{"id":"https://openalex.org/W2949310776","doi":"https://doi.org/10.1093/bioinformatics/btw138","title":"D3M: detection of differential distributions of methylation levels","display_name":"D3M: detection of differential distributions of methylation levels","publication_year":2016,"publication_date":"2016-03-11","ids":{"openalex":"https://openalex.org/W2949310776","doi":"https://doi.org/10.1093/bioinformatics/btw138","mag":"2949310776","pmid":"https://pubmed.ncbi.nlm.nih.gov/27153581"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw138","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw138","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103144232","display_name":"Yusuke Matsui","orcid":"https://orcid.org/0000-0003-3977-4313"},"institutions":[{"id":"https://openalex.org/I60134161","display_name":"Nagoya University","ror":"https://ror.org/04chrp450","country_code":"JP","type":"education","lineage":["https://openalex.org/I60134161"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Yusuke Matsui","raw_affiliation_strings":["1 Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan","institution_ids":["https://openalex.org/I60134161"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051623223","display_name":"Masahiro Mizuta","orcid":"https://orcid.org/0000-0001-6767-8834"},"institutions":[{"id":"https://openalex.org/I205349734","display_name":"Hokkaido University","ror":"https://ror.org/02e16g702","country_code":"JP","type":"education","lineage":["https://openalex.org/I205349734"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Masahiro Mizuta","raw_affiliation_strings":["2 Information Initiative Center, Hokkaido University, Sapporo 060-0811, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 Information Initiative Center, Hokkaido University, Sapporo 060-0811, Japan","institution_ids":["https://openalex.org/I205349734"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101469434","display_name":"Satoshi Ito","orcid":"https://orcid.org/0000-0002-8464-7535"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Satoshi Ito","raw_affiliation_strings":["3 Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088167618","display_name":"Satoru Miyano","orcid":"https://orcid.org/0000-0002-1753-6616"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Satoru Miyano","raw_affiliation_strings":["3 Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009811167","display_name":"Teppei Shimamura","orcid":"https://orcid.org/0000-0003-2994-872X"},"institutions":[{"id":"https://openalex.org/I60134161","display_name":"Nagoya University","ror":"https://ror.org/04chrp450","country_code":"JP","type":"education","lineage":["https://openalex.org/I60134161"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Teppei Shimamura","raw_affiliation_strings":["1 Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan","institution_ids":["https://openalex.org/I60134161"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5009811167","https://openalex.org/A5103144232"],"corresponding_institution_ids":["https://openalex.org/I60134161"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.5126,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.72580758,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"32","issue":"15","first_page":"2248","last_page":"2255"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.4957999885082245,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.4957999885082245,"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":0.13459999859333038,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.12359999865293503,"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/interpretability","display_name":"Interpretability","score":0.7123328447341919},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.5848420858383179},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5501530766487122},{"id":"https://openalex.org/keywords/methylation","display_name":"Methylation","score":0.5140520334243774},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47362393140792847},{"id":"https://openalex.org/keywords/epigenetics","display_name":"Epigenetics","score":0.4328840374946594},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.422977089881897},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3391345739364624},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.32834410667419434},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.28414052724838257},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.23686566948890686},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16035383939743042},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10074460506439209},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.08048757910728455}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.7123328447341919},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.5848420858383179},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5501530766487122},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.5140520334243774},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47362393140792847},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.4328840374946594},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.422977089881897},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3391345739364624},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32834410667419434},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.28414052724838257},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.23686566948890686},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16035383939743042},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10074460506439209},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.08048757910728455},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btw138","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw138","pdf_url":null,"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:27153581","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27153581","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:32/15/2248","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/15/2248","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"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G313148667","display_name":null,"funder_award_id":"15H05912","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G4955043931","display_name":"Transcription