{"id":"https://openalex.org/W2183363900","doi":"https://doi.org/10.2390/biecoll-jib-2013-231","title":"Improving the performance of Transposable Elements detection tools","display_name":"Improving the performance of Transposable Elements detection tools","publication_year":2013,"publication_date":"2013-01-01","ids":{"openalex":"https://openalex.org/W2183363900","doi":"https://doi.org/10.2390/biecoll-jib-2013-231","mag":"2183363900","pmid":"https://pubmed.ncbi.nlm.nih.gov/24231145"},"language":"en","primary_location":{"id":"pmid:24231145","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24231145","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":"Journal of integrative bioinformatics","raw_type":null},"type":"article","indexed_in":["datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://repositorio.inesctec.pt/handle/123456789/7070","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016378511","display_name":"Tiago Loureiro","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Loureiro, Tiago","raw_affiliation_strings":["DEI & Faculdade de Engenharia, Universidade do Porto, Portugal"],"affiliations":[{"raw_affiliation_string":"DEI & Faculdade de Engenharia, Universidade do Porto, Portugal","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054960351","display_name":"Rui Camacho","orcid":"https://orcid.org/0000-0003-0940-3554"},"institutions":[{"id":"https://openalex.org/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Camacho, Rui","raw_affiliation_strings":["University of Porto"],"affiliations":[{"raw_affiliation_string":"University of Porto","institution_ids":["https://openalex.org/I182534213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015978945","display_name":"Jorge Vieira","orcid":"https://orcid.org/0000-0001-7032-5220"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Vieira, Jorge","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5003291220","display_name":"Nuno A. Fonseca","orcid":"https://orcid.org/0000-0003-4832-578X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Fonseca, Nuno A.","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5016378511"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.9251,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.82666482,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"10","issue":"3","first_page":"231","last_page":"231"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9984999895095825,"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":0.9984999895095825,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9983999729156494,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9914000034332275,"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/transposable-element","display_name":"Transposable element","score":0.7830716371536255},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7700467705726624},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6462664008140564},{"id":"https://openalex.org/keywords/transpose","display_name":"Transpose","score":0.596697986125946},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5683769583702087},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.4636102616786957},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4348880648612976},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.42527979612350464},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14792442321777344},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12456732988357544},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.0921686589717865}],"concepts":[{"id":"https://openalex.org/C4918238","wikidata":"https://www.wikidata.org/wiki/Q121438","display_name":"Transposable element","level":4,"score":0.7830716371536255},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7700467705726624},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6462664008140564},{"id":"https://openalex.org/C200106649","wikidata":"https://www.wikidata.org/wiki/Q223683","display_name":"Transpose","level":3,"score":0.596697986125946},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5683769583702087},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.4636102616786957},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4348880648612976},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.42527979612350464},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14792442321777344},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12456732988357544},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0921686589717865},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C158693339","wikidata":"https://www.wikidata.org/wiki/Q190524","display_name":"Eigenvalues and eigenvectors","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"pmid:24231145","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24231145","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":"Journal of integrative bioinformatics","raw_type":null},{"id":"pmh:oai:repositorio.inesctec.pt:123456789/7070","is_oa":true,"landing_page_url":"http://repositorio.inesctec.pt/handle/123456789/7070","pdf_url":"http://repositorio.inesctec.pt/handle/123456789/7070","source":{"id":"https://openalex.org/S4306402433","display_name":"Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"journal