{"id":"https://openalex.org/W2139028033","doi":"https://doi.org/10.1093/nar/gkv257","title":"A new approach for annotation of transposable elements using small RNA mapping","display_name":"A new approach for annotation of transposable elements using small RNA mapping","publication_year":2015,"publication_date":"2015-03-26","ids":{"openalex":"https://openalex.org/W2139028033","doi":"https://doi.org/10.1093/nar/gkv257","mag":"2139028033","pmid":"https://pubmed.ncbi.nlm.nih.gov/25813049","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/4513842"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkv257","doi":"https://doi.org/10.1093/nar/gkv257","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkv257","pdf_url":"https://academic.oup.com/nar/article-pdf/43/13/e84/17433887/gkv257.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/43/13/e84/17433887/gkv257.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015047867","display_name":"Moa\u00efne El Baidouri","orcid":"https://orcid.org/0000-0002-5023-3457","observed_orcids":["https://orcid.org/0000-0002-5023-3457"]},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Moaine El\u00a0Baidouri","raw_affiliation_strings":["Center for Applied Genetic Technologies. University of Georgia, 111, Riverbend Dr., Athens, GA 30602, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Applied Genetic Technologies. University of Georgia, 111, Riverbend Dr., Athens, GA 30602, USA","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012842459","display_name":"Kyung Do Kim","orcid":"https://orcid.org/0000-0001-5296-2349","observed_orcids":["https://orcid.org/0000-0001-5296-2349"]},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kyung Do Kim","raw_affiliation_strings":["Center for Applied Genetic Technologies. University of Georgia, 111, Riverbend Dr., Athens, GA 30602, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Applied Genetic Technologies. University of Georgia, 111, Riverbend Dr., Athens, GA 30602, USA","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076953317","display_name":"Brian L. Abernathy","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brian Abernathy","raw_affiliation_strings":["Center for Applied Genetic Technologies. University of Georgia, 111, Riverbend Dr., Athens, GA 30602, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Applied Genetic Technologies. University of Georgia, 111, Riverbend Dr., Athens, GA 30602, USA","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026757656","display_name":"Siwaret Arikit","orcid":"https://orcid.org/0000-0002-2964-1886","observed_orcids":["https://orcid.org/0000-0002-2964-1886"]},"institutions":[{"id":"https://openalex.org/I4405261003","display_name":"Delaware Biotechnology Institute","ror":"https://ror.org/04m1ydt32","country_code":"US","type":"facility","lineage":["https://openalex.org/I4405261003","https://openalex.org/I86501945"]},{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Siwaret Arikit","raw_affiliation_strings":["Delaware Biotechnology Institute and Department of Plant & Soil Sciences, University of Delaware, Newark, DE 19711, USA","Delaware Biotechnology Institute and Department of Plant and Soil Sciences University of Delaware Newark DE 19711 USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Delaware Biotechnology Institute and Department of Plant & Soil Sciences, University of Delaware, Newark, DE 19711, USA","institution_ids":["https://openalex.org/I4405261003","https://openalex.org/I86501945"]},{"raw_affiliation_string":"Delaware Biotechnology Institute and Department of Plant and Soil Sciences University of Delaware Newark DE 19711 USA","institution_ids":["https://openalex.org/I4405261003","https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086631884","display_name":"Florian Maumus","orcid":"https://orcid.org/0000-0001-7325-0527","observed_orcids":["https://orcid.org/0000-0001-7325-0527"]},"institutions":[{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Florian Maumus","raw_affiliation_strings":["INRA, UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles 78026, France","INRA, UR1164 URGI\u2014Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles 78026, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INRA, UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles 78026, France","institution_ids":["https://openalex.org/I4210088668"]},{"raw_affiliation_string":"INRA, UR1164 URGI\u2014Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles 78026, France","institution_ids":["https://openalex.org/I4210088668"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025702012","display_name":"Olivier Panaud","orcid":"https://orcid.org/0000-0002-9292-503X","observed_orcids":["https://orcid.org/0000-0002-9292-503X"]},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I151295451","display_name":"Universit\u00e9 de Perpignan","ror":"https://ror.org/03am2jy38","country_code":"FR","type":"education","lineage":["https://openalex.org/I151295451"]},{"id":"https://openalex.org/I4210130438","display_name":"Laboratoire G\u00e9nome et D\u00e9veloppement des Plantes","ror":"https://ror.org/038207k30","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I151295451","https://openalex.org/I4210096427","https://openalex.org/I4210130438"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Olivier Panaud","raw_affiliation_strings":["Universit\u00e9 de Perpignan Via Domitia. Laboratoire G\u00e9nome et D\u00e9veloppement des Plantes. UMR5096 CNRS/UPVD., 52, avenue Paul Alduy. 