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

MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data

(2012) Shihao Shen et al.   NUCLEIC ACIDS RESEARCH

FDM: a graph-based statistical method to detect differential transcription using RNA-seq data

(2011) Darshan Singh et al.   BIOINFORMATICS

SpliceTrap: a method to quantify alternative splicing under single cellular conditions

(2011) Jie Wu et al.   BIOINFORMATICS

CD44 splice isoform switching in human and mouse epithelium is essential for epithelial-mesenchymal transition and breast cancer progression

(2011) Rhonda L. Brown et al.   JOURNAL OF CLINICAL INVESTIGATION

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

A probabilistic framework for aligning paired-end RNA-seq data

(2010) Yin Hu et al.   BIOINFORMATICS

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Alternative expression analysis by RNA sequencing

(2010) Malachi Griffith et al.   NATURE METHODS

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

Detection of splice junctions from paired-end RNA-seq data by SpliceMap

(2010) K. F. Au et al.   NUCLEIC ACIDS RESEARCH

A two-parameter generalized Poisson model to improve the analysis of RNA-seq data

(2010) Sudeep Srivastava et al.   NUCLEIC ACIDS RESEARCH

rQuant.web: a tool for RNA-Seq-based transcript quantitation

(2010) R. Bohnert et al.   NUCLEIC ACIDS RESEARCH

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

Statistical inferences for isoform expression in RNA-Seq

(2009) Hui Jiang et al.   BIOINFORMATICS

De novo transcriptome assembly with ABySS

(2009) I. Birol et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

ErbB4 Splice Variants Cyt1 and Cyt2 Differ by 16 Amino Acids and Exert Opposing Effects on the Mammary Epithelium In Vivo

(2009) R. S. Muraoka-Cook et al.   MOLECULAR AND CELLULAR BIOLOGY

Sequence-non-specific effects of RNA interference triggers and microRNA regulators

(2009) Marta Olejniczak et al.   NUCLEIC ACIDS RESEARCH

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Genome-wide analysis of transcript isoform variation in humans

(2008) Tony Kwan et al.   NATURE GENETICS

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Whole genome exon arrays identify differential expression of alternatively spliced, cancer-related genes in lung cancer

(2008) Liqiang Xi et al.   NUCLEIC ACIDS RESEARCH

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

(2008) M. Sultan et al.   SCIENCE

Comprehensive Analysis of Affymetrix Exon Arrays Using BioConductor

(2008) Michał J Okoniewski et al.   PLoS Computational Biology