{"id":"https://openalex.org/W4402839059","doi":"https://doi.org/10.1093/bib/bbae467","title":"3t-seq: automatic gene expression analysis of single-copy genes, transposable elements, and tRNAs from RNA-seq data","display_name":"3t-seq: automatic gene expression analysis of single-copy genes, transposable elements, and tRNAs from RNA-seq data","publication_year":2024,"publication_date":"2024-09-23","ids":{"openalex":"https://openalex.org/W4402839059","doi":"https://doi.org/10.1093/bib/bbae467","pmid":"https://pubmed.ncbi.nlm.nih.gov/39322626"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae467","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae467","pdf_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae467/59335334/bbae467.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"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"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae467/59335334/bbae467.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5113401496","display_name":"Francesco Tabaro","orcid":null},"institutions":[{"id":"https://openalex.org/I4210111367","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/01yr73893","country_code":"IT","type":"government","lineage":["https://openalex.org/I4210111367","https://openalex.org/I4210138560"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Francesco Tabaro","raw_affiliation_strings":["Epigenetics and Neurobiology Unit, EMBL Rome, European Molecular Biology Laboratory , Via Ercole Ramarini 32, Monterotondo 00015,"],"affiliations":[{"raw_affiliation_string":"Epigenetics and Neurobiology Unit, EMBL Rome, European Molecular Biology Laboratory , Via Ercole Ramarini 32, Monterotondo 00015,","institution_ids":["https://openalex.org/I4210111367"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5114233831","display_name":"Matthieu Boulard","orcid":null},"institutions":[{"id":"https://openalex.org/I4210111367","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/01yr73893","country_code":"IT","type":"government","lineage":["https://openalex.org/I4210111367","https://openalex.org/I4210138560"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Matthieu Boulard","raw_affiliation_strings":["Epigenetics and Neurobiology Unit, EMBL Rome, European Molecular Biology Laboratory , Via Ercole Ramarini 32, Monterotondo 00015,"],"affiliations":[{"raw_affiliation_string":"Epigenetics and Neurobiology Unit, EMBL Rome, European Molecular Biology Laboratory , Via Ercole Ramarini 32, Monterotondo 00015,","institution_ids":["https://openalex.org/I4210111367"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5113401496"],"corresponding_institution_ids":["https://openalex.org/I4210111367"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.2437,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.58406224,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"25","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9997000098228455,"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"}},"topics":[{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9997000098228455,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9988999962806702,"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":0.9983000159263611,"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/rna-seq","display_name":"RNA-Seq","score":0.679753839969635},{"id":"https://openalex.org/keywords/transposable-element","display_name":"Transposable element","score":0.5846871137619019},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5536497831344604},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5160355567932129},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5121605396270752},{"id":"https://openalex.org/keywords/polyadenylation","display_name":"Polyadenylation","score":0.46337878704071045},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.44690531492233276},{"id":"https://openalex.org/keywords/transfer-rna","display_name":"Transfer RNA","score":0.4134385287761688},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4067722260951996},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.3927677869796753},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.35493403673171997},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.285545289516449}],"concepts":[{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.679753839969635},{"id":"https://openalex.org/C4918238","wikidata":"https://www.wikidata.org/wiki/Q121438","display_name":"Transposable element","level":4,"score":0.5846871137619019},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5536497831344604},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5160355567932129},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5121605396270752},{"id":"https://openalex.org/C142575336","wikidata":"https://www.wikidata.org/wiki/Q412148","display_name":"Polyadenylation","level":4,"score":0.46337878704071045},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.44690531492233276},{"id":"https://openalex.org/C153957851","wikidata":"https://www.wikidata.org/wiki/Q201448","display_name":"Transfer RNA","level":4,"score":0.4134385287761688},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4067722260951996},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.3927677869796753},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.35493403673171997},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.285545289516449}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012343","descriptor_name":"RNA, Transfer","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012343","descriptor_name":"RNA, Transfer","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012343","descriptor_name":"RNA, Transfer","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012343","descriptor_name":"RNA, Transfer","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae467","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae467","pdf_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae467/59335334/bbae467.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"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":"pmid:39322626","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39322626","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11424182","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11424182","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11424182/pdf/bbae467.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae467","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae467","pdf_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae467/59335334/bbae467.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320314023","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/050589e39"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4402839059.pdf","grobid_xml":"https://content.openalex.org/works/W4402839059.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1999574084","https://openalex.org/W2029623390","https://openalex.org/W2046241907","https://openalex.org/W2088612061","https://openalex.org/W2096652998","https://openalex.org/W2102619694","https://openalex.org/W2104005232","https://openalex.org/W2126419817","https://openalex.org/W2131271579","https://openalex.org/W2138207763","https://openalex.org/W2156274673","https://openalex.org/W2169456326","https://openalex.org/W2170551349","https://openalex.org/W2179438025","https://openalex.org/W2205690268","https://openalex.org/W2223836536","https://openalex.org/W2236822143","https://openalex.org/W2267092331","https://openalex.org/W2432815617","https://openalex.org/W2538665045","https://openalex.org/W2589026194","https://openalex.org/W2592811885","https://openalex.org/W2770935577","https://openalex.org/W2799170276","https://openalex.org/W2908644729","https://openalex.org/W2963367647","https://openalex.org/W2998336860","https://openalex.org/W3006653136","https://openalex.org/W3036426980","https://openalex.org/W3081933993","https://openalex.org/W3110764155","https://openalex.org/W3111152985","https://openalex.org/W3112468480","https://openalex.org/W3113761085","https://openalex.org/W3118238647","https://openalex.org/W3122109253","https://openalex.org/W3148902524","https://openalex.org/W3186309583","https://openalex.org/W3195010157","https://openalex.org/W4210296660","https://openalex.org/W4210644165","https://openalex.org/W4229948506","https://openalex.org/W4362660267","https://openalex.org/W6746248141","https://openalex.org/W6786498093"],"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":{"RNA":[0,25,64],"sequencing":[1,55,123],"is":[2,74,81,167,173],"the":[3,161],"gold-standard":[4],"method":[5,154],"to":[6,52,83,141,155],"quantify":[7,142],"transcriptomic":[8],"changes":[9],"between":[10],"two":[11],"conditions.":[12],"The":[13],"overwhelming":[14],"majority":[15],"of":[16,87,101],"data":[17,124],"analysis":[18,100,119],"methods":[19,140],"available":[20,174],"are":[21,45,57,61,68],"focused":[22],"on":[23,164],"polyadenylated":[24],"transcribed":[26,62],"from":[27,33,103,121],"single-copy":[28,104],"genes":[29],"and":[30,48,67,107,114,125,134,145,172],"overlook":[31],"transcripts":[32,102],"repeated":[34],"sequences":[35],"such":[36],"as":[37],"transposable":[38],"elements":[39,44],"(TEs).":[40],"These":[41],"self-autonomous":[42],"genetic":[43],"increasingly":[46],"studied,":[47],"specialized":[49],"tools":[50],"designed":[51],"handle":[53],"multimapping":[54],"reads":[56],"available.":[58],"Transfer":[59],"RNAs":[60],"by":[63],"polymerase":[65],"III":[66],"essential":[69],"for":[70,77,96,117,147],"protein":[71],"translation.":[72],"There":[73],"a":[75,93],"need":[76],"integrated":[78,97],"software":[79,157],"that":[80,159],"able":[82],"analyze":[84],"multiple":[85],"types":[86],"RNA.":[88],"Here,":[89],"