{"id":"https://openalex.org/W4410603856","doi":"https://doi.org/10.3389/fbinf.2025.1575346","title":"MORE-RNAseq: a pipeline for quantifying retrotransposition-capable LINE1 expression based on RNA-seq data","display_name":"MORE-RNAseq: a pipeline for quantifying retrotransposition-capable LINE1 expression based on RNA-seq data","publication_year":2025,"publication_date":"2025-05-22","ids":{"openalex":"https://openalex.org/W4410603856","doi":"https://doi.org/10.3389/fbinf.2025.1575346","pmid":"https://pubmed.ncbi.nlm.nih.gov/40475058"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2025.1575346","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1575346","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1575346/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1575346/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068325499","display_name":"Yutaka Nakachi","orcid":"https://orcid.org/0000-0003-1964-2495"},"institutions":[{"id":"https://openalex.org/I96036126","display_name":"Kumamoto University","ror":"https://ror.org/02cgss904","country_code":"JP","type":"education","lineage":["https://openalex.org/I96036126"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Yutaka Nakachi","raw_affiliation_strings":["Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan","institution_ids":["https://openalex.org/I96036126"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026166611","display_name":"Jianbin Du","orcid":"https://orcid.org/0000-0003-1496-660X"},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]},{"id":"https://openalex.org/I4210133397","display_name":"Jiangxi Mental Health Center","ror":"https://ror.org/03j5jkz79","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210133397"]},{"id":"https://openalex.org/I96036126","display_name":"Kumamoto University","ror":"https://ror.org/02cgss904","country_code":"JP","type":"education","lineage":["https://openalex.org/I96036126"]}],"countries":["CN","JP"],"is_corresponding":false,"raw_author_name":"Jianbin Du","raw_affiliation_strings":["Department of Geriatric Psychiatry, The Affiliated Mental Health Center of Jiangnan University, Wuxi, China","Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Geriatric Psychiatry, The Affiliated Mental Health Center of Jiangnan University, Wuxi, China","institution_ids":["https://openalex.org/I111599522","https://openalex.org/I4210133397"]},{"raw_affiliation_string":"Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan","institution_ids":["https://openalex.org/I96036126"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084229829","display_name":"Risa Watanabe","orcid":"https://orcid.org/0000-0002-0186-9029"},"institutions":[{"id":"https://openalex.org/I96036126","display_name":"Kumamoto University","ror":"https://ror.org/02cgss904","country_code":"JP","type":"education","lineage":["https://openalex.org/I96036126"]},{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["JP","US"],"is_corresponding":false,"raw_author_name":"Risa Watanabe","raw_affiliation_strings":["Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan","Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan","institution_ids":["https://openalex.org/I96036126"]},{"raw_affiliation_string":"Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yutaro Yanagida","orcid":null},"institutions":[{"id":"https://openalex.org/I96036126","display_name":"Kumamoto University","ror":"https://ror.org/02cgss904","country_code":"JP","type":"education","lineage":["https://openalex.org/I96036126"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yutaro Yanagida","raw_affiliation_strings":["Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan","institution_ids":["https://openalex.org/I96036126"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085717963","display_name":"Miki Bundo","orcid":"https://orcid.org/0000-0002-5786-0509"},"institutions":[{"id":"https://openalex.org/I96036126","display_name":"Kumamoto University","ror":"https://ror.org/02cgss904","country_code":"JP","type":"education","lineage":["https://openalex.org/I96036126"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Miki Bundo","raw_affiliation_strings":["Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan","institution_ids":["https://openalex.org/I96036126"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032229122","display_name":"Kazuya Iwamoto","orcid":"https://orcid.org/0000-0002-1780-692X"},"institutions":[{"id":"https://openalex.org/I96036126","display_name":"Kumamoto University","ror":"https://ror.org/02cgss904","country_code":"JP","type":"education","lineage":["https://openalex.org/I96036126"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Kazuya Iwamoto","raw_affiliation_strings":["Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan","institution_ids":["https://openalex.org/I96036126"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5032229122","https://openalex.org/A5068325499"],"corresponding_institution_ids":["https://openalex.org/I96036126"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.07678817,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"5","issue":null,"first_page":"1575346","last_page":"1575346"},"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9832000136375427,"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/T10981","display_name":"Cytomegalovirus and herpesvirus research","score":0.9815000295639038,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7518750429153442},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.7176192998886108},{"id":"https://openalex.org/keywords/retrotransposon","display_name":"Retrotransposon","score":0.6797027587890625},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4085806906223297},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.39627805352211},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.37599262595176697},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3620803654193878},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.3182351589202881},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.208414226770401},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1932353675365448},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.14699825644493103},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.054272472858428955},{"id":"https://openalex.org/keywords/transposable-element","display_name":"Transposable