Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data

Discovery and Classification of Fusion Transcripts in Prostate Cancer and Normal Prostate Tissue

(2015) Jian-Hua Luo et al.   AMERICAN JOURNAL OF PATHOLOGY

Functional inflammatory profiles distinguish myelin-reactive T cells from patients with multiple sclerosis

(2015) Yonghao Cao et al.   Science Translational Medicine

Proteome- and Transcriptome-Driven Reconstruction of the Human Myocyte Metabolic Network and Its Use for Identification of Markers for Diabetes

(2015) Leif Väremo et al.   Cell Reports

JAFFA: High sensitivity transcriptome-focused fusion gene detection

(2015) Nadia M Davidson et al.   Genome Medicine

Novel Fusion Transcripts Associate with Progressive Prostate Cancer

(2014) Yan P. Yu et al.   AMERICAN JOURNAL OF PATHOLOGY

Chimera: a Bioconductor package for secondary analysis of fusion products

(2014) Marco Beccuti et al.   BIOINFORMATICS

PRADA: pipeline for RNA sequencing data analysis

(2014) Wandaliz Torres-García et al.   BIOINFORMATICS

Open-access synthetic spike-in mRNA-seq data for cancer gene fusions

(2014) Waibhav D Tembe et al.   BMC GENOMICS

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

ChiTaRS 2.1—an improved database of the chimeric transcripts and RNA-seq data with novel sense–antisense chimeric RNA transcripts

(2014) Milana Frenkel-Morgenstern et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Chenglin Liu et al.   BMC BIOINFORMATICS

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

BreakTrans: uncovering the genomic architecture of gene fusions

(2013) Ken Chen et al.   GENOME BIOLOGY

Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript

(2012) Matteo Benelli et al.   BIOINFORMATICS

BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data

(2012) K. Chen et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin 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

Evidence of a Functional Estrogen Receptor in Parathyroid Adenomas

(2012) Felix Haglund et al.   JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

DNA methylome analysis using short bisulfite sequencing data

(2012) Felix Krueger et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data

(2012) Milana Frenkel-Morgenstern et al.   NUCLEIC ACIDS RESEARCH

RNA-seq Reveals Novel Transcriptome of Genes and Their Isoforms in Human Pulmonary Microvascular Endothelial Cells Treated with Thrombin

(2012) Li Qin Zhang et al.   PLoS One

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

Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs

(2011) Marcus Kinsella et al.   BIOINFORMATICS

Comparative analysis of algorithms for next-generation sequencing read alignment

(2011) M. Ruffalo et al.   BIOINFORMATICS

FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq

(2011) Yang Li et al.   BIOINFORMATICS

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

(2011) Huanying Ge et al.   BIOINFORMATICS

ChimeraScan: a tool for identifying chimeric transcription in sequencing data

(2011) Matthew K. Iyer et al.   BIOINFORMATICS

Mapping copy number variation by population-scale genome sequencing

(2011) Ryan E. Mills et al.   NATURE

A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines

(2011) Yan W. Asmann et al.   NUCLEIC ACIDS 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

Integrative analysis of the melanoma transcriptome

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

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

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

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Mutation-associated fusion cancer genes in solid tumors

(2009) F. J. Kaye   MOLECULAR CANCER THERAPEUTICS

Implications of chimaeric non-co-linear transcripts

(2009) Thomas R. Gingeras   NATURE

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

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH