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MOTIVATION Next-generation sequencing allows us to sequence reads from a microbial environment using single-cell sequencing or metagenomic sequencing technologies. However, both technologies suffer from the problem that sequencing depth of different regions of a genome or genomes from different species are highly uneven. Most existing genome assemblers(More)
The de Bruijn graph assembly approach breaks reads into k-mers before assembling them into contigs. The string graph approach forms contigs by connecting two reads with k or more overlapping nucleotides. Both approaches must deal with the following problems: false-positive vertices, due to erroneous reads; gap problem, due to non-uniform coverage; branching(More)
MOTIVATION Next-generation sequencing techniques allow us to generate reads from a microbial environment in order to analyze the microbial community. However, assembling of a set of mixed reads from different species to form contigs is a bottleneck of metagenomic research. Although there are many assemblers for assembling reads from a single genome, there(More)
MOTIVATION RNA sequencing based on next-generation sequencing technology is effective for analyzing transcriptomes. Like de novo genome assembly, de novo transcriptome assembly does not rely on any reference genome or additional annotation information, but is more difficult. In particular, isoforms can have very uneven expression levels (e.g. 1:100), which(More)
BACKGROUND The conformational conversion of the host-derived cellular prion protein (PrP(C)) into the disease-associated scrapie isoform (PrP(Sc)) is responsible for the pathogenesis of transmissible spongiform encephalopathies (TSEs). Various single-point mutations in PrP(C)s could cause structural changes and thereby distinctly influence the(More)
Much work has been done to address the need for incentive models in real deployed peer-to-peer networks. In this paper, we discuss problems found with the incentive model in a large, deployed peer-to-peer network, Maze. We evaluate several alternatives, and propose an incentive system that generates preferences for well-behaved nodes while correctly(More)
The recessive tall rice (Oryza sativa) mutant elongated uppermost internode (eui) is morphologically normal until its final internode elongates drastically at the heading stage. The stage-specific developmental effect of the eui mutation has been used in the breeding of hybrid rice to improve the performance of heading in male sterile cultivars. We found(More)
Limited by the laboratory technique, traditional microorganism research usually focuses on one single individual species. This significantly limits the deep analysis of intricate biological processes among complex microorganism communities. With the rapid development of genome sequencing techniques, the traditional research methods of microorganisms based(More)
MOTIVATION With the rapid development of next-generation sequencing techniques, metagenomics, also known as environmental genomics, has emerged as an exciting research area that enables us to analyze the microbial environment in which we live. An important step for metagenomic data analysis is the identification and taxonomic characterization of DNA(More)
—We are in an age where people are paying increasing attention to energy conservation around the world. The heating and airconditioning systems of buildings introduce one of the largest chunk of energy expenses. In this paper, we make a key observation that after a meeting or a class ends in a room, the indoor temperature will not immediately increase to(More)