RNA-seq data with biological variation

(2012) Peter Glaus et al.   BIOINFORMATICS

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

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Modelling and simulating generic RNA-Seq experiments with the flux simulator

(2012) Thasso Griebel et al.   NUCLEIC ACIDS RESEARCH

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads

(2011) Ernest Turro et al.   GENOME BIOLOGY

Testing overall and moderator effects in random effects meta-regression

(2010) Hilde M. Huizenga et al.   BRITISH JOURNAL OF MATHEMATICAL & STATISTICAL PSYCHOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation

(2008) Luis López-Maury et al.   NATURE REVIEWS GENETICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS