{"id":"https://openalex.org/W4403211625","doi":"https://doi.org/10.1109/cibcb58642.2024.10702140","title":"Classification of LTR Retrotransposons via Interaction Prediction","display_name":"Classification of LTR Retrotransposons via Interaction Prediction","publication_year":2024,"publication_date":"2024-08-27","ids":{"openalex":"https://openalex.org/W4403211625","doi":"https://doi.org/10.1109/cibcb58642.2024.10702140"},"language":"en","primary_location":{"id":"doi:10.1109/cibcb58642.2024.10702140","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb58642.2024.10702140","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5113117388","display_name":"Silvana C. S. Cardoso","orcid":null},"institutions":[{"id":"https://openalex.org/I177909021","display_name":"Universidade Federal de S\u00e3o Carlos","ror":"https://ror.org/00qdc6m37","country_code":"BR","type":"education","lineage":["https://openalex.org/I177909021"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Silvana C. S. Cardoso","raw_affiliation_strings":["Federal University of S&#x00E3;o Carlos,Department of Physics,Brazil"],"affiliations":[{"raw_affiliation_string":"Federal University of S&#x00E3;o Carlos,Department of Physics,Brazil","institution_ids":["https://openalex.org/I177909021"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088024942","display_name":"Douglas Silva Domingues","orcid":"https://orcid.org/0000-0002-1290-0853"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Douglas S. Domingues","raw_affiliation_strings":["Escola Superior de Agricultura Luiz de Queiroz, Universidade de S&#x00E3;o Paulo,Departamento de Gen&#x00E9;tica,Brazil"],"affiliations":[{"raw_affiliation_string":"Escola Superior de Agricultura Luiz de Queiroz, Universidade de S&#x00E3;o Paulo,Departamento de Gen&#x00E9;tica,Brazil","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051358440","display_name":"Alexandre Rossi Paschoal","orcid":"https://orcid.org/0000-0002-8887-0582"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Alexandre R. Paschoal","raw_affiliation_strings":["Federal University of Technology,Department of Computer Science,Brazil"],"affiliations":[{"raw_affiliation_string":"Federal University of Technology,Department of Computer Science,Brazil","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045524441","display_name":"Carlos Norberto Fischer","orcid":"https://orcid.org/0000-0002-5598-6263"},"institutions":[{"id":"https://openalex.org/I879563668","display_name":"Universidade Estadual Paulista (Unesp)","ror":"https://ror.org/00987cb86","country_code":"BR","type":"education","lineage":["https://openalex.org/I879563668"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Carlos N. Fischer","raw_affiliation_strings":["Matem&#x00E1;tica Aplicada e Computa&#x00E7;&#x00E3;o, Universidade Estadual Paulista,Departamento de Estat&#x00ED;stica,Brazil"],"affiliations":[{"raw_affiliation_string":"Matem&#x00E1;tica Aplicada e Computa&#x00E7;&#x00E3;o, Universidade Estadual Paulista,Departamento de Estat&#x00ED;stica,Brazil","institution_ids":["https://openalex.org/I879563668"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066866262","display_name":"Ricardo Cerri","orcid":"https://orcid.org/0000-0002-2582-1695"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ricardo Cerri","raw_affiliation_strings":["Instituto de Ci&#x00EA;ncias Matem&#x00E1;ticas e de Computa&#x00E7;ao, &#x02DC; Universidade de S&#x00E3;o Paulo,Department of Computer Science,Brazil"],"affiliations":[{"raw_affiliation_string":"Instituto de Ci&#x00EA;ncias Matem&#x00E1;ticas e de Computa&#x00E7;ao, &#x02DC; Universidade de S&#x00E3;o Paulo,Department of Computer Science,Brazil","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5113117388"],"corresponding_institution_ids":["https://openalex.org/I177909021"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.09625906,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9822999835014343,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9822999835014343,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9397000074386597,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/retrotransposon","display_name":"Retrotransposon","score":0.8216747045516968},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6281628608703613},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.35981371998786926},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1748376488685608},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.13547393679618835},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13307729363441467},{"id":"https://openalex.org/keywords/transposable-element","display_name":"Transposable