A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

Circular Intronic Long Noncoding RNAs

(2013) Yang Zhang et al.   MOLECULAR CELL

Natural RNA circles function as efficient microRNA sponges

(2013) Thomas B. Hansen et al.   NATURE

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The p53 isoforms are differentially modified by Mdm2

(2012) Suzanne Camus et al.   CELL CYCLE

Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts

(2012) M. Frenkel-Morgenstern et al.   GENOME RESEARCH

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Circular RNAs are abundant, conserved, and associated with ALU repeats

(2012) W. R. Jeck et al.   RNA

A novel and well-defined benchmarking method for second generation read mapping

(2011) Manuel Holtgrewe et al.   BMC BIOINFORMATICS

Stearoyl CoA desaturase (SCD) facilitates proliferation of prostate cancer cells through enhancement of androgen receptor transactivation

(2011) Seung-Jin Kim et al.   MOLECULES AND CELLS

Transcriptome-wide discovery of circular RNAs in Archaea

(2011) Miri Danan et al.   NUCLEIC ACIDS RESEARCH

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

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

A global analysis of C. elegans trans-splicing

(2010) M. A. Allen et al.   GENOME RESEARCH

Integrative analysis of the melanoma transcriptome

(2010) M. F. Berger et al.   GENOME RESEARCH

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

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

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Massively parallel sequencing of the polyadenylated transcriptome of C. elegans

(2009) L. W. Hillier et al.   GENOME RESEARCH

Implications of chimaeric non-co-linear transcripts

(2009) Thomas R. Gingeras   NATURE

ASTD: The Alternative Splicing and Transcript Diversity database

(2008) Gautier Koscielny et al.   GENOMICS