66860 Perpignan Cedex, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 de Perpignan Via Domitia. Laboratoire G\u00e9nome et D\u00e9veloppement des Plantes. UMR5096 CNRS/UPVD., 52, avenue Paul Alduy. 66860 Perpignan Cedex, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I151295451","https://openalex.org/I4210130438"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076526804","display_name":"Blake C. Meyers","orcid":"https://orcid.org/0000-0003-3436-6097","observed_orcids":["https://orcid.org/0000-0003-3436-6097"]},"institutions":[{"id":"https://openalex.org/I4405261003","display_name":"Delaware Biotechnology Institute","ror":"https://ror.org/04m1ydt32","country_code":"US","type":"facility","lineage":["https://openalex.org/I4405261003","https://openalex.org/I86501945"]},{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Blake C. Meyers","raw_affiliation_strings":["Delaware Biotechnology Institute and Department of Plant & Soil Sciences, University of Delaware, Newark, DE 19711, USA","Delaware Biotechnology Institute and Department of Plant and Soil Sciences University of Delaware Newark DE 19711 USA"],"raw_orcid":"https://orcid.org/0000-0003-3436-6097","affiliations":[{"raw_affiliation_string":"Delaware Biotechnology Institute and Department of Plant & Soil Sciences, University of Delaware, Newark, DE 19711, USA","institution_ids":["https://openalex.org/I4405261003","https://openalex.org/I86501945"]},{"raw_affiliation_string":"Delaware Biotechnology Institute and Department of Plant and Soil Sciences University of Delaware Newark DE 19711 USA","institution_ids":["https://openalex.org/I4405261003","https://openalex.org/I86501945"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101826297","display_name":"Scott A. Jackson","orcid":"https://orcid.org/0000-0002-3172-1607","observed_orcids":["https://orcid.org/0000-0002-3172-1607"]},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Scott A. Jackson","raw_affiliation_strings":["Center for Applied Genetic Technologies. University of Georgia, 111, Riverbend Dr., Athens, GA 30602, USA sjackson@uga.edu","1Center for Applied Genetic Technologies. University of Georgia, 111, Riverbend Dr., Athens, GA 30602, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Applied Genetic Technologies. University of Georgia, 111, Riverbend Dr., Athens, GA 30602, USA sjackson@uga.edu","institution_ids":["https://openalex.org/I165733156"]},{"raw_affiliation_string":"1Center for Applied Genetic Technologies. University of Georgia, 111, Riverbend Dr., Athens, GA 30602, USA","institution_ids":["https://openalex.org/I165733156"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5101826297"],"corresponding_institution_ids":["https://openalex.org/I165733156"],"apc_list":{"value":3992,"currency":"USD","value_usd":3992},"apc_paid":{"value":3992,"currency":"USD","value_usd":3992},"fwci":5.2439,"has_fulltext":true,"cited_by_count":29,"citation_normalized_percentile":{"value":0.94861157,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"43","issue":"13","first_page":"e84","last_page":"e84"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9970999956130981,"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":0.9970999956130981,"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":0.0020000000949949026,"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/T10184","display_name":"Plant Molecular Biology Research","score":0.00039999998989515007,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/transposable-elements","display_name":"transposable elements","score":0.9739999771118164},{"id":"https://openalex.org/keywords/transposon-annotation","display_name":"transposon annotation","score":0.8489999771118164},{"id":"https://openalex.org/keywords/24-nt-sirnas","display_name":"24-nt siRNAs","score":0.9020000100135803},{"id":"https://openalex.org/keywords/transposon-silencing","display_name":"transposon silencing","score":0.8309999704360962},{"id":"https://openalex.org/keywords/plant-genome","display_name":"plant