Comparative study of bioinformatic tools for the identification of chimeric RNAs from RNA Sequencing

The landscape of chimeric RNAs in non-diseased tissues and cells

(2020) Sandeep Singh et al.   NUCLEIC ACIDS RESEARCH

The landscape of chimeric RNAs in bladder urothelial carcinoma

(2019) Dingjun Zhu et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

ChiTaRS 5.0: the comprehensive database of chimeric transcripts matched with druggable fusions and 3D chromatin maps

(2019) Deepak Balamurali et al.   NUCLEIC ACIDS RESEARCH

STAR Chimeric Post for rapid detection of circular RNA and fusion transcripts

(2018) Nicholas K Akers et al.   BIOINFORMATICS

A fast detection of fusion genes from paired-end RNA-seq data

(2018) Trung Nghia Vu et al.   BMC GENOMICS

The Landscape and Implications of Chimeric RNAs in Cervical Cancer

(2018) Peng Wu et al.   EBioMedicine

ChimeRScope: a novel alignment-free algorithm for fusion transcript prediction using paired-end RNA-Seq data

(2017) You Li et al.   NUCLEIC ACIDS RESEARCH

GFusion: an Effective Algorithm to Identify Fusion Genes from Cancer RNA-Seq Data

(2017) Jian Zhao et al.   Scientific Reports

Chimeric RNAs in cancer and normal physiology

(2017) Katarzyna Chwalenia et al.   Wiley Interdisciplinary Reviews-RNA

confFuse: High-Confidence Fusion Gene Detection across Tumor Entities

(2017) Zhiqin Huang et al.   Frontiers in Genetics

Recurrent chimeric fusion RNAs in non-cancer tissues and cells

(2016) Mihaela Babiceanu et al.   NUCLEIC ACIDS RESEARCH

Identifying fusion transcripts using next generation sequencing

(2016) Shailesh Kumar et al.   Wiley Interdisciplinary Reviews-RNA

InFusion: Advancing Discovery of Fusion Genes and Chimeric Transcripts from Deep RNA-Sequencing Data

(2016) Konstantin Okonechnikov et al.   PLoS One

Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data

(2016) Shailesh Kumar et al.   Scientific Reports

INTEGRATE: gene fusion discovery using whole genome and transcriptome data

(2015) Jin Zhang et al.   GENOME RESEARCH

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

(2015) Silvia Liu et al.   NUCLEIC ACIDS RESEARCH

JAFFA: High sensitivity transcriptome-focused fusion gene detection

(2015) Nadia M Davidson et al.   Genome Medicine

Discovery of CTCF-Sensitive Cis-Spliced Fusion RNAs between Adjacent Genes in Human Prostate Cells

(2015) Fujun Qin et al.   PLoS Genetics

A novel transcript,VNN1-AB, as a biomarker for colorectal cancer

(2014) Marthe Løvf et al.   INTERNATIONAL JOURNAL OF CANCER

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

Transcription-Mediated Chimeric RNAs in Prostate Cancer: Time to Revisit Old Hypothesis?

(2014) Guoping Ren et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

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

(2013) Matteo Carrara et al.   BMC BIOINFORMATICS

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

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

A Chimeric RNA Characteristic of Rhabdomyosarcoma in Normal Myogenesis Process

(2013) H. Yuan et al.   Cancer Discovery

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

(2013) Wenlong Jia et al.   GENOME BIOLOGY

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

(2012) Matteo Benelli et al.   BIOINFORMATICS

Detection of Redundant Fusion Transcripts as Biomarkers or Disease-Specific Therapeutic Targets in Breast Cancer

(2012) Y. W. Asmann et al.   CANCER RESEARCH

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

FusionFinder: A Software Tool to Identify Expressed Gene Fusion Candidates from RNA-Seq Data

(2012) Richard W. Francis et al.   PLoS One

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

(2012) Sara Kangaspeska et al.   PLoS One

Chimeric Transcript Generated by cis-Splicing of Adjacent Genes Regulates Prostate Cancer Cell Proliferation

(2012) Yanmei Zhang et al.   Cancer Discovery

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

ChimeraScan: a tool for identifying chimeric transcription in sequencing data

(2011) Matthew K. Iyer et al.   BIOINFORMATICS

Gene fusions and RNA trans-splicing in normal and neoplastic human cells

(2011) Hui Li et al.   CELL CYCLE

Transcriptional consequences of genomic structural aberrations in breast cancer

(2011) K. Inaki et al.   GENOME RESEARCH

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

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

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

TFG, a target of chromosome translocations in lymphoma and soft tissue tumors, fuses to GPR128 in healthy individuals

(2009) A. Chase et al.   HAEMATOLOGICA

Transcriptome sequencing to detect gene fusions in cancer

(2009) Christopher A. Maher et al.   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