Detection of generic differential RNA processing events from RNA-seq data

Differential expression analysis of RNA-seq data at single-base resolution

(2014) A. C. Frazee et al.   BIOSTATISTICS

Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems

(2014) Ruolin Liu et al.   BMC BIOINFORMATICS

Long Noncoding RNA Modulates Alternative Splicing Regulators in Arabidopsis

(2014) Florian Bardou et al.   DEVELOPMENTAL CELL

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

(2013) Ning Leng et al.   BIOINFORMATICS

Accurate detection of differential RNA processing

(2013) Philipp Drewe et al.   NUCLEIC ACIDS RESEARCH

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

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

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

DiffSplice: the genome-wide detection of differential splicing events with RNA-seq

(2012) Yin Hu et al.   NUCLEIC ACIDS RESEARCH

Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis

(2012) P. Nicolas et al.   SCIENCE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Transcriptome genetics using second generation sequencing in a Caucasian population

(2010) Stephen B. Montgomery et al.   NATURE

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

(2009) S. A. Filichkin et al.   GENOME RESEARCH

Intronic noncoding RNAs and splicing

(2008) John W.S. Brown et al.   TRENDS IN PLANT SCIENCE