genome","score":0.6919999718666077},{"id":"https://openalex.org/keywords/arabidopsis","display_name":"Arabidopsis","score":0.8790000081062317},{"id":"https://openalex.org/keywords/rice","display_name":"rice","score":0.9980000257492065},{"id":"https://openalex.org/keywords/soybean","display_name":"soybean","score":0.9190000295639038},{"id":"https://openalex.org/keywords/de-novo-annotation","display_name":"de novo annotation","score":0.7900000214576721}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8852444291114807},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.8362337946891785},{"id":"https://openalex.org/C4918238","wikidata":"https://www.wikidata.org/wiki/Q121438","display_name":"Transposable element","level":4,"score":0.7809398174285889},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6737088561058044},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5861939191818237},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.5282527208328247},{"id":"https://openalex.org/C2779341050","wikidata":"https://www.wikidata.org/wiki/Q24287527","display_name":"Small RNA","level":4,"score":0.48137786984443665},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.46778687834739685},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.4449284076690674},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.28101563453674316},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.2283293604850769}],"mesh":[{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D012275","descriptor_name":"Oryza","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012275","descriptor_name":"Oryza","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012275","descriptor_name":"Oryza","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012275","descriptor_name":"Oryza","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013025","descriptor_name":"Glycine max","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013025","descriptor_name":"Glycine max","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013025","descriptor_name":"Glycine max","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013025","descriptor_name":"Glycine max","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020071","descriptor_name":"Interspersed Repetitive Sequences","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020071","descriptor_name":"Interspersed Repetitive Sequences","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020071","descriptor_name":"Interspersed Repetitive Sequences","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020071","descriptor_name":"Interspersed Repetitive Sequences","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1093/nar/gkv257","doi":"https://doi.org/10.1093/nar/gkv257","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkv257","pdf_url":"https://academic.oup.com/nar/article-pdf/43/13/e84/17433887/gkv257.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4513842","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4513842","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"},{"id":"pmid:25813049","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25813049","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,"listed_in":[],"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":"Nucleic acids research","raw_type":"Journal Article"},{"id":"pmh:oai:udspace.udel.edu:19716/17246","doi":null,"is_oa":true,"landing_page_url":"http://udspace.udel.edu/handle/19716/17246","pdf_url":"https://udspace.udel.edu/bitstreams/9eab6856-4645-47aa-b2c4-4b3cf835f961/download","source":{"id":"https://openalex.org/S4377196565","display_name":"Library, Museums and Press - UDSpace (University of Delaware)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I86501945","host_organization_name":"University of Delaware","host_organization_lineage":["https://openalex.org/I86501945"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/","raw_type":"Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.805.1938","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.805.1938","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/bf/a2/gkv257.PMC4513842.pdf","raw_type":"text"},{"id":"pmh:oai:HAL:hal-01215276v1","doi":null,"is_oa":true,"landing_page_url":"https://hal.science/hal-01215276","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4405252976","host_organization_name":"Centre pour la Communication Scientifique Directe","host_organization_lineage":["https://openalex.org/I4405252976"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt8wv5f9fb","doi":null,"is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/8wv5f9fb","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research, vol 43, iss 13","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/nar/gkv257","doi":"https://doi.org/10.1093/nar/gkv257","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkv257","pdf_url":"https://academic.oup.com/nar/article-pdf/43/13/e84/17433887/gkv257.