{"id":"https://openalex.org/W3121126297","doi":"https://doi.org/10.1109/tcbb.2021.3049366","title":"FBCwPlaid: A Functional Biclustering Analysis of Epi-Transcriptome Profiling Data Via a Weighted Plaid Model","display_name":"FBCwPlaid: A Functional Biclustering Analysis of Epi-Transcriptome Profiling Data Via a Weighted Plaid Model","publication_year":2021,"publication_date":"2021-01-05","ids":{"openalex":"https://openalex.org/W3121126297","doi":"https://doi.org/10.1109/tcbb.2021.3049366","mag":"3121126297","pmid":"https://pubmed.ncbi.nlm.nih.gov/33400655"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2021.3049366","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3049366","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5102962088","display_name":"Shutao Chen","orcid":"https://orcid.org/0000-0001-6188-2631"},"institutions":[{"id":"https://openalex.org/I25757504","display_name":"China University of Mining and Technology","ror":"https://ror.org/01xt2dr21","country_code":"CN","type":"education","lineage":["https://openalex.org/I25757504"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shutao Chen","raw_affiliation_strings":["Engineering Research Center of Intelligent Control for Underground Space, Ministry of Education, China University of Mining and Technology, Xuzhou, China","School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China"],"raw_orcid":"https://orcid.org/0000-0001-6188-2631","affiliations":[{"raw_affiliation_string":"Engineering Research Center of Intelligent Control for Underground Space, Ministry of Education, China University of Mining and Technology, Xuzhou, China","institution_ids":["https://openalex.org/I25757504"]},{"raw_affiliation_string":"School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China","institution_ids":["https://openalex.org/I25757504"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100351875","display_name":"Lin Zhang","orcid":"https://orcid.org/0000-0002-7404-5231"},"institutions":[{"id":"https://openalex.org/I25757504","display_name":"China University of Mining and Technology","ror":"https://ror.org/01xt2dr21","country_code":"CN","type":"education","lineage":["https://openalex.org/I25757504"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lin Zhang","raw_affiliation_strings":["Engineering Research Center of Intelligent Control for Underground Space, Ministry of Education, China University of Mining and Technology, Xuzhou, China","School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China"],"raw_orcid":"https://orcid.org/0000-0002-7404-5231","affiliations":[{"raw_affiliation_string":"Engineering Research Center of Intelligent Control for Underground Space, Ministry of Education, China University of Mining and Technology, Xuzhou, China","institution_ids":["https://openalex.org/I25757504"]},{"raw_affiliation_string":"School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China","institution_ids":["https://openalex.org/I25757504"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085660877","display_name":"Lin L\u00fc","orcid":"https://orcid.org/0000-0002-2803-6297"},"institutions":[{"id":"https://openalex.org/I25757504","display_name":"China University of Mining and Technology","ror":"https://ror.org/01xt2dr21","country_code":"CN","type":"education","lineage":["https://openalex.org/I25757504"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lin Lu","raw_affiliation_strings":["Engineering Research Center of Intelligent Control for Underground Space, Ministry of Education, China University of Mining and Technology, Xuzhou, China","School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Engineering Research Center of Intelligent Control for Underground Space, Ministry of Education, China University of Mining and Technology, Xuzhou, China","institution_ids":["https://openalex.org/I25757504"]},{"raw_affiliation_string":"School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China","institution_ids":["https://openalex.org/I25757504"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062986831","display_name":"Jia Meng","orcid":"https://orcid.org/0000-0003-3455-205X"},"institutions":[{"id":"https://openalex.org/I69356397","display_name":"Xi\u2019an Jiaotong-Liverpool University","ror":"https://ror.org/03zmrmn05","country_code":"CN","type":"education","lineage":["https://openalex.org/I69356397"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jia Meng","raw_affiliation_strings":["Department of Biological Sciences, AI University Re-search Center, Xi&#x0027;an Jiaotong-Liverpool University, Suzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, AI University Re-search Center, Xi&#x0027;an Jiaotong-Liverpool University, Suzhou, China","institution_ids":["https://openalex.org/I69356397"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113566766","display_name":"Hui Liu","orcid":"https://orcid.org/0000-0001-8845-4813"},"institutions":[{"id":"https://openalex.org/I25757504","display_name":"China University of Mining and Technology","ror":"https://ror.org/01xt2dr21","country_code":"CN","type":"education","lineage":["https://openalex.org/I25757504"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hui Liu","raw_affiliation_strings":["Engineering Research Center of Intelligent Control for Underground Space, Ministry of Education, China University of Mining and Technology, Xuzhou, China","School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Engineering Research Center of Intelligent Control for Underground Space, Ministry of Education, China University of Mining and Technology, Xuzhou, China","institution_ids":["https://openalex.org/I25757504"]},{"raw_affiliation_string":"School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China","institution_ids":["https://openalex.org/I25757504"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.8723,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.71230026,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":99},"biblio":{"volume":"19","issue":"3","first_page":"1640","last_page":"1650"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":1.0,"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/T11482","display_name":"RNA modifications and cancer","score":1.0,"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/T13157","display_name":"Cancer-related gene regulation","score":0.995199978351593,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9819999933242798,"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/biclustering","display_name":"Biclustering","score":0.8004816174507141},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.6284895539283752},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6041635870933533},{"id":"https://openalex.org/keywords/rna-methylation","display_name":"RNA methylation","score":0.5923702716827393},{"id":"https://openalex.org/keywords/methylation","display_name":"Methylation","score":0.5891767740249634},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4322127103805542},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.41122376918792725},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.39939913153648376},{"id":"https://openalex.org/keywords/methyltransferase","display_name":"Methyltransferase","score":0.34366026520729065},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2703925371170044},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.25777310132980347},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2527529299259186},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.22916772961616516},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2243560552597046}],"concepts":[{"id":"https://openalex.org/C144817290","wikidata":"https://www.wikidata.org/wiki/Q2976575","display_name":"Biclustering","level":5,"score":0.8004816174507141},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.6284895539283752},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6041635870933533},{"id":"https://openalex.org/C2909856833","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"RNA methylation","level":5,"score":0.5923702716827393},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.5891767740249634},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4322127103805542},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.41122376918792725},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.39939913153648376},{"id":"https://openalex.org/C91965660","wikidata":"https://www.wikidata.org/wiki/Q415875","display_name":"Methyltransferase","level":4,"score":0.34366026520729065},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2703925371170044},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.25777310132980347},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2527529299259186},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22916772961616516},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2243560552597046},{"id":"https://openalex.org/C33704608","wikidata":"https://www.wikidata.org/wiki/Q5014717","display_name":"CURE data clustering algorithm","level":4,"score":0.0},{"id":"https://openalex.org/C94641424","wikidata":"https://www.wikidata.org/wiki/Q5172845","display_name":"Correlation clustering","level":3,"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":"D008745","descriptor_name":"Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008745","descriptor_name":"Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008745","descriptor_name":"Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2021.3049366","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3049366","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33400655","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33400655","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1143551653","display_name":null,"funder_award_id":"61971422","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5450572105","display_name":null,"funder_award_id":"31871337","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G981807214","display_name":null,"funder_award_id":"2015XKQY21","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":58,"referenced_works":["https://openalex.org/W776567260","https://openalex.org/W1593486402","https://openalex.org/W1650797637","https://openalex.org/W1933156045","https://openalex.org/W1941339056","https://openalex.org/W1953890763","https://openalex.org/W1971774865","https://openalex.org/W1991807334","https://openalex.org/W2007429249","https://openalex.org/W2008887283","https://openalex.org/W2009002761","https://openalex.org/W2011131953","https://openalex.org/W2015696149","https://openalex.org/W2022770379","https://openalex.org/W2023416945","https://openalex.org/W2035618305","https://openalex.org/W2050791777","https://openalex.org/W2062821957","https://openalex.org/W2064787891","https://openalex.org/W2065847836","https://openalex.org/W2071930821","https://openalex.org/W2078964320","https://openalex.org/W2080278541","https://openalex.org/W2091235283","https://openalex.org/W2095916340","https://openalex.org/W2102872651","https://openalex.org/W2105883975","https://openalex.org/W2110065044","https://openalex.org/W2137318078","https://openalex.org/W2140729960","https://openalex.org/W2144544802","https://openalex.org/W2153976088","https://openalex.org/W2161488150","https://openalex.org/W2164852392","https://openalex.org/W2165547003","https://openalex.org/W2167616678","https://openalex.org/W2169231639","https://openalex.org/W2180404227","https://openalex.org/W2195615921","https://openalex.org/W2269054226","https://openalex.org/W2462807123","https://openalex.org/W2508638967","https://openalex.org/W2563912688","https://openalex.org/W2592658054","https://openalex.org/W2597375791","https://openalex.org/W2616848081","https://openalex.org/W2632544498","https://openalex.org/W2754499625","https://openalex.org/W2767731367","https://openalex.org/W2769630486","https://openalex.org/W2791790309","https://openalex.org/W2793785833","https://openalex.org/W2806565274","https://openalex.org/W2808202500","https://openalex.org/W2912369228","https://openalex.org/W2946834045","https://openalex.org/W3092365280","https://openalex.org/W6635743399"],"related_works":["https://openalex.org/W46965905","https://openalex.org/W2089104969","https://openalex.org/W2003083382","https://openalex.org/W3147900171","https://openalex.org/W3172822044","https://openalex.org/W2779653945","https://openalex.org/W2475490100","https://openalex.org/W4296034215","https://openalex.org/W3049201654","https://openalex.org/W2054210259"],"abstract_inverted_index":{"Recent":[0],"studies":[1,6],"have":[2],"shown":[3],"that":[4,92,173,193,199],"in-depth":[5],"on":[7,62,135],"epi-transcriptomic":[8],"patterns":[9,161,195],"of":[10,34,105,138,147],"N6-methyladenosine":[11],"(m":[12],"<sup":[13,47,184],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[14,48,185],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">6</sup>":[15,49,186],"A)":[16],"may":[17,125,205],"help":[18],"understand":[19],"its":[20],"complex":[21],"functions":[22],"and":[23,85,164,168],"co-regulatory":[24],"mechanisms.":[25],"Since":[26],"most":[27],"biclustering":[28,58],"algorithms":[29],"are":[30,179,196],"developed":[31],"in":[32,127,176,207],"scenarios":[33],"gene":[35],"expression":[36,94,103],"analysis,":[37],"which":[38,148],"does":[39],"not":[40],"share":[41],"the":[42,63,69,90],"same":[43],"characteristics":[44],"with":[45],"m":[46,183],"A":[50,187],"methylation":[51,97,140,203],"profile,":[52],"we":[53],"propose":[54],"a":[55,150,153],"weighted":[56],"Plaid":[57],"model":[59],"(FBCwPlaid)":[60],"based":[61],"Lagrange":[64],"multiplier":[65],"method":[66],"to":[67,110,152,182],"discover":[68],"potential":[70],"functional":[71],"patterns.":[72],"Each":[73],"pattern":[74,178],"is":[75],"achieved":[76],"by":[77],"minimizing":[78],"approximation":[79],"error":[80],"between":[81],"FBCwPlaid":[82,117,131],"predicted":[83],"value":[84],"real":[86],"data.":[87],"To":[88],"address":[89],"issue":[91],"site":[93,107],"level":[95,98],"determines":[96],"confidence,":[99],"it":[100],"uses":[101],"RNA":[102],"levels":[104],"each":[106,146,177],"as":[108],"weights":[109],"make":[111],"lower":[112],"expressed":[113],"sites":[114,124,141,174],"less":[115],"confident.":[116],"also":[118],"allows":[119],"overlapping":[120],"biclusters,":[121],"indicating":[122,198],"some":[123,194,200],"participate":[126],"multiple":[128],"biological":[129],"functions.":[130],"was":[132],"then":[133],"applied":[134],"MeRIP-Seq":[136],"data":[137],"69,446":[139],"under":[142],"32":[143],"experimental":[144],"conditions,":[145],"represented":[149],"stimulus":[151],"particular":[154],"cell":[155,209],"line":[156],"or":[157,211],"environment.":[158],"Finally,":[159],"three":[160],"were":[162],"discovered,":[163],"further":[165],"pathway":[166],"analysis":[167],"enzyme":[169],"specificity":[170],"test":[171],"showed":[172,192],"involved":[175],"highly":[180],"relevant":[181],"methyltransferases.":[188],"Further":[189],"detailed":[190],"analyses":[191],"condition-specific,":[197],"specific":[201,208],"sites\u2019":[202],"profiles":[204],"occur":[206],"lines":[210],"conditions.":[212]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
