Chunxiao Wu

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MOTIVATION Comrad is a novel algorithmic framework for the integrated analysis of RNA-Seq and whole genome shotgun sequencing (WGSS) data for the purposes of discovering genomic rearrangements and aberrant transcripts. The Comrad framework leverages the advantages of both RNA-Seq and WGSS data, providing accurate classification of rearrangements as(More)
BACKGROUND The genomes of many epithelial tumors exhibit extensive chromosomal rearrangements. All classes of genome rearrangements can be identified using end sequencing profiling, which relies on paired-end sequencing of cloned tumor genomes. RESULTS In the present study brain, breast, ovary, and prostate tumors, along with three breast cancer cell(More)
Complex Genomic Rearrangements (CGRs) are emerging as a new feature of cancer genomes. CGRs are characterized by multiple genomic breakpoints, and thus have the potential to simultaneously affect multiple genes, fusing some genes and interrupting other genes. Analysis of high-throughput whole genome shotgun sequencing (WGSS) is beginning to facilitate the(More)
Complex genomic rearrangements (CGRs) are emerging as a new feature of cancer genomes. CGRs are characterized by multiple genomic breakpoints and thus have the potential to simultaneously affect multiple genes, fusing some genes and interrupting other genes. Analysis of high-throughput whole-genome shotgun sequencing (WGSS) is beginning to facilitate the(More)
RNA editing modifies the sequence of primary transcripts, potentially resulting in profound effects to RNA structure and protein-coding sequence. Recent analyses of RNA sequence data are beginning to provide insights into the distribution of RNA editing across the entire transcriptome, but there are few published matched whole genome and transcriptome(More)
Supplemental nFuse pipeline overview The nFuse method builds upon Comrad (McPherson et al., 2011b), our previous work on rearrangement detection in matched RNA-seq and WGSS. We begin this section by briefly describing Comrad, then describe significant differences between Comrad and nFuse. An overview of the nFuse pipeline is shown in Figure 1.
Motivation: Comrad is a novel algorithmic framework for the integrated analysis of RNA-Seq and Whole Genome Shotgun Sequencing (WGSS) data for the purposes of discovering genomic rearrangements and aberrant transcripts. The Comrad framework leverages the advantages of both RNA-Seq and WGSS data, providing accurate classification of rearrangements as(More)
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