Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data

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

(2011) Marcus Kinsella et al.   BIOINFORMATICS

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

(2011) Andrew McPherson et al.   PLoS Computational Biology

A probabilistic framework for aligning paired-end RNA-seq data

(2010) Yin Hu et al.   BIOINFORMATICS

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing

(2010) Iman Hajirasouliha et al.   BIOINFORMATICS

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery

(2010) Fereydoun Hormozdiari et al.   BIOINFORMATICS

Integrative analysis of the melanoma transcriptome

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

Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing

(2010) D. Pflueger et al.   GENOME RESEARCH

Database resources of the National Center for Biotechnology Information

(2010) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Jonathan Houseley et al.   PLoS One

FusionSeq: a modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data

(2010) Andrea Sboner et al.   GENOME BIOLOGY

SLC45A3-ELK4 Is a Novel and Frequent Erythroblast Transformation-Specific Fusion Transcript in Prostate Cancer

(2009) D. S. Rickman et al.   CANCER RESEARCH

Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes

(2009) F. Hormozdiari et al.   GENOME RESEARCH

Functional Pre- mRNAtrans-Splicing of Coactivator CoAA and Corepressor RBM4 during Stem/Progenitor Cell Differentiation

(2009) Yang S. Brooks et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Transcriptome sequencing to detect gene fusions in cancer

(2009) Christopher A. Maher et al.   NATURE

A small-cell lung cancer genome with complex signatures of tobacco exposure

(2009) Erin D. Pleasance et al.   NATURE

MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions

(2009) Seunghak Lee et al.   NATURE METHODS

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

The UCSC Genome Browser database: update 2010

(2009) B. Rhead et al.   NUCLEIC ACIDS RESEARCH

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

Estimation and assessment of raw copy numbers at the single locus level

(2008) H. Bengtsson et al.   BIOINFORMATICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

A Neoplastic Gene Fusion Mimics Trans-Splicing of RNAs in Normal Human Cells

(2008) H. Li et al.   SCIENCE

Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer

(2008) Ali Bashir et al.   PLoS Computational Biology