{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T05:22:06Z","timestamp":1674883326892},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: With the spreading technique of mass sequencing, nucleosome positions and scores for their intensity have become available through several previous studies in yeast, but relatively few studies have specifically aimed to determine the score of nucleosome stability. Based on mass sequencing data, we proposed a nucleosome center score (NCS) for quantifying nucleosome stability by measuring shifts of the nucleosome center, and then mapping NCS scores to nucleosome positions in Brogaard et al.\u2019s study.<\/jats:p>\n               <jats:p>Results: We demonstrated the efficiency of NCS by known preference of A\/T-based tracts for nucleosome formation, and showed that central nucleosomal DNA is more sensitive to A\/T-based tracts than outer regions, which corresponds to the central histone tetramer-dominated region. We also found significant flanking preference around nucleosomal DNA for A\/T-based dinucleotides, suggesting that neighboring sequences could affect nucleosome stability. Finally, the difference between results of NCS and Brogaard et al.\u2019s scores was addressed and discussed.<\/jats:p>\n               <jats:p>Contacts: \u00a0jchiang@mail.ncku.edu.tw<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt621","type":"journal-article","created":{"date-parts":[[2013,11,1]],"date-time":"2013-11-01T06:53:15Z","timestamp":1383288795000},"page":"761-767","source":"Crossref","is-referenced-by-count":0,"title":["NCS: incorporating positioning data to quantify nucleosome stability in yeast"],"prefix":"10.1093","volume":"30","author":[{"given":"Jung-Hsien","family":"Chiang","sequence":"first","affiliation":[{"name":"Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan 70101, Taiwan"}]},{"given":"Chan-Hsien","family":"Lin","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan 70101, Taiwan"}]}],"member":"286","published-online":{"date-parts":[[2013,10,31]]},"reference":[{"key":"2023012710442462900_btt621-B1","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1038\/nature05632","article-title":"Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome","volume":"446","author":"Albert","year":"2007","journal-title":"Nature"},{"key":"2023012710442462900_btt621-B2","doi-asserted-by":"crossref","first-page":"3093","DOI":"10.1093\/nar\/gkq1279","article-title":"Nucleosome accessibility governed by the dimer\/tetramer interface","volume":"39","author":"Bohm","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012710442462900_btt621-B3","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1038\/nature11142","article-title":"A map of nucleosome positions in yeast at base-pair resolution","volume":"486","author":"Brogaard","year":"2012","journal-title":"Nature"},{"key":"2023012710442462900_btt621-B4","doi-asserted-by":"crossref","first-page":"e15754","DOI":"10.1371\/journal.pone.0015754","article-title":"The effect of micrococcal nuclease digestion on nucleosome positioning data","volume":"5","author":"Chung","year":"2010","journal-title":"PloS One"},{"key":"2023012710442462900_btt621-B5","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1016\/j.bbagrm.2012.01.008","article-title":"Perfect and imperfect nucleosome positioning in yeast","volume":"1819","author":"Cole","year":"2012","journal-title":"Biochimica et Biophysica Acta"},{"key":"2023012710442462900_btt621-B6","doi-asserted-by":"crossref","first-page":"D918","DOI":"10.1093\/nar\/gkr1055","article-title":"The UCSC Genome Browser database: extensions and updates 2011","volume":"40","author":"Dreszer","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023012710442462900_btt621-B7","doi-asserted-by":"crossref","first-page":"e1000216","DOI":"10.1371\/journal.pcbi.1000216","article-title":"Distinct modes of regulation by chromatin encoded through nucleosome positioning signals","volume":"4","author":"Field","year":"2008","journal-title":"PLoS Comput. 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