{"id":"https://openalex.org/W3025472913","doi":"https://doi.org/10.1093/bioinformatics/btaa519","title":"DeepTE: a computational method for <i>de novo</i> classification of transposons with convolutional neural network","display_name":"DeepTE: a computational method for <i>de novo</i> classification of transposons with convolutional neural network","publication_year":2020,"publication_date":"2020-05-12","ids":{"openalex":"https://openalex.org/W3025472913","doi":"https://doi.org/10.1093/bioinformatics/btaa519","mag":"3025472913","pmid":"https://pubmed.ncbi.nlm.nih.gov/32415954"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa519","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa519","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/15/4269/33796677/btaa519.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/36/15/4269/33796677/btaa519.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064484262","display_name":"Haidong Yan","orcid":"https://orcid.org/0000-0002-9903-2672"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Haidong Yan","raw_affiliation_strings":["School of Plant and Environmental Sciences (SPES), Virginia Tech , Blacksburg, VA 24061, USA"],"affiliations":[{"raw_affiliation_string":"School of Plant and Environmental Sciences (SPES), Virginia Tech , Blacksburg, VA 24061, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087701636","display_name":"Aureliano Bombarely","orcid":"https://orcid.org/0000-0001-6257-8914"},"institutions":[{"id":"https://openalex.org/I189158943","display_name":"University of Milan","ror":"https://ror.org/00wjc7c48","country_code":"IT","type":"education","lineage":["https://openalex.org/I189158943"]},{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["IT","US"],"is_corresponding":false,"raw_author_name":"Aureliano Bombarely","raw_affiliation_strings":["Department of Life Sciences, University of Milan , Milan 20122, Italy","School of Plant and Environmental Sciences (SPES), Virginia Tech , Blacksburg, VA 24061, USA"],"affiliations":[{"raw_affiliation_string":"Department of Life Sciences, University of Milan , Milan 20122, Italy","institution_ids":["https://openalex.org/I189158943"]},{"raw_affiliation_string":"School of Plant and Environmental Sciences (SPES), Virginia Tech , Blacksburg, VA 24061, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100448209","display_name":"Song Li","orcid":"https://orcid.org/0000-0002-8133-3944"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Song Li","raw_affiliation_strings":["Graduate Program in Genetics, Bioinformatics and Computational Biology (GBCB), Virginia Tech , Blacksburg, VA 24061, USA","School of Plant and Environmental Sciences (SPES), Virginia Tech , Blacksburg, VA 24061, USA"],"affiliations":[{"raw_affiliation_string":"Graduate Program in Genetics, Bioinformatics and Computational Biology (GBCB), Virginia Tech , Blacksburg, VA 24061, USA","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"School of Plant and Environmental Sciences (SPES), Virginia Tech , Blacksburg, VA 24061, USA","institution_ids":["https://openalex.org/I859038795"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100448209"],"corresponding_institution_ids":["https://openalex.org/I859038795"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":13.2125,"has_fulltext":true,"cited_by_count":202,"citation_normalized_percentile":{"value":0.98795984,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"36","issue":"15","first_page":"4269","last_page":"4275"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9995999932289124,"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":0.9919000267982483,"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/convolutional-neural-network","display_name":"Convolutional neural network","score":0.7939091324806213},{"id":"https://openalex.org/keywords/transposable-element","display_name":"Transposable element","score":0.7325288653373718},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.7075487375259399},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6421110033988953},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6341024041175842},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5439070463180542},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5262688398361206},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4227029085159302},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3940720856189728},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.36823707818984985},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3240423798561096},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2628113627433777},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1242654025554657},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1057349145412445},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.06546372175216675}],"concepts":[{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.7939091324806213},{"id":"https://openalex.org/C4918238","wikidata":"https://www.wikidata.org/wiki/Q121438","display_name":"Transposable