{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,3,30]],"date-time":"2022-03-30T21:24:04Z","timestamp":1648675444458},"reference-count":37,"publisher":"World Scientific Pub Co Pte Lt","issue":"06","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2014,12]]},"abstract":"<jats:p> Whole-genome bisulfite sequencing (WGBS) is an approach of growing importance. It is the only approach that provides a comprehensive picture of the genome-wide DNA methylation profile. However, obtaining a sufficient amount of genome and read coverage typically requires high sequencing costs. Bioinformatics tools can reduce this cost burden by improving the quality of sequencing data. We have developed a statistical method Ajusted Local Kernel Smoother (AKSmooth) that can accurately and efficiently reconstruct the single CpG methylation estimate across the entire methylome using low-coverage bisulfite sequencing (Bi-Seq) data. We demonstrate the AKSmooth performance on the low-coverage (~ 4\u00d7) DNA methylation profiles of three human colon cancer samples and matched controls. Under the best set of parameters, AKSmooth-curated data showed high concordance with the gold standard high-coverage sample (Pearson 0.90), outperforming the popular analogous method. In addition, AKSmooth showed computational efficiency with runtime benchmark over 4.5 times better than the reference tool. To summarize, AKSmooth is a simple and efficient tool that can provide an accurate human colon methylome estimation profile from low-coverage WGBS data. The proposed method is implemented in R and is available at https:\/\/github.com\/Junfang\/AKSmooth . <\/jats:p>","DOI":"10.1142\/s0219720014420050","type":"journal-article","created":{"date-parts":[[2014,11,14]],"date-time":"2014-11-14T01:22:12Z","timestamp":1415928132000},"page":"1442005","source":"Crossref","is-referenced-by-count":0,"title":["AKSmooth: Enhancing low-coverage bisulfite sequencing data via kernel-based smoothing"],"prefix":"10.1142","volume":"12","author":[{"given":"Junfang","family":"Chen","sequence":"first","affiliation":[{"name":"Center for Bioinformatics, Saarland University, Saarbr\u00fccken 66123, Germany"},{"name":"Department of Genetics, Saarland University, Saarbr\u00fccken 66123, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pavlo","family":"Lutsik","sequence":"additional","affiliation":[{"name":"Department of Genetics, Saarland University, Saarbr\u00fccken 66123, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruslan","family":"Akulenko","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, Saarland University, Saarbr\u00fccken 66123, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J\u00f6rn","family":"Walter","sequence":"additional","affiliation":[{"name":"Department of Genetics, Saarland University, Saarbr\u00fccken 66123, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Volkhard","family":"Helms","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, Saarland University, Saarbr\u00fccken 66123, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"219","published-online":{"date-parts":[[2015,1,2]]},"reference":[{"key":"rf1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.97.10.5237"},{"key":"rf2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1002389"},{"key":"rf3","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/10.8.2709"},{"key":"rf4","doi-asserted-by":"publisher","DOI":"10.1016\/S0896-6273(01)00325-7"},{"key":"rf5","doi-asserted-by":"publisher","DOI":"10.1038\/5947"},{"key":"rf6","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(00)81155-1"},{"key":"rf7","doi-asserted-by":"publisher","DOI":"10.1038\/366362a0"},{"key":"rf8","doi-asserted-by":"publisher","DOI":"10.1016\/S1568-1637(03)00010-2"},{"key":"rf9","doi-asserted-by":"publisher","DOI":"10.1038\/72785"},{"key":"rf10","doi-asserted-by":"crossref","first-page":"988","DOI":"10.1177\/153537020422901002","volume":"229","author":"Davis C. 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