{"id":"https://openalex.org/W3207035374","doi":"https://doi.org/10.1093/bib/bbab417","title":"Locus-specific expression analysis of transposable elements","display_name":"Locus-specific expression analysis of transposable elements","publication_year":2021,"publication_date":"2021-09-14","ids":{"openalex":"https://openalex.org/W3207035374","doi":"https://doi.org/10.1093/bib/bbab417","mag":"3207035374","pmid":"https://pubmed.ncbi.nlm.nih.gov/34664075","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/8769692"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbab417","doi":"https://doi.org/10.1093/bib/bbab417","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbab417","pdf_url":"https://academic.oup.com/bib/article-pdf/23/1/bbab417/42231098/bbab417.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["ccf-b","cwts-core","doaj","dongbi-b","doyens","jufo-2","ki-jl-2","medline","norway-2","oarl","poland-140","russia-white-list-1"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/23/1/bbab417/42231098/bbab417.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5012338094","display_name":"Robert J. Schwarz","orcid":"https://orcid.org/0000-0002-0654-0943","observed_orcids":["https://orcid.org/0000-0002-0654-0943"]},"institutions":[{"id":"https://openalex.org/I4210127789","display_name":"Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)","ror":"https://ror.org/039a53269","country_code":"DE","type":"facility","lineage":["https://openalex.org/I315704651","https://openalex.org/I4210127789"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Robert Schwarz","raw_affiliation_strings":["Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11, 07745 Jena, Germany"],"raw_orcid":"https://orcid.org/0000-0002-0654-0943","affiliations":[{"raw_affiliation_string":"Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11, 07745 Jena, Germany","institution_ids":["https://openalex.org/I4210127789"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050788414","display_name":"Philipp Koch","orcid":"https://orcid.org/0000-0003-2825-7943","observed_orcids":["https://orcid.org/0000-0003-2825-7943"]},"institutions":[{"id":"https://openalex.org/I4210127789","display_name":"Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)","ror":"https://ror.org/039a53269","country_code":"DE","type":"facility","lineage":["https://openalex.org/I315704651","https://openalex.org/I4210127789"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Philipp Koch","raw_affiliation_strings":["CF Life Science Computing, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11, 07745 Jena, Germany"],"raw_orcid":"https://orcid.org/0000-0003-2825-7943","affiliations":[{"raw_affiliation_string":"CF Life Science Computing, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11, 07745 Jena, Germany","institution_ids":["https://openalex.org/I4210127789"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080194003","display_name":"Jeanne Wilbrandt","orcid":"https://orcid.org/0000-0002-0363-3837","observed_orcids":["https://orcid.org/0000-0002-0363-3837"]},"institutions":[{"id":"https://openalex.org/I4210127789","display_name":"Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)","ror":"https://ror.org/039a53269","country_code":"DE","type":"facility","lineage":["https://openalex.org/I315704651","https://openalex.org/I4210127789"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jeanne Wilbrandt","raw_affiliation_strings":["CF Life Science Computing, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11, 07745 Jena, Germany"],"raw_orcid":"https://orcid.org/0000-0002-0363-3837","affiliations":[{"raw_affiliation_string":"CF Life Science Computing, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11, 07745 Jena, Germany","institution_ids":["https://openalex.org/I4210127789"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070930800","display_name":"Steve Hoffmann","orcid":"https://orcid.org/0000-0002-5239-7201","observed_orcids":["https://orcid.org/0000-0002-5239-7201"]},"institutions":[{"id":"https://openalex.org/I4210127789","display_name":"Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)","ror":"https://ror.org/039a53269","country_code":"DE","type":"facility","lineage":["https://openalex.org/I315704651","https://openalex.org/I4210127789"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Steve Hoffmann","raw_affiliation_strings":["Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11, 07745 Jena, Germany"],"raw_orcid":"https://orcid.org/0000-0002-5239-7201","affiliations":[{"raw_affiliation_string":"Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11, 07745 