Computer Science Research Works

Permanent URI for this collectionhttp://hdl.handle.net/1903/1593

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    SIMPL-R and Its Application to Large, Sparse Matrix Problems
    (1974-07) McHugh, John; Basili, Victor
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    TopHat-Fusion: an algorithm for discovery of novel fusion transcripts
    (2011-08-11) Kim, Daehwan; Salzberg, Steven L
    TopHat-Fusion is an algorithm designed to discover transcripts representing fusion gene products, which result from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome. TopHat-Fusion is an enhanced version of TopHat, an efficient program that aligns RNA-seq reads without relying on existing annotation. Because it is independent of gene annotation, TopHat-Fusion can discover fusion products deriving from known genes, unknown genes and unannotated splice variants of known genes. Using RNA-seq data from breast and prostate cancer cell lines, we detected both previously reported and novel fusions with solid supporting evidence. TopHat-Fusion is available at http://tophat-fusion.sourceforge.net/.