{"id":"https://openalex.org/W2513256266","doi":"https://doi.org/10.1093/bioinformatics/btw562","title":"Prediction of nucleosome positioning by the incorporation of frequencies and distributions of three different nucleotide segment lengths into a general pseudo k-tuple nucleotide composition","display_name":"Prediction of nucleosome positioning by the incorporation of frequencies and distributions of three different nucleotide segment lengths into a general pseudo k-tuple nucleotide composition","publication_year":2016,"publication_date":"2016-08-25","ids":{"openalex":"https://openalex.org/W2513256266","doi":"https://doi.org/10.1093/bioinformatics/btw562","mag":"2513256266","pmid":"https://pubmed.ncbi.nlm.nih.gov/27563027"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw562","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw562","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/1/42/25140246/btw562.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/1/42/25140246/btw562.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5036650358","display_name":"Akinori Awazu","orcid":"https://orcid.org/0000-0002-0778-021X"},"institutions":[{"id":"https://openalex.org/I113306721","display_name":"Hiroshima University","ror":"https://ror.org/03t78wx29","country_code":"JP","type":"education","lineage":["https://openalex.org/I113306721"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Akinori Awazu","raw_affiliation_strings":["Department of Mathematical and Life Sciences, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima, Japan","Research Center for Mathematics on Chromatin Live Dynamics, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematical and Life Sciences, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima, Japan","institution_ids":["https://openalex.org/I113306721"]},{"raw_affiliation_string":"Research Center for Mathematics on Chromatin Live Dynamics, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima, Japan","institution_ids":["https://openalex.org/I113306721"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5036650358"],"corresponding_institution_ids":["https://openalex.org/I113306721"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.9593,"has_fulltext":false,"cited_by_count":30,"citation_normalized_percentile":{"value":0.91228639,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"33","issue":"1","first_page":"42","last_page":"48"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.5838000178337097,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.5838000178337097,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.34709998965263367,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12946","display_name":"Fractal and DNA sequence analysis","score":0.04610000178217888,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/nucleosome","display_name":"Nucleosome","score":0.8763188719749451},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.5735881328582764},{"id":"https://openalex.org/keywords/caenorhabditis-elegans","display_name":"Caenorhabditis elegans","score":0.546916127204895},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5260762572288513},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.515108048915863},{"id":"https://openalex.org/keywords/drosophila-melanogaster","display_name":"Drosophila melanogaster","score":0.49136415123939514},{"id":"https://openalex.org/keywords/nucleotide","display_name":"Nucleotide","score":0.49034857749938965},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4529097378253937},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4465213418006897},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.4402201473712921},{"id":"https://openalex.org/keywords/histone","display_name":"Histone","score":0.4292069375514984},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.17024004459381104}],"concepts":[{"id":"https://openalex.org/C84772758","wikidata":"https://www.wikidata.org/wiki/Q271794","display_name":"Nucleosome","level":4,"score":0.8763188719749451},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.5735881328582764},{"id":"https://openalex.org/C2778944004","wikidata":"https://www.wikidata.org/wiki/Q91703","display_name":"Caenorhabditis elegans","level":3,"score":0.546916127204895},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5260762572288513},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.515108048915863},{"id":"https://openalex.org/C2780104201","wikidata":"https://www.wikidata.org/wiki/Q130888","display_name":"Drosophila melanogaster","level":3,"score":0.49136415123939514},{"id":"https://openalex.org/C512185932","wikidata":"https://www.wikidata.org/wiki/Q28745","display_name":"Nucleotide","level":3,"score":0.49034857749938965},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4529097378253937},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4465213418006897},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.4402201473712921},{"id":"https://openalex.org/C64927066","wikidata":"https://www.wikidata.org/wiki/Q36293","display_name":"Histone","level":3,"score":0.4292069375514984},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17024004459381104}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D042002","descriptor_name":"Chromatin Assembly and Disassembly","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D042002","descriptor_name":"Chromatin Assembly and Disassembly","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D042002","descriptor_name":"Chromatin Assembly and Disassembly","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btw562","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw562","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/1/42/25140246/btw562.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:27563027","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27563027","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:33/1/42","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/33/1/42","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:5860184","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5860184","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw562","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw562","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/1/42/25140246/btw562.