Jena, Germany","institution_ids":["https://openalex.org/I4210127789"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5012338094","https://openalex.org/A5070930800"],"corresponding_institution_ids":["https://openalex.org/I4210127789"],"apc_list":{"value":3894,"currency":"USD","value_usd":3894},"apc_paid":{"value":3894,"currency":"USD","value_usd":3894},"fwci":1.6512,"has_fulltext":true,"cited_by_count":27,"citation_normalized_percentile":{"value":0.82604605,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":99},"biblio":{"volume":"23","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.8359000086784363,"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":0.8359000086784363,"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":0.15160000324249268,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.003000000026077032,"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-elements","display_name":"transposable elements","score":1.0},{"id":"https://openalex.org/keywords/transposable-element-expression","display_name":"transposable element expression","score":0.5709999799728394},{"id":"https://openalex.org/keywords/differential-gene-expression","display_name":"differential gene expression","score":0.7289999723434448},{"id":"https://openalex.org/keywords/paired-end-sequencing","display_name":"paired-end sequencing","score":0.7950000166893005},{"id":"https://openalex.org/keywords/telescopes","display_name":"telescopes","score":0.9829999804496765},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.6470000147819519},{"id":"https://openalex.org/keywords/histone-modifications","display_name":"histone modifications","score":0.8970000147819519},{"id":"https://openalex.org/keywords/genomic-stability","display_name":"genome stability","score":0.6669999957084656},{"id":"https://openalex.org/keywords/non-model-organisms","display_name":"non-model organisms","score":0.6449999809265137}],"concepts":[{"id":"https://openalex.org/C4918238","wikidata":"https://www.wikidata.org/wiki/Q121438","display_name":"Transposable element","level":4,"score":0.8530078530311584},{"id":"https://openalex.org/C84597430","wikidata":"https://www.wikidata.org/wiki/Q106227","display_name":"Locus (genetics)","level":3,"score":0.6431966423988342},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.5792374610900879},{"id":"https://openalex.org/C2910146623","wikidata":"https://www.wikidata.org/wiki/Q121438","display_name":"DNA Transposable Elements","level":5,"score":0.5372175574302673},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5325813293457031},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4365103840827942},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3974733054637909},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3402308225631714},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2109675109386444},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.20116525888442993},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbab417","doi":"https://doi.org/10.1093/bib/bbab417","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbab417","pdf_url":"https://academic.oup.com/bib/article-pdf/23/1/bbab417/42231098/bbab417.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["ccf-b","cwts-core","doaj","dongbi-b","doyens","jufo-2","ki-jl-2","medline","norway-2","oarl","poland-140","russia-white-list-1"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8769692","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8769692","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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Brief Bioinform","raw_type":"Text"},{"id":"pmid:34664075","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34664075","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":"Briefings in bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:frl.publisso.de:frl:6475600","doi":null,"is_oa":true,"landing_page_url":"https://repository.publisso.de/resource/frl:6475600","pdf_url":null,"source":{"id":"https://openalex.org/S4306402606","display_name":"Informationszentrum Lebenswissenschaften (ZB MED)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210112663","host_organization_name":"ZB MED - Information Centre for Life Sciences","host_organization_lineage":["https://openalex.org/I4210112663"],"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://lobid.org/resources/99370677667606441#!, 23(1):bbab417","raw_type":"Zeitschriftenartikel"}],"best_oa_location":{"id":"doi:10.1093/bib/bbab417","doi":"https://doi.org/10.1093/bib/bbab417","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbab417","pdf_url":"https://academic.oup.com/bib/article-pdf/23/1/bbab417/42231098/bbab417.