{"id":"https://openalex.org/W4282030442","doi":"https://doi.org/10.1093/bioinformatics/btac354","title":"ExplorATE: a new pipeline to explore active transposable elements from RNA-seq data","display_name":"ExplorATE: a new pipeline to explore active transposable elements from RNA-seq data","publication_year":2022,"publication_date":"2022-05-24","ids":{"openalex":"https://openalex.org/W4282030442","doi":"https://doi.org/10.1093/bioinformatics/btac354","pmid":"https://pubmed.ncbi.nlm.nih.gov/35608310"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac354","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac354","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/13/3361/49884019/btac354.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/38/13/3361/49884019/btac354.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000780397","display_name":"Martin M. Femenias","orcid":"https://orcid.org/0000-0002-2690-6666"},"institutions":[{"id":"https://openalex.org/I4210142366","display_name":"Centro Cient\u00edfico Tecnol\u00f3gico Patag\u00f3nico","ror":"https://ror.org/049xnr573","country_code":"AR","type":"facility","lineage":["https://openalex.org/I151201029","https://openalex.org/I4210123736","https://openalex.org/I4210142366","https://openalex.org/I4387155568"]}],"countries":["AR"],"is_corresponding":true,"raw_author_name":"Martin M Femenias","raw_affiliation_strings":["Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas, Instituto Patag\u00f3nico para el Estudio de los Ecosistemas Continentales (IPEEC-CONICET) , Puerto Madryn, CT U9120ACD, Argentina"],"affiliations":[{"raw_affiliation_string":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas, Instituto Patag\u00f3nico para el Estudio de los Ecosistemas Continentales (IPEEC-CONICET) , Puerto Madryn, CT U9120ACD, Argentina","institution_ids":["https://openalex.org/I4210142366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101728335","display_name":"Juan C. Santos","orcid":"https://orcid.org/0000-0002-7777-8094"},"institutions":[{"id":"https://openalex.org/I142823887","display_name":"St. John's University","ror":"https://ror.org/00bgtad15","country_code":"US","type":"education","lineage":["https://openalex.org/I142823887"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Juan C Santos","raw_affiliation_strings":["Department of Biological Sciences, St. John's University , Queens, NY 11439, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, St. John's University , Queens, NY 11439, USA","institution_ids":["https://openalex.org/I142823887"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050199826","display_name":"Jack W. Sites","orcid":"https://orcid.org/0000-0002-3860-6484"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jack W Sites","raw_affiliation_strings":["Department of Biology and M.L. Bean Life Science Museum, Brigham Young University (BYU) , Provo, UT 84602, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology and M.L. Bean Life Science Museum, Brigham Young University (BYU) , Provo, UT 84602, USA","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039204103","display_name":"Luciano Javier \u00c1vila","orcid":"https://orcid.org/0000-0003-4641-6581"},"institutions":[{"id":"https://openalex.org/I4210142366","display_name":"Centro Cient\u00edfico Tecnol\u00f3gico Patag\u00f3nico","ror":"https://ror.org/049xnr573","country_code":"AR","type":"facility","lineage":["https://openalex.org/I151201029","https://openalex.org/I4210123736","https://openalex.org/I4210142366","https://openalex.org/I4387155568"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"Luciano J Avila","raw_affiliation_strings":["Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas, Instituto Patag\u00f3nico para el Estudio de los Ecosistemas Continentales (IPEEC-CONICET) , Puerto Madryn, CT U9120ACD, Argentina"],"affiliations":[{"raw_affiliation_string":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas, Instituto Patag\u00f3nico para el Estudio de los Ecosistemas Continentales (IPEEC-CONICET) , Puerto Madryn, CT U9120ACD, Argentina","institution_ids":["https://openalex.org/I4210142366"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024030384","display_name":"Mariana Morando","orcid":"https://orcid.org/0000-0002-9640-6704"},"institutions":[{"id":"https://openalex.org/I4210142366","display_name":"Centro Cient\u00edfico Tecnol\u00f3gico Patag\u00f3nico","ror":"https://ror.org/049xnr573","country_code":"AR","type":"facility","lineage":["https://openalex.org/I151201029","https://openalex.org/I4210123736","https://openalex.org/I4210142366","https://openalex.org/I4387155568"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"Mariana Morando","raw_affiliation_strings":["Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas, Instituto Patag\u00f3nico para el Estudio de los Ecosistemas Continentales (IPEEC-CONICET) , Puerto Madryn, CT U9120ACD, Argentina"],"affiliations":[{"raw_affiliation_string":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas, Instituto Patag\u00f3nico para el Estudio de los Ecosistemas Continentales (IPEEC-CONICET) , Puerto Madryn, CT U9120ACD, Argentina","institution_ids":["https://openalex.org/I4210142366"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5000780397"],"corresponding_institution_ids":["https://openalex.org/I4210142366"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.0528,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.80305935,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"38","issue":"13","first_page":"3361","last_page":"3366"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9987000226974487,"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":0.988099992275238,"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":0.7068200707435608},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.700251042842865},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6444196105003357},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6265674233436584},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5724151730537415},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5340826511383057},{"id":"https://openalex.org/keywords/spurious-relationship","display_name":"Spurious