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

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