Kris Popendorf

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MOTIVATION The accurate detection of orthologous segments (also referred to as syntenic segments) plays a key role in comparative genomics, as it is useful for inferring genome rearrangement scenarios and computing whole-genome alignments. Although a number of algorithms for detecting orthologous segments have been proposed, none of them contain a framework(More)
BACKGROUND Bacillus subtilis natto is closely related to the laboratory standard strain B. subtilis Marburg 168, and functions as a starter for the production of the traditional Japanese food "natto" made from soybeans. Although re-sequencing whole genomes of several laboratory domesticated B. subtilis 168 derivatives has already been attempted using short(More)
BACKGROUND With the number of available genome sequences increasing rapidly, the magnitude of sequence data required for multiple-genome analyses is a challenging problem. When large-scale rearrangements break the collinearity of gene orders among genomes, genome comparison algorithms must first identify sets of short well-conserved sequences present in(More)
Traditional publish / subscribe systems offer a range of expressive subscription languages for constraints, but restrict the publish operation to be a single published object that contains only constants and no constraints. We have introduced a novel generalization of publish / subscribe called symmetric publish / subscribe where both publications and(More)
UNLABELLED Since tens of millions of chemical compounds have been accumulated in public chemical databases, fast comprehensive computational methods to predict interactions between chemical compounds and proteins are needed for virtual screening of lead compounds. Previously, we proposed a novel method for predicting protein-chemical interactions using(More)
SUMMARY Existing SAM visualization tools like 'samtools tview' (Li et al., 2009) are limited to a small region of the genome, and tools like Tablet (Milne et al., 2010) are limited to a relatively small number of reads and may fail outright on large datasets. We need to visualize complex ChIP-Seq and RNA-Seq features such as polarity as well as coverage(More)
Traditional publish / subscribe systems offer a range of expressive subscription languages for constraints, but restrict the publish operation to be a single published object that contains only constants and no constraints. We have introduced a novel generalization of publish / subscribe called symmetric publish / subscribe where both publications and(More)
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