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G5949325361","display_name":"Comparative-, Functional-, and Epi-Genomics of Legumes and Nodule Formation","funder_award_id":"1339194","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G899590796","display_name":"Leveraging Untapped Genetic Diversity in Soybean","funder_award_id":"1229956","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"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2139028033.pdf","grobid_xml":"https://content.openalex.org/works/W2139028033.grobid-xml"},"referenced_works_count":58,"referenced_works":["https://openalex.org/W85367672","https://openalex.org/W1494075612","https://openalex.org/W1585076338","https://openalex.org/W1964388814","https://openalex.org/W1968458420","https://openalex.org/W1974122526","https://openalex.org/W1979576560","https://openalex.org/W1984891757","https://openalex.org/W1985624299","https://openalex.org/W2000054174","https://openalex.org/W2005205149","https://openalex.org/W2012986985","https://openalex.org/W2014818969","https://openalex.org/W2021344630","https://openalex.org/W2022438258","https://openalex.org/W2024578708","https://openalex.org/W2028839461","https://openalex.org/W2036551273","https://openalex.org/W2040553259","https://openalex.org/W2049466086","https://openalex.org/W2054851865","https://openalex.org/W2059099579","https://openalex.org/W2059864757","https://openalex.org/W2059979506","https://openalex.org/W2060141463","https://openalex.org/W2070143111","https://openalex.org/W2071501400","https://openalex.org/W2076498407","https://openalex.org/W2079308685","https://openalex.org/W2082819719","https://openalex.org/W2083697678","https://openalex.org/W2084820917","https://openalex.org/W2085185449","https://openalex.org/W2094923272","https://openalex.org/W2101844654","https://openalex.org/W2102619694","https://openalex.org/W2109072112","https://openalex.org/W2112814753","https://openalex.org/W2122711136","https://openalex.org/W2122954888","https://openalex.org/W2124351063","https://openalex.org/W2129581281","https://openalex.org/W2131374955","https://openalex.org/W2144268209","https://openalex.org/W2145694678","https://openalex.org/W2156873474","https://openalex.org/W2158070006","https://openalex.org/W2161734718","https://openalex.org/W2163346964","https://openalex.org/W2163471569","https://openalex.org/W2166241520","https://openalex.org/W2170551349","https://openalex.org/W2171619188","https://openalex.org/W2436899892","https://openalex.org/W2460496335","https://openalex.org/W2462305122","https://openalex.org/W2482833590","https://openalex.org/W2979243399"],"related_works":["https://openalex.org/W3043200021","https://openalex.org/W2994632914","https://openalex.org/W2510855016","https://openalex.org/W3041568474","https://openalex.org/W1240908203","https://openalex.org/W4376255607","https://openalex.org/W3048836161","https://openalex.org/W2166281646","https://openalex.org/W2917498696","https://openalex.org/W2807605914"],"abstract_inverted_index":{"Transposable":[0],"elements":[1],"(TEs)":[2],"are":[3,24,86],"mobile":[4],"genomic":[5],"DNA":[6],"sequences":[7],"found":[8],"in":[9,112,131],"most":[10],"organisms.":[11],"They":[12],"so":[13],"densely":[14],"populate":[15],"the":[16,26,30,40,61],"genomes":[17],"of":[18,33,63,89,110],"many":[19,34],"eukaryotic":[20],"species":[21],"that":[22,78,85,119],"they":[23],"often":[25],"major":[27],"constituents.":[28],"With":[29],"rapid":[31],"generation":[32],"plant":[35],"genome":[36],"sequencing":[37],"projects":[38],"over":[39],"past":[41],"few":[42],"decades,":[43],"there":[44],"is":[45,134],"an":[46],"urgent":[47],"need":[48],"for":[49,56,65,73,106,126,136],"improved":[50],"TE":[51,76,90,129],"annotation":[52,77,109,130],"as":[53,80],"a":[54,70,81,87],"prerequisite":[55],"genome-wide":[57],"studies.":[58],"Analogous":[59],"to":[60],"use":[62,94],"RNA-seq":[64],"gene":[66],"annotation,":[67],"we":[68],"propose":[69],"new":[71,96],"method":[72],"de":[74,107,127],"novo":[75,108,128],"uses":[79],"guide":[82],"24":[83],"nt-siRNAs":[84],"part":[88],"silencing":[91],"pathways.":[92],"We":[93],"this":[95,120],"approach,":[97],"called":[98],"TASR":[99],"(for":[100],"Transposon":[101],"Annotation":[102],"using":[103],"Small":[104],"RNAs),":[105],"TEs":[111],"Arabidopsis,":[113],"rice":[114],"and":[115,117],"soybean":[116],"demonstrate":[118],"strategy":[121],"can":[122],"be":[123],"successfully":[124],"applied":[125],"plants.Executable":[132],"PERL":[133],"available":[135],"download":[137],"from:":[138],"http://tasr-pipeline.sourceforge.net/.":[139]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":4},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1}],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2016-06-24T00:00:00"}