CRAC: an integrated approach to the analysis of RNA-seq reads

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Thasso Griebel et al.   NUCLEIC ACIDS RESEARCH

Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant

(2011) H. H. Al-Balool et al.   GENOME RESEARCH

Mechanistic Control of Carcinoembryonic Antigen-related Cell Adhesion Molecule-1 (CEACAM1) Splice Isoforms by the Heterogeneous Nuclear Ribonuclear Proteins hnRNP L, hnRNP A1, and hnRNP M

(2011) Kenneth J. Dery et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing

(2011) K. Kannan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of fusion genes in breast cancer by paired-end RNA-sequencing

(2011) Henrik Edgren et al.   GENOME BIOLOGY

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

(2011) Daehwan Kim et al.   GENOME BIOLOGY

GASSST: global alignment short sequence search tool

(2010) Guillaume Rizk et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

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

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

Heat Shock Protein 60 Regulation of the Mitochondrial Permeability Transition Pore in Tumor Cells

(2010) J. C. Ghosh et al.   CANCER RESEARCH

Diverse somatic mutation patterns and pathway alterations in human cancers

(2010) Zhengyan Kan et al.   NATURE

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Advances in understanding cancer genomes through second-generation sequencing

(2010) Matthew Meyerson et al.   NATURE REVIEWS GENETICS

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

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

Apparent Non-Canonical Trans-Splicing Is Generated by Reverse Transcriptase In Vitro

(2010) Jonathan Houseley et al.   PLoS One

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

Commonality but Diversity in Cancer Gene Fusions

(2009) Terence H. Rabbitts   CELL

Transcriptome sequencing to detect gene fusions in cancer

(2009) Christopher A. Maher et al.   NATURE

Implications of chimaeric non-co-linear transcripts

(2009) Thomas R. Gingeras   NATURE

Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity

(2009) Nicolas Philippe et al.   NUCLEIC ACIDS RESEARCH

Chimeric transcript discovery by paired-end transcriptome sequencing

(2009) C. A. Maher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

A Neoplastic Gene Fusion Mimics Trans-Splicing of RNAs in Normal Human Cells

(2008) H. Li et al.   SCIENCE