relationship","score":0.5115140676498413},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.46014201641082764},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4361554980278015},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4071066379547119},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.270302414894104},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1864756941795349},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18198329210281372},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.16184785962104797},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.1478019654750824}],"concepts":[{"id":"https://openalex.org/C4918238","wikidata":"https://www.wikidata.org/wiki/Q121438","display_name":"Transposable element","level":4,"score":0.7068200707435608},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.700251042842865},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6444196105003357},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6265674233436584},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5724151730537415},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5340826511383057},{"id":"https://openalex.org/C97256817","wikidata":"https://www.wikidata.org/wiki/Q1462316","display_name":"Spurious relationship","level":2,"score":0.5115140676498413},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.46014201641082764},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4361554980278015},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4071066379547119},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.270302414894104},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1864756941795349},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18198329210281372},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.16184785962104797},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.1478019654750824},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac354","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac354","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/13/3361/49884019/btac354.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:35608310","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35608310","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:ri.conicet.gov.ar:11336/170981","is_oa":true,"landing_page_url":"http://hdl.handle.net/11336/170981","pdf_url":null,"source":{"id":"https://openalex.org/S4306401400","display_name":"Conicet","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210104196","host_organization_name":"Centro Cient\u00edfico Tecnol\u00f3gico - Nordeste","host_organization_lineage":["https://openalex.org/I4210104196"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac354","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac354","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/13/3361/49884019/btac354.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":[{"id":"https://metadata.un.org/sdg/14","score":0.6299999952316284,"display_name":"Life below water"}],"awards":[{"id":"https://openalex.org/G1200585956","display_name":null,"funder_award_id":"PICT2015-1252","funder_id":"https://openalex.org/F4320337954","funder_display_name":"Fondo para la Investigaci\u00f3n Cient\u00edfica y Tecnol\u00f3gica"},{"id":"https://openalex.org/G4179741312","display_name":null,"funder_award_id":"PICT2011-0784","funder_id":"https://openalex.org/F4320337954","funder_display_name":"Fondo para la Investigaci\u00f3n Cient\u00edfica y Tecnol\u00f3gica"},{"id":"https://openalex.org/G4705618542","display_name":null,"funder_award_id":"2016372","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6329547617","display_name":null,"funder_award_id":"DEB-2016372","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320312458","display_name":"St. John's University","ror":"https://ror.org/00bgtad15"},{"id":"https://openalex.org/F4320337954","display_name":"Fondo para la Investigaci\u00f3n Cient\u00edfica y Tecnol\u00f3gica","ror":"https://ror.org/03stxzb56"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4282030442.pdf","grobid_xml":"https://content.openalex.org/works/W4282030442.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1999574084","https://openalex.org/W2042086471","https://openalex.org/W2046137036","https://openalex.org/W2059864757","https://openalex.org/W2062026173","https://openalex.org/W2065771268","https://openalex.org/W2077879161","https://openalex.org/W2090978648","https://openalex.org/W2095595375","https://openalex.org/W2096652998","https://openalex.org/W2107201454","https://openalex.org/W2114104545","https://openalex.org/W2148725552","https://openalex.org/W2152222332","https://openalex.org/W2179438025","https://openalex.org/W2538665045","https://openalex.org/W2553413375","https://openalex.org/W2556763090","https://openalex.org/W2584829257","https://openalex.org/W2587213787","https://openalex.org/W2592811885","https://openalex.org/W2749706640","https://openalex.org/W2788876413","https://openalex.org/W2789843538","https://openalex.org/W2803834849","https://openalex.org/W2805084391","https://openalex.org/W2822240849","https://openalex.org/W2892332606","https://openalex.org/W2911642321","https://openalex.org/W2951722482","https://openalex.org/W2972280986","https://openalex.org/W2989996227","https://openalex.org/W2994632914","https://openalex.org/W2998336860","https://openalex.org/W3000279131","https://openalex.org/W3005162899","https://openalex.org/W3005320228","https://openalex.org/W3015812144","https://openalex.org/W3017049640","https://openalex.org/W3036325257","https://openalex.org/W3083664261","https://openalex.org/W6728970545"],"related_works":["https://openalex.org/W2053969879","https://openalex.org/W2082641564","https://openalex.org/W2107333779","https://openalex.org/W2790772971","https://openalex.org/W3211333492","https://openalex.org/W3215901263","https://openalex.org/W2059021908","https://openalex.org/W2121332208","https://openalex.org/W1964419640","https://openalex.org/W820151157"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2}],"updated_date":"2026-04-14T08:04:32.555800","created_date":"2025-10-10T00:00:00"}
