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dc.contributor.authorZhong, Cuncong
dc.contributor.authorZhang, Shaojie
dc.identifier.citationZhong, C., & Zhang, S. (2019, August 30). Accurate and Efficient Mapping of the Cross-Linked microRNA-mRNA Duplex Reads. iScience, 18, 11-19.en_US
dc.descriptionThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.en_US
dc.description.abstractMicroRNA (miRNA) trans-regulates the stability of many mRNAs and controls their expression levels. Reconstruction of the miRNA-mRNA interactome is key to the understanding of the miRNA regulatory network and related biological processes. However, existing miRNA target prediction methods are limited to canonical miRNA-mRNA interactions and have high false prediction rates. Other experimental methods are low throughput and cannot be used to probe genome-wide interactions. To address this challenge, the Cross-linking Ligation and Sequencing of Hybrids (CLASH) technology was developed for high-throughput probing of transcriptome-wide microRNA-mRNA interactions in vivo. The mapping of duplex reads, chimeras of two ultra-short RNA strands, poses computational challenges to current mapping and alignment methods. To address this issue, we developed CLAN (CrossLinked reads ANalysis toolkit). CLAN generated a comparable mapping of singular reads to other tools, and significantly outperformed in mapping simulated and real CLASH duplex reads, offering a potential application to other next-generation sequencing-based duplex-read-generating technologies.en_US
dc.publisherCell Pressen_US
dc.rights© 2019 The Author(s).en_US
dc.titleAccurate and Efficient Mapping of the Cross-Linked microRNA-mRNA Duplex Readsen_US
kusw.kuauthorZhong, Cuncong
kusw.kudepartmentElectrical Engineering & Computer Scienceen_US
kusw.oaversionScholarly/refereed, publisher versionen_US
kusw.oapolicyThis item meets KU Open Access policy criteria.en_US

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© 2019 The Author(s).
Except where otherwise noted, this item's license is described as: © 2019 The Author(s).