JAFFA: High sensitivity transcriptome-focused fusion gene detection

RNA-seq of 272 gliomas revealed a novel, recurrentPTPRZ1-METfusion transcript in secondary glioblastomas

(2014) Zhao-Shi Bao et al.   GENOME RESEARCH

Assessment of the Impact of Using a Reference Transcriptome in Mapping Short RNA-Seq Reads

(2014) Shanrong Zhao   PLoS One

FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq

(2013) Chenglin Liu et al.   BMC BIOINFORMATICS

State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues?

(2013) Matteo Carrara et al.   BMC BIOINFORMATICS

Optimizing de novo assembly of short-read RNA-seq data for phylogenomics

(2013) Ya Yang et al.   BMC GENOMICS

Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency

(2013) C.-S. Wu et al.   GENOME RESEARCH

Identification of recurrentFGFR3fusion genes in lung cancer through kinome-centred RNA sequencing

(2013) Ian J Majewski et al.   JOURNAL OF PATHOLOGY

Systematic evaluation of spliced alignment programs for RNA-seq data

(2013) Pär G Engström et al.   NATURE METHODS

State-of-the-Art Fusion-Finder Algorithms Sensitivity and Specificity

(2013) Matteo Carrara et al.   Biomed Research International

SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data

(2013) Wenlong Jia et al.   GENOME BIOLOGY

Bpipe: a tool for running and managing bioinformatics pipelines

(2012) Simon P. Sadedin et al.   BIOINFORMATICS

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives

(2012) Q. Wang et al.   BRIEFINGS IN BIOINFORMATICS

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

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

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Reanalysis of RNA-Sequencing Data Reveals Several Additional Fusion Genes with Multiple Isoforms

(2012) Sara Kangaspeska et al.   PLoS One

RNA-Seq Mapping and Detection of Gene Fusions with a Suffix Array Algorithm

(2012) Onur Sakarya et al.   PLoS Computational Biology

FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution

(2011) Huanying Ge et al.   BIOINFORMATICS

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples

(2011) Serban Nacu et al.   BMC Medical Genomics

Transcriptional consequences of genomic structural aberrations in breast cancer

(2011) K. Inaki et al.   GENOME RESEARCH

deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data

(2011) Andrew McPherson et al.   PLoS Computational Biology

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

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

(2010) Jonathan Houseley et al.   PLoS One

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

Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line

(2009) Qi Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Short Homologous Sequences Are Strongly Associated with the Generation of Chimeric RNAs in Eukaryotes

(2008) Xin Li et al.   JOURNAL OF MOLECULAR EVOLUTION