element","level":4,"score":0.7325288653373718},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.7075487375259399},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6421110033988953},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6341024041175842},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5439070463180542},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5262688398361206},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4227029085159302},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3940720856189728},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.36823707818984985},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3240423798561096},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2628113627433777},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1242654025554657},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1057349145412445},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06546372175216675},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaa519","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa519","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/15/4269/33796677/btaa519.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:32415954","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32415954","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:digital.csic.es:10261/416178","is_oa":false,"landing_page_url":"http://hdl.handle.net/10261/416178","pdf_url":null,"source":{"id":"https://openalex.org/S4306400616","display_name":"DIGITAL.CSIC (Spanish National Research Council (CSIC))","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I134820265","host_organization_name":"Consejo Superior de Investigaciones Cient\u00edficas","host_organization_lineage":["https://openalex.org/I134820265"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:air.unimi.it:2434/798658","is_oa":true,"landing_page_url":"http://hdl.handle.net/2434/798658","pdf_url":null,"source":{"id":"https://openalex.org/S4306400516","display_name":"Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I189158943","host_organization_name":"University of Milan","host_organization_lineage":["https://openalex.org/I189158943"],"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":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa519","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa519","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/15/4269/33796677/btaa519.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/15","display_name":"Life in Land","score":0.49000000953674316}],"awards":[{"id":"https://openalex.org/G3890658974","display_name":null,"funder_award_id":"Hatch","funder_id":"https://openalex.org/F4320306114","funder_display_name":"U.S. Department of Agriculture"},{"id":"https://openalex.org/G6441438290","display_name":null,"funder_award_id":"USDA Hatch","funder_id":"https://openalex.org/F4320306114","funder_display_name":"U.S. Department of Agriculture"}],"funders":[{"id":"https://openalex.org/F4320306114","display_name":"U.S. Department of Agriculture","ror":"https://ror.org/01na82s61"},{"id":"https://openalex.org/F4320309646","display_name":"Virginia Polytechnic Institute and State University","ror":"https://ror.org/02smfhw86"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3025472913.pdf","grobid_xml":"https://content.openalex.org/works/W3025472913.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1123205372","https://openalex.org/W1482190741","https://openalex.org/W1835750348","https://openalex.org/W1963918196","https://openalex.org/W1967297336","https://openalex.org/W1984259444","https://openalex.org/W1988581590","https://openalex.org/W2014704298","https://openalex.org/W2021081566","https://openalex.org/W2021344630","https://openalex.org/W2046842005","https://openalex.org/W2054254276","https://openalex.org/W2059864757","https://openalex.org/W2076063813","https://openalex.org/W2076092946","https://openalex.org/W2082330286","https://openalex.org/W2083697678","https://openalex.org/W2085708372","https://openalex.org/W2110367804","https://openalex.org/W2120583228","https://openalex.org/W2132141594","https://openalex.org/W2134783286","https://openalex.org/W2163960662","https://openalex.org/W2169859562","https://openalex.org/W2198606573","https://openalex.org/W2222590335","https://openalex.org/W2259812802","https://openalex.org/W2343416635","https://openalex.org/W2345512687","https://openalex.org/W2433743436","https://openalex.org/W2467672047","https://openalex.org/W2605266783","https://openalex.org/W2768337983","https://openalex.org/W2772231999","https://openalex.org/W2808191239","https://openalex.org/W2855293443","https://openalex.org/W2892332606","https://openalex.org/W2895144975","https://openalex.org/W2900520464","https://openalex.org/W2901901698","https://openalex.org/W2917498696","https://openalex.org/W2929108854","https://openalex.org/W2935703330"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2053969879","https://openalex.org/W2082641564","https://openalex.org/W2107333779","https://openalex.org/W3108190435","https://openalex.org/W2790772971","https://openalex.org/W1964419640","https://openalex.org/W1906262170"],"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":23},{"year":2025,"cited_by_count":75},{"year":2024,"cited_by_count":47},{"year":2023,"cited_by_count":26},{"year":2022,"cited_by_count":21},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":4}],"updated_date":"2026-04-16T08:26:57.006410","created_date":"2020-05-21T00:00:00"}