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["ccf-b","cwts-core","doaj","dongbi-b","doyens","jufo-2","ki-jl-2","medline","norway-2","oarl","poland-140","russia-white-list-1"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G6278642807","display_name":null,"funder_award_id":"03.136.2018","funder_id":"https://openalex.org/F4320324316","funder_display_name":"Klaus Tschira Stiftung"},{"id":"https://openalex.org/G7369326042","display_name":"de.NBI - Partner - de.STAIR","funder_award_id":"031L0106D","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320313941","display_name":"Friedrich-Schiller-Universit\u00e4t Jena","ror":"https://ror.org/05qpz1x62"},{"id":"https://openalex.org/F4320315885","display_name":"Australian Government","ror":"https://ror.org/0314h5y94"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320324316","display_name":"Klaus Tschira Stiftung","ror":"https://ror.org/052jep661"},{"id":"https://openalex.org/F4320324900","display_name":"Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn","ror":"https://ror.org/041nas322"},{"id":"https://openalex.org/F4320334763","display_name":"Leibniz-Gemeinschaft","ror":"https://ror.org/01n6r0e97"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3207035374.pdf","grobid_xml":"https://content.openalex.org/works/W3207035374.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1528634627","https://openalex.org/W1970091573","https://openalex.org/W1973094248","https://openalex.org/W2017621914","https://openalex.org/W2029868997","https://openalex.org/W2059864757","https://openalex.org/W2065461553","https://openalex.org/W2095595375","https://openalex.org/W2096652998","https://openalex.org/W2102619694","https://openalex.org/W2107333779","https://openalex.org/W2136605542","https://openalex.org/W2150453771","https://openalex.org/W2154146356","https://openalex.org/W2169456326","https://openalex.org/W2170687235","https://openalex.org/W2179438025","https://openalex.org/W2183090108","https://openalex.org/W2236767140","https://openalex.org/W2273566024","https://openalex.org/W2378183100","https://openalex.org/W2429031812","https://openalex.org/W2529931326","https://openalex.org/W2538665045","https://openalex.org/W2592811885","https://openalex.org/W2743624002","https://openalex.org/W2770935577","https://openalex.org/W2792712613","https://openalex.org/W2908644729","https://openalex.org/W2911642321","https://openalex.org/W2921681769","https://openalex.org/W2960706517","https://openalex.org/W2976891460","https://openalex.org/W3036325257","https://openalex.org/W4212903522","https://openalex.org/W4399639445"],"related_works":["https://openalex.org/W3036325257","https://openalex.org/W4306952466","https://openalex.org/W6888800062","https://openalex.org/W3189501930","https://openalex.org/W2096652998","https://openalex.org/W4287447425","https://openalex.org/W4411276458","https://openalex.org/W3213438581","https://openalex.org/W7147447298","https://openalex.org/W2807605914"],"abstract_inverted_index":{"Transposable":[0],"elements":[1],"(TEs)":[2],"have":[3],"been":[4],"associated":[5],"with":[6],"many,":[7],"frequently":[8],"detrimental,":[9],"biological":[10],"roles.":[11],"Consequently,":[12],"the":[13,34,43,63,76,80,100,109],"regulations":[14],"of":[15,37,49,67,82,103,106,141],"TEs,":[16],"e.g.":[17],"via":[18],"DNA-methylation":[19],"and":[20,30,56,65,92,133,151],"histone":[21],"modifications,":[22],"are":[23],"considered":[24],"critical":[25],"for":[26,124,145],"maintaining":[27],"genomic":[28],"integrity":[29],"other":[31],"functions.":[32],"Still,":[33],"high-throughput":[35],"study":[36,87],"TEs":[38,107],"is":[39,72],"usually":[40],"limited":[41],"to":[42,74,115],"family":[44],"or":[45],"consensus-sequence":[46],"level":[47,81],"because":[48],"alignment":[50],"problems":[51],"prompted":[52],"by":[53],"high-sequence":[54],"similarities":[55,91],"short":[57,93],"read":[58,94],"lengths.":[59],"To":[60],"entirely":[61],"comprehend":[62],"effects":[64],"reasons":[66],"TE":[68,77,118,142],"expression,":[69],"however,":[70],"it":[71],"necessary":[73],"assess":[75],"expression":[78,105,119,147],"at":[79,108],"individual":[83],"instances.":[84],"Our":[85],"simulation":[86],"demonstrates":[88],"that":[89,131],"sequence":[90],"lengths":[95],"do":[96],"not":[97],"rule":[98],"out":[99],"accurate":[101],"assessment":[102],"(differential)":[104],"instance-level.":[110],"With":[111],"only":[112],"slight":[113],"modifications":[114],"existing":[116],"methods,":[117],"analysis":[120],"works":[121],"surprisingly":[122],"well":[123],"conventional":[125],"paired-end":[126],"sequencing":[127],"data.":[128],"We":[129],"find":[130],"SalmonTE":[132],"Telescope":[134],"can":[135],"accurately":[136],"tally":[137],"a":[138],"considerable":[139],"amount":[140],"instances,":[143],"allowing":[144],"differential":[146],"recovery":[148],"in":[149],"model":[150],"non-model":[152],"organisms.":[153]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2021-10-25T00:00:00"}