regulatory network atlas for functional ncRNA search","funder_award_id":"15K12139","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G6366613923","display_name":"Statistical Models for Fractionated Irradiation","funder_award_id":"25540008","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G848035828","display_name":"Bayesian modeling for analyzing, integrating and understanding of intracellular metabolic shifts","funder_award_id":"15H05325","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W158759942","https://openalex.org/W1598395355","https://openalex.org/W1831033366","https://openalex.org/W1963480915","https://openalex.org/W1963604057","https://openalex.org/W1984807040","https://openalex.org/W1996816592","https://openalex.org/W2025183726","https://openalex.org/W2056040742","https://openalex.org/W2076423950","https://openalex.org/W2087933354","https://openalex.org/W2096099115","https://openalex.org/W2107776519","https://openalex.org/W2110065044","https://openalex.org/W2113088508","https://openalex.org/W2123174009","https://openalex.org/W2125865219","https://openalex.org/W2129269004","https://openalex.org/W2129836734","https://openalex.org/W2144751786","https://openalex.org/W2146512944","https://openalex.org/W2150936392","https://openalex.org/W2167942713","https://openalex.org/W2169353806","https://openalex.org/W2212660284","https://openalex.org/W2328111639","https://openalex.org/W2338990760","https://openalex.org/W3021971632","https://openalex.org/W3106526220","https://openalex.org/W4245050711","https://openalex.org/W4292156489","https://openalex.org/W6678814708","https://openalex.org/W6688325169"],"related_works":["https://openalex.org/W2214376880","https://openalex.org/W3212149434","https://openalex.org/W2073893804","https://openalex.org/W2291484187","https://openalex.org/W2902329290","https://openalex.org/W2139872319","https://openalex.org/W2052355316","https://openalex.org/W2046964473","https://openalex.org/W2107880877","https://openalex.org/W2151182744"],"abstract_inverted_index":{"MOTIVATION:":[0],"DNA":[1],"methylation":[2,20,33,40,120],"is":[3,35,196],"an":[4,141],"important":[5],"epigenetic":[6],"modification":[7],"related":[8],"to":[9,36,63],"a":[10,68,78,89],"variety":[11],"of":[12,28,32,84,95,98,116,131,144],"diseases":[13],"including":[14],"cancers.":[15],"We":[16,87,127],"focus":[17],"on":[18,101,123],"the":[19,29,38,65,108,124,129,132,145,152],"data":[21,50,172,208],"from":[22,173,199],"Illumina's":[23],"Infinium":[24],"HumanMethylation450":[25],"BeadChip.":[26],"One":[27],"key":[30],"issues":[31],"analysis":[34],"detect":[37,107],"differential":[39,96],"sites":[41],"between":[42,134],"case":[43,135],"and":[44,58,77,136,139,158,168,186],"control":[45,137],"groups.":[46],"Previous":[47],"approaches":[48],"describe":[49],"with":[51,163],"simple":[52],"summary":[53,69,143],"statistics":[54],"or":[55,203],"kernel":[56,79],"function,":[57],"then":[59],"use":[60],"statistical":[61],"tests":[62],"determine":[64],"difference.":[66],"However,":[67],"statistics-based":[70],"approach":[71,81],"cannot":[72],"capture":[73],"complicated":[74],"underlying":[75,117],"structure,":[76],"function-based":[80],"lacks":[82],"interpretability":[83],"results.":[85,146],"RESULTS:":[86],"propose":[88],"novel":[90],"method":[91,105,154,181],"D(3)M,":[92],"for":[93],"detection":[94],"distribution":[97],"methylation,":[99],"based":[100,122],"distribution-valued":[102],"data.":[103],"Our":[104],"can":[106],"differences":[109],"in":[110,119],"high-order":[111],"moments,":[112],"such":[113],"as":[114],"shapes":[115],"distributions":[118],"profiles,":[121],"Wasserstein":[125],"metric.":[126],"test":[128],"significance":[130],"difference":[133],"groups":[138],"provide":[140],"interpretable":[142],"The":[147,174],"simulation":[148],"results":[149,161],"show":[150,178],"that":[151,179],"proposed":[153],"achieves":[155],"promising":[156],"accuracy":[157],"shows":[159],"favorable":[160],"compared":[162],"previous":[164],"methods.":[165],"Glioblastoma":[166],"multiforme":[167],"lower":[169],"grade":[170],"glioma":[171],"Cancer":[175],"Genome":[176],"Atlas":[177],"our":[180],"supports":[182],"recent":[183],"biological":[184],"advances":[185],"suggests":[187],"new":[188],"insights.":[189],"AVAILABILITY":[190],"AND":[191],"IMPLEMENTATION:":[192],"R":[193],"implemented":[194],"code":[195],"freely":[197],"available":[198,210],"https://github.com/ymatts/D3M/":[200],"CONTACT:":[201],"ymatsui@med.nagoya-u.ac.jp":[202],"shimamura@med.nagoya-u.ac.jp":[204],"SUPPLEMENTARY":[205],"INFORMATION:":[206],"Supplementary":[207],"are":[209],"at":[211],"Bioinformatics":[212],"online.":[213]},"counts_by_year":[{"year":2021,"cited_by_count":4},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2}],"updated_date":"2026-07-13T07:31:44.756512","created_date":"2025-10-10T00:00:00"}