element","score":0.053067922592163086}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7518750429153442},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.7176192998886108},{"id":"https://openalex.org/C7029365","wikidata":"https://www.wikidata.org/wiki/Q413988","display_name":"Retrotransposon","level":5,"score":0.6797027587890625},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4085806906223297},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.39627805352211},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.37599262595176697},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3620803654193878},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3182351589202881},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.208414226770401},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1932353675365448},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.14699825644493103},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.054272472858428955},{"id":"https://openalex.org/C4918238","wikidata":"https://www.wikidata.org/wiki/Q121438","display_name":"Transposable element","level":4,"score":0.053067922592163086}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/fbinf.2025.1575346","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1575346","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1575346/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40475058","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40475058","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:80842d4361bf424ba35c7ab9395624e1","is_oa":true,"landing_page_url":"https://doaj.org/article/80842d4361bf424ba35c7ab9395624e1","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 5 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12138260","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12138260","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,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Front Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2025.1575346","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1575346","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1575346/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410603856.pdf"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1508644246","https://openalex.org/W1981252886","https://openalex.org/W2025890473","https://openalex.org/W2026798838","https://openalex.org/W2096652998","https://openalex.org/W2111203527","https://openalex.org/W2111657144","https://openalex.org/W2114924552","https://openalex.org/W2145214649","https://openalex.org/W2151464048","https://openalex.org/W2153586836","https://openalex.org/W2166506784","https://openalex.org/W2168909179","https://openalex.org/W2533759132","https://openalex.org/W2538665045","https://openalex.org/W2557584271","https://openalex.org/W2592811885","https://openalex.org/W2745178135","https://openalex.org/W2908644729","https://openalex.org/W2911642321","https://openalex.org/W2921681769","https://openalex.org/W3094671770","https://openalex.org/W3146579363","https://openalex.org/W3180809905","https://openalex.org/W4287447425","https://openalex.org/W4310434702","https://openalex.org/W4319294944","https://openalex.org/W4367672459"],"related_works":["https://openalex.org/W4394359997","https://openalex.org/W4362511652","https://openalex.org/W4362511917","https://openalex.org/W4362511922","https://openalex.org/W4362485688","https://openalex.org/W4362530184","https://openalex.org/W4362530193","https://openalex.org/W2904597490","https://openalex.org/W4362485661","https://openalex.org/W4394365953"],"abstract_inverted_index":{"Retrotransposon":[0],"long":[1],"interspersed":[2],"nuclear":[3],"element-1":[4],"(LINE-1,":[5],"L1)":[6],"constitutes":[7],"a":[8,32,88,211],"large":[9],"proportion":[10],"of":[11,17,50,56,63,65,76,93,108,111,114,117,125,137,157,214,229],"the":[12,25,48,61,74,115,126,145,154,161,177,183,218,227],"mammalian":[13],"genome.":[14],"A":[15],"fraction":[16],"L1s,":[18],"which":[19,180],"have":[20],"no":[21,203],"deleterious":[22],"mutations":[23],"in":[24,47,100,164,217,231],"structure,":[26],"can":[27],"amplify":[28],"their":[29],"copies":[30],"via":[31],"process":[33],"called":[34],"retrotransposition":[35],"(RT).":[36],"RT":[37],"affects":[38],"genome":[39],"stability":[40],"and":[41,44,102,120,139,167,196,209,234],"gene":[42],"expression":[43,55,92,109,116,216],"is":[45,68],"involved":[46],"pathogenesis":[49],"many":[51],"hereditary":[52],"diseases.":[53],"Measuring":[54],"RT-capable":[57],"L1s":[58],"(rc-L1s)":[59],"among":[60],"hundreds":[62],"thousands":[64],"non":[66],"rc-L1s":[67,94,122,175,230],"an":[69],"essential":[70],"step":[71],"to":[72,132,194,225],"understand":[73,226],"impact":[75],"RT.":[77],"We":[78,129,152,170,189],"developed":[79],"mobile":[80],"element-originated":[81],"read":[82],"enrichment":[83],"from":[84,144],"RNA-seq":[85,135,200,239],"data":[86,136,201],"(MORE-RNAseq),":[87],"pipeline":[89],"for":[90,106,186],"calculating":[91],"using":[95,237],"manually":[96],"curated":[97],"L1":[98,150,207],"references":[99],"humans":[101],"mice.":[103],"MORE-RNAseq":[104,131],"allows":[105],"quantification":[107],"levels":[110],"overall":[112,162],"(sum":[113],"all":[118],"rc-L1s)":[119],"individual":[121],"with":[123,202],"consideration":[124],"genomic":[127],"context.":[128],"applied":[130,191],"publicly":[133],"available":[134,244],"human":[138,198],"mouse":[140],"cancer":[141],"cell":[142],"lines":[143],"studies":[146],"that":[147],"reported":[148],"increased":[149],"expression.":[151],"found":[153,210],"significant":[155,212],"increase":[156,213],"rc-L1":[158,215],"expressions":[159],"at":[160,176,245],"level":[163],"both":[165],"inter-":[166],"intragenic":[168],"contexts.":[169],"also":[171,190],"identified":[172],"differentially":[173],"expressed":[174],"locus":[178],"level,":[179],"will":[181,223],"be":[182],"important":[184],"candidates":[185],"downstream":[187],"analysis.":[188],"our":[192],"method":[193,222],"young":[195],"aged":[197,219],"muscle":[199],"prior":[204],"information":[205],"about":[206],"expression,":[208],"samples.":[220],"Our":[221],"contribute":[224],"role":[228],"various":[232],"physiological":[233],"pathophysiological":[235],"conditions":[236],"standard":[238],"data.":[240],"All":[241],"scripts":[242],"are":[243],"https://github.com/molbrain/MORE-RNAseq.":[246]},"counts_by_year":[],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}