OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds

PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data

(2012) Yanju Zhang et al.   BIOINFORMATICS

TrueSight: a new algorithm for splice junction detection using RNA-seq

(2012) Yang Li et al.   NUCLEIC ACIDS RESEARCH

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data

(2011) Songbo Huang et al.   Frontiers in Genetics

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Expansion of the eukaryotic proteome by alternative splicing

(2010) Timothy W. Nilsen et al.   NATURE

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

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

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

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

Integrative Modeling Defines the Nova Splicing-Regulatory Network and Its Combinatorial Controls

(2010) C. Zhang et al.   SCIENCE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

RNA and Disease

(2009) Thomas A. Cooper et al.   CELL

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines

(2008) John C Castle 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

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS