Computer Science Research Works

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

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Author: search.filters.author.Kim, Daehwan

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    TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    (Springer Nature, 2013-04-25) Kim, Daehwan; Pertea, Geo; Trapnell, Cole; Pimentel, Harold; Kelley, Ryan; Salzberg, Steven L
    TopHat is a popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper, we describe TopHat2, which incorporates many significant enhancements to TopHat. TopHat2 can align reads of various lengths produced by the latest sequencing technologies, while allowing for variable-length indels with respect to the reference genome. In addition to de novo spliced alignment, TopHat2 can align reads across fusion breaks, which can occur after genomic translocations. TopHat2 combines the ability to identify novel splice sites with direct mapping to known transcripts, producing sensitive and accurate alignments, even for highly repetitive genomes or in the presence of pseudogenes. TopHat2 is available at http://ccb.jhu.edu/software/tophat .
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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/.