Browsing by Author "Wang, Zhong"

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    Hybrid error correction and de novo assembly of single-molecule sequencing reads.
    (Nat Biotechnol, 2012-07-01) Koren, Sergey; Schatz, Michael C; Walenz, Brian P; Martin, Jeffrey; Howard, Jason T; Ganapathy, Ganeshkumar; Wang, Zhong; Rasko, David A; McCombie, W Richard; Jarvis, Erich D; Adam M Phillippy
    Single-molecule sequencing instruments can generate multikilobase sequences with the potential to greatly improve genome and transcriptome assembly. However, the error rates of single-molecule reads are high, which has limited their use thus far to resequencing bacteria. To address this limitation, we introduce a correction algorithm and assembly strategy that uses short, high-fidelity sequences to correct the error in single-molecule sequences. We demonstrate the utility of this approach on reads generated by a PacBio RS instrument from phage, prokaryotic and eukaryotic whole genomes, including the previously unsequenced genome of the parrot Melopsittacus undulatus, as well as for RNA-Seq reads of the corn (Zea mays) transcriptome. Our long-read correction achieves >99.9% base-call accuracy, leading to substantially better assemblies than current sequencing strategies: in the best example, the median contig size was quintupled relative to high-coverage, second-generation assemblies. Greater gains are predicted if read lengths continue to increase, including the prospect of single-contig bacterial chromosome assembly.
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    The prevalence and regulation of antisense transcripts in Schizosaccharomyces pombe.
    (PLoS One, 2010-12-20) Ni, Ting; Tu, Kang; Wang, Zhong; Song, Shen; Wu, Han; Xie, Bin; Scott, Kristin C; Grewal, Shiv I; Gao, Yuan; Zhu, Jun
    A strand-specific transcriptome sequencing strategy, directional ligation sequencing or DeLi-seq, was employed to profile antisense transcriptome of Schizosaccharomyces pombe. Under both normal and heat shock conditions, we found that polyadenylated antisense transcripts are broadly expressed while distinct expression patterns were observed for protein-coding and non-coding loci. Dominant antisense expression is enriched in protein-coding genes involved in meiosis or stress response pathways. Detailed analyses further suggest that antisense transcripts are independently regulated with respect to their sense transcripts, and diverse mechanisms might be potentially involved in the biogenesis and degradation of antisense RNAs. Taken together, antisense transcription may have profound impacts on global gene regulation in S. pombe.