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320311405","display_name":"Japan Agency for Medical Research and Development","ror":"https://ror.org/004rtk039"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":88,"referenced_works":["https://openalex.org/W1149957381","https://openalex.org/W1494484168","https://openalex.org/W1807324513","https://openalex.org/W1943237984","https://openalex.org/W1964243769","https://openalex.org/W1968916935","https://openalex.org/W1971057981","https://openalex.org/W1976582164","https://openalex.org/W1980971292","https://openalex.org/W1983808106","https://openalex.org/W1991141438","https://openalex.org/W1991794321","https://openalex.org/W1996852546","https://openalex.org/W1998291732","https://openalex.org/W2002197756","https://openalex.org/W2003613304","https://openalex.org/W2004874474","https://openalex.org/W2010979687","https://openalex.org/W2016597274","https://openalex.org/W2022965734","https://openalex.org/W2026710881","https://openalex.org/W2029873987","https://openalex.org/W2033072260","https://openalex.org/W2034070267","https://openalex.org/W2035090437","https://openalex.org/W2036329916","https://openalex.org/W2047187013","https://openalex.org/W2049361027","https://openalex.org/W2050042672","https://openalex.org/W2066124661","https://openalex.org/W2069545688","https://openalex.org/W2072152932","https://openalex.org/W2075176419","https://openalex.org/W2077838441","https://openalex.org/W2079100340","https://openalex.org/W2079830359","https://openalex.org/W2080569293","https://openalex.org/W2082247817","https://openalex.org/W2085493431","https://openalex.org/W2091505355","https://openalex.org/W2095759849","https://openalex.org/W2101536723","https://openalex.org/W2106372318","https://openalex.org/W2106448802","https://openalex.org/W2107649894","https://openalex.org/W2109157139","https://openalex.org/W2109268993","https://openalex.org/W2113512405","https://openalex.org/W2114024619","https://openalex.org/W2115219137","https://openalex.org/W2120026469","https://openalex.org/W2121851992","https://openalex.org/W2124266758","https://openalex.org/W2129759388","https://openalex.org/W2131291563","https://openalex.org/W2133095756","https://openalex.org/W2134314200","https://openalex.org/W2138045300","https://openalex.org/W2139166279","https://openalex.org/W2140964565","https://openalex.org/W2142260709","https://openalex.org/W2147734340","https://openalex.org/W2154109129","https://openalex.org/W2155453721","https://openalex.org/W2157215357","https://openalex.org/W2158038881","https://openalex.org/W2161414637","https://openalex.org/W2167764944","https://openalex.org/W2167954129","https://openalex.org/W2170033314","https://openalex.org/W2170604299","https://openalex.org/W2217901696","https://openalex.org/W2264592275","https://openalex.org/W2296312486","https://openalex.org/W2313411748","https://openalex.org/W2323161552","https://openalex.org/W2334348844","https://openalex.org/W2345938495","https://openalex.org/W2413285763","https://openalex.org/W2439245561","https://openalex.org/W2472513547","https://openalex.org/W2598495276","https://openalex.org/W2774947529","https://openalex.org/W3156302520","https://openalex.org/W4285719527","https://openalex.org/W6680166665","https://openalex.org/W6692998215","https://openalex.org/W6735888752"],"related_works":["https://openalex.org/W4313474347","https://openalex.org/W2587366952","https://openalex.org/W2993659554","https://openalex.org/W2393920775","https://openalex.org/W2183871674","https://openalex.org/W390558816","https://openalex.org/W4385516583","https://openalex.org/W2014093629","https://openalex.org/W3216649527","https://openalex.org/W1980411169"],"abstract_inverted_index":{"MOTIVATION:":[0],"Nucleosome":[1,34],"positioning":[2,23,35,139],"plays":[3],"important":[4],"roles":[5],"in":[6,61,72],"many":[7],"eukaryotic":[8],"intranuclear":[9],"processes,":[10],"such":[11],"as":[12,128],"transcriptional":[13],"regulation":[14],"and":[15,67,69,91,118,125,140],"chromatin":[16],"structure":[17],"formation.":[18],"The":[19],"investigations":[20],"of":[21,29,43,46,53,58,64],"nucleosome":[22,123,138],"rules":[24],"provide":[25],"a":[26,40,49,65,101],"deeper":[27],"understanding":[28],"these":[30],"intracellular":[31],"processes.":[32],"RESULTS:":[33],"prediction":[36,103],"was":[37,97,112],"performed":[38],"using":[39],"model":[41,96,111],"consisting":[42],"three":[44],"types":[45],"variables":[47],"characterizing":[48],"DNA":[50,73],"sequence-the":[51],"number":[52,57],"five-nucleotide":[54],"sequences,":[55],"the":[56,94,106,116,131,143],"three-nucleotide":[59],"combinations":[60],"one":[62],"period":[63],"helix,":[66],"mono-":[68],"di-nucleotide":[70],"distributions":[71],"fragments.":[74],"Using":[75],"recently":[76,107],"proposed":[77,108],"stringent":[78],"benchmark":[79],"datasets":[80],"with":[81],"low":[82],"biases":[83],"for":[84],"Saccharomyces":[85],"cerevisiae,":[86],"Homo":[87],"sapiens,":[88],"Caenorhabditis":[89],"elegans":[90],"Drosophila":[92],"melanogaster,":[93],"present":[95],"shown":[98],"to":[99,114],"have":[100],"better":[102],"performance":[104],"than":[105],"predictors.":[109],"This":[110],"able":[113],"display":[115],"common":[117],"organism-dependent":[119],"factors":[120,145],"that":[121],"affect":[122],"forming":[124],"inhibiting":[126],"sequences":[127],"well.":[129],"Therefore,":[130],"predictors":[132],"developed":[133],"here":[134],"can":[135],"accurately":[136],"predict":[137],"help":[141],"determine":[142],"key":[144],"influencing":[146],"this":[147],"process.":[148],"CONTACT:":[149],"awa@hiroshima-u.ac.jpSupplementary":[150],"information:":[151],"Supplementary":[152],"data":[153],"are":[154],"available":[155],"at":[156],"Bioinformatics":[157],"online.":[158]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":4}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