article"},{"id":"pmh:oai:biecoll.ub.uni-bielefeld.de:5309","is_oa":false,"landing_page_url":"http://biecoll.ub.uni-bielefeld.de/volltexte/2013/5309/","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://journal.imbio.de/article.php?aid=231","raw_type":"Journal Article"},{"id":"doi:10.2390/biecoll-jib-2013-231","is_oa":true,"landing_page_url":"https://doi.org/10.2390/biecoll-jib-2013-231","pdf_url":null,"source":{"id":"https://openalex.org/S4306401670","display_name":"PUB \u2013 Publications at Bielefeld University (Bielefeld University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20121455","host_organization_name":"Bielefeld University","host_organization_lineage":["https://openalex.org/I20121455"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"pmh:oai:repositorio.inesctec.pt:123456789/7070","is_oa":true,"landing_page_url":"http://repositorio.inesctec.pt/handle/123456789/7070","pdf_url":"http://repositorio.inesctec.pt/handle/123456789/7070","source":{"id":"https://openalex.org/S4306402433","display_name":"Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"journal article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1167214205","display_name":null,"funder_award_id":"COMPETE","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G1578237752","display_name":null,"funder_award_id":"COMPETE","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G160550121","display_name":null,"funder_award_id":"-FEDER-","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G1716593420","display_name":null,"funder_award_id":"-FEDER-","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G5348594205","display_name":null,"funder_award_id":"FEDER","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G6299983296","display_name":null,"funder_award_id":"PTDC/","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G7049410507","display_name":null,"funder_award_id":"Portuguese Foundation for Science","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G7900078432","display_name":null,"funder_award_id":"PTDC/","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G8319216165","display_name":null,"funder_award_id":"01-0124-FEDER-022701","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G8570012161","display_name":null,"funder_award_id":"unknown","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G8868700560","display_name":null,"funder_award_id":"FCOMP-01-0124-FEDER","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G943999617","display_name":null,"funder_award_id":"Technology","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"}],"funders":[{"id":"https://openalex.org/F4320324086","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612"},{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2183363900.pdf","grobid_xml":"https://content.openalex.org/works/W2183363900.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W1570448133","https://openalex.org/W1968050693","https://openalex.org/W1975445958","https://openalex.org/W1999078569","https://openalex.org/W1999930403","https://openalex.org/W2029195137","https://openalex.org/W2033049603","https://openalex.org/W2050228332","https://openalex.org/W2054373621","https://openalex.org/W2069712815","https://openalex.org/W2071501400","https://openalex.org/W2113506551","https://openalex.org/W2122954888","https://openalex.org/W2123646732","https://openalex.org/W2129581281","https://openalex.org/W2136145671"],"related_works":["https://openalex.org/W3095837879","https://openalex.org/W2606530940","https://openalex.org/W2977884694","https://openalex.org/W2510855016","https://openalex.org/W2917498696","https://openalex.org/W1536808921","https://openalex.org/W2436899892","https://openalex.org/W2460331461","https://openalex.org/W2072285646","https://openalex.org/W2990895847"],"abstract_inverted_index":{"Transposable":[0],"Elements":[1],"(TE)":[2],"are":[3,18],"sequences":[4],"of":[5,54,63,87,92],"DNA":[6],"that":[7,99],"move":[8],"and":[9,29,40,67,70,95],"transpose":[10],"within":[11],"a":[12],"genome.":[13],"TEs,":[14],"as":[15],"mutation":[16],"agents,":[17],"quite":[19],"important":[20],"for":[21],"their":[22,81,100],"role":[23],"in":[24,89],"both":[25],"genome":[26],"alteration":[27],"diseases":[28],"on":[30,50],"species":[31],"evolution.":[32],"Several":[33],"tools":[34,69,97],"have":[35],"been":[36],"developed":[37],"to":[38,79],"discover":[39],"annotate":[41],"TEs":[42,65,93],"but":[43],"no":[44],"single":[45],"tool":[46],"achieves":[47],"good":[48],"results":[49,86],"all":[51],"different":[52],"types":[53],"TEs.":[55],"In":[56],"this":[57],"paper":[58],"we":[59],"evaluate":[60],"the":[61],"performance":[62,101],"several":[64],"detection":[66,83,94],"annotation":[68,96],"investigate":[71],"if":[72],"Machine":[73],"Learning":[74],"techniques":[75],"can":[76,102],"be":[77,103],"used":[78],"improve":[80],"overall":[82],"accuracy.":[84],"The":[85],"an":[88],"silico":[90],"evaluation":[91],"indicate":[98],"improved":[104],"by":[105],"using":[106],"machine":[107],"learning":[108],"constructed":[109],"classifiers.":[110]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":7},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