element","score":0.113371342420578}],"concepts":[{"id":"https://openalex.org/C7029365","wikidata":"https://www.wikidata.org/wiki/Q413988","display_name":"Retrotransposon","level":5,"score":0.8216747045516968},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6281628608703613},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.35981371998786926},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1748376488685608},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.13547393679618835},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13307729363441467},{"id":"https://openalex.org/C4918238","wikidata":"https://www.wikidata.org/wiki/Q121438","display_name":"Transposable element","level":4,"score":0.113371342420578},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/cibcb58642.2024.10702140","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb58642.2024.10702140","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/13","score":0.4099999964237213,"display_name":"Climate action"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W55768394","https://openalex.org/W59589783","https://openalex.org/W1967542092","https://openalex.org/W2008840001","https://openalex.org/W2021344630","https://openalex.org/W2033049603","https://openalex.org/W2059864757","https://openalex.org/W2069458148","https://openalex.org/W2071501400","https://openalex.org/W2119331235","https://openalex.org/W2127774996","https://openalex.org/W2130212962","https://openalex.org/W2132141594","https://openalex.org/W2169859562","https://openalex.org/W2170960297","https://openalex.org/W2608035254","https://openalex.org/W2800198679","https://openalex.org/W2800240915","https://openalex.org/W2892332606","https://openalex.org/W2897216915","https://openalex.org/W2903975631","https://openalex.org/W2947464213","https://openalex.org/W2965883971","https://openalex.org/W3025472913","https://openalex.org/W4311049139","https://openalex.org/W6716194921","https://openalex.org/W6790425969","https://openalex.org/W6791467293"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W4285312541","https://openalex.org/W4211158134","https://openalex.org/W2606486591","https://openalex.org/W2358072366","https://openalex.org/W3152031548","https://openalex.org/W2361710902","https://openalex.org/W2041009366","https://openalex.org/W1969846117"],"abstract_inverted_index":{"Transposable":[0],"Elements":[1],"(TEs)":[2],"are":[3,18,205],"genetic":[4,13],"sequences":[5,66,91,105],"that":[6,203],"can":[7],"relocate":[8],"within":[9],"the":[10,46,52,80,100,107,114,122,130,138,156,159,171,181,187,215],"genome,":[11],"promoting":[12],"diversity.":[14],"In":[15,129],"eukaryotes,":[16],"TEs":[17],"classified":[19,154],"into":[20,155],"classes,":[21],"subclasses,":[22],"orders,":[23],"superfamilies,":[24,98],"families,":[25],"and":[26,67,96,125,173,199,207],"subfamilies.":[27],"LTR":[28,49,89],"retrotransposons":[29,50],"(LTR-RT)":[30],"constitute":[31],"an":[32],"order":[33],"in":[34,145,186,213],"this":[35,41],"taxonomy.":[36],"The":[37,85,150,193],"main":[38],"objective":[39],"of":[40,48,106,142,180,189],"study":[42],"is":[43,134,152],"to":[44,61,71,78,93,121,178,209],"investigate":[45,79],"classification":[47,131],"at":[51],"superfamily":[53,157],"level.":[54],"Predictive":[55],"Bi-Clustering":[56],"Trees":[57],"(PBCTs)":[58],"were":[59,76,165],"used":[60,77,184],"predict":[62],"interactions":[63],"between":[64],"LTR-RT":[65,123,148],"conserved":[68,108,126],"protein":[69],"domains":[70,109],"achieve":[72],"this.":[73],"Two":[74],"datasets":[75],"relationships":[81],"among":[82],"different":[83],"superfamilies.":[84],"first":[86],"dataset":[87,102],"contained":[88],"retrotransposon":[90],"assigned":[92],"Copia,":[94],"Gypsy,":[95],"Bel-Pao":[97],"while":[99],"second":[101],"included":[103],"consensus":[104],"for":[110,170],"each":[111],"superfamily.":[112,217],"Thus,":[113],"PBCT":[115],"decision":[116],"tree":[117],"tests":[118],"could":[119],"relate":[120],"sequence":[124,151],"domain":[127,144],"attributes.":[128],"process,":[132],"interaction":[133],"interpreted":[135],"as":[136,167],"either":[137],"presence":[139],"or":[140],"absence":[141],"a":[143,146],"given":[147],"sequence.":[149],"then":[153],"with":[158],"most":[160,182],"predicted":[161],"domains.":[162],"Precision-recall":[163],"curves":[164],"adopted":[166],"evaluation":[168],"metrics":[169],"method,":[172],"its":[174],"performance":[175],"was":[176],"compared":[177],"some":[179],"commonly":[183],"models":[185],"task":[188],"transposable":[190],"element":[191],"classification.":[192],"experiments":[194],"conducted":[195],"on":[196],"D.":[197],"melanogaster":[198],"A.":[200],"thaliana":[201],"showed":[202],"PBCTs":[204],"promising":[206],"comparable":[208],"other":[210],"methods,":[211],"especially":[212],"classifying":[214],"Gypsy":[216]},"counts_by_year":[],"updated_date":"2025-12-27T23:08:20.325037","created_date":"2025-10-10T00:00:00"}
