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Open AccessBarnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies
Chimeric transcripts, including partial and internal tandem duplications (PTDs, ITDs) and gene fusions, are important in the detection, prognosis, and treatment of human cancers.
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Article
The clonal and mutational evolution spectrum of primary triple-negative breast cancers
Primary triple-negative breast cancers are shown to vary widely and continuously in the degree of clonal evolution and mutational content at the time of diagnosis, with implications for future studies of the d...
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Article
De novo assembly and analysis of RNA-seq data
The Trans-ABySS pipeline is an integrated approach for transcript assembly and analysis to identify new mRNA isoforms and structures.
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Personalized oncogenomics
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Open AccessEvolution of an adenocarcinoma in response to selection by targeted kinase inhibitors
Adenocarcinomas of the tongue are rare and represent the minority (20 to 25%) of salivary gland tumors affecting the tongue. We investigated the utility of massively parallel sequencing to characterize an aden...
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Open AccessGenomic analysis of a rare human tumor
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Article
Conserved role of intragenic DNA methylation in regulating alternative promoters
DNA methylation plays an important role in the maintenance of cell identity through its effect on gene expression. Methylation of 5′ promoters is known to suppress gene expression, while the role of intragenic...
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Article
Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin
Marco Marra and colleagues identify somatic mutations in EZH2 in diffuse large B-cell lymphomas and follicular lymphomas. EZH2 is a histone methyltransferase that participates in trimethylation of H3 Lys27 (H3K27...
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Article
Open AccessMutational evolution in a lobular breast tumour profiled at single nucleotide resolution
Next-generation sequencing approaches have been used to investigate the genomes and transcriptomes of an oestrogen-receptor-α-positive metastatic lobular breast cancer from a patient — rather than from a cell ...
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Article
Open AccessIdentification of a set of genes showing regionally enriched expression in the mouse brain
The Pleiades Promoter Project aims to improve gene therapy by designing human mini-promoters (< 4 kb) that drive gene expression in specific brain regions or cell-types of therapeutic interest. Our goal was to...
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Article
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
We developed a method, ChIP-sequencing (ChIP-seq), combining chromatin immunoprecipitation (ChIP) and massively parallel sequencing to identify mammalian DNA sequences bound by transcription factors in vivo. We u...
