RNA-Seq Mapping and Detection of Gene Fusions with a Suffix Array Algorithm
Published 2012 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
RNA-Seq Mapping and Detection of Gene Fusions with a Suffix Array Algorithm
Authors
Keywords
-
Journal
PLoS Computational Biology
Volume 8, Issue 4, Pages e1002464
Publisher
Public Library of Science (PLoS)
Online
2012-04-06
DOI
10.1371/journal.pcbi.1002464
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- EML4-ALK Fusion Lung Cancer: A Rare Acquired Event
- (2015) Sven Perner et al. NEOPLASIA
- Estimation of alternative splicing isoform frequencies from RNA-Seq data
- (2011) Marius Nicolae et al. Algorithms for Molecular Biology
- Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs
- (2011) Marcus Kinsella et al. BIOINFORMATICS
- RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
- (2011) Bo Li et al. BMC BIOINFORMATICS
- Transcriptional consequences of genomic structural aberrations in breast cancer
- (2011) K. Inaki et al. GENOME RESEARCH
- 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
- 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
- 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
- A probabilistic framework for aligning paired-end RNA-seq data
- (2010) Yin Hu et al. BIOINFORMATICS
- MicroRNAs and Cellular Phenotypy
- (2010) Kenneth S. Kosik CELL
- Integrative analysis of the melanoma transcriptome
- (2010) M. F. Berger et al. GENOME RESEARCH
- Optimization of de novo transcriptome assembly from next-generation sequencing data
- (2010) Y. Surget-Groba 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
- Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
- (2010) Mitchell Guttman et al. NATURE BIOTECHNOLOGY
- Androgen-induced TOP2B-mediated double-strand breaks and prostate cancer gene rearrangements
- (2010) Michael C Haffner et al. NATURE GENETICS
- Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma
- (2010) Nallasivam Palanisamy et al. NATURE MEDICINE
- De novo assembly and analysis of RNA-seq data
- (2010) Gordon Robertson et al. NATURE METHODS
- Anaplastic Lymphoma Kinase Inhibition in Non–Small-Cell Lung Cancer
- (2010) Eunice L. Kwak et al. NEW ENGLAND JOURNAL OF MEDICINE
- Detection of splice junctions from paired-end RNA-seq data by SpliceMap
- (2010) K. F. Au et al. NUCLEIC ACIDS RESEARCH
- FusionSeq: a modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data
- (2010) Andrea Sboner et al. GENOME BIOLOGY
- Global and unbiased detection of splice junctions from RNA-seq data
- (2010) Adam Ameur et al. GENOME BIOLOGY
- RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data
- (2009) Nicole Cloonan et al. BIOINFORMATICS
- De novo transcriptome assembly with ABySS
- (2009) I. Birol et al. BIOINFORMATICS
- TopHat: discovering splice junctions with RNA-Seq
- (2009) Cole Trapnell et al. BIOINFORMATICS
- Nuclear Receptor-Induced Chromosomal Proximity and DNA Breaks Underlie Specific Translocations in Cancer
- (2009) Chunru Lin et al. CELL
- Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding
- (2009) K. J. McKernan et al. GENOME RESEARCH
- Circos: An information aesthetic for comparative genomics
- (2009) M. Krzywinski et al. GENOME RESEARCH
- Transcriptome sequencing to detect gene fusions in cancer
- (2009) Christopher A. Maher et al. NATURE
- Direct RNA sequencing
- (2009) Fatih Ozsolak et al. NATURE
- mRNA-Seq whole-transcriptome analysis of a single cell
- (2009) Fuchou Tang et al. NATURE METHODS
- Recurrent fusion of MYB and NFIB transcription factor genes in carcinomas of the breast and head and neck
- (2009) M. Persson 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
- Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing
- (2009) M. Yassour et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Optimal spliced alignments of short sequence reads
- (2008) F. De Bona et al. BIOINFORMATICS
- EML4-ALK Fusion Gene and Efficacy of an ALK Kinase Inhibitor in Lung Cancer
- (2008) J. P. Koivunen et al. CLINICAL CANCER RESEARCH
- A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome
- (2008) O. A. Hampton et al. GENOME RESEARCH
- Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
- (2008) D. R. Zerbino et al. GENOME RESEARCH
- Alternative isoform regulation in human tissue transcriptomes
- (2008) Eric T. Wang et al. NATURE
- Stem cell transcriptome profiling via massive-scale mRNA sequencing
- (2008) Nicole Cloonan et al. NATURE METHODS
- Mapping and quantifying mammalian transcriptomes by RNA-Seq
- (2008) Ali Mortazavi et al. NATURE METHODS
- RNA-Seq: a revolutionary tool for transcriptomics
- (2008) Zhong Wang et al. NATURE REVIEWS GENETICS
- The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing
- (2008) U. Nagalakshmi et al. SCIENCE
- Annotating genomes with massive-scale RNA sequencing
- (2008) France Denoeud et al. GENOME BIOLOGY
Find the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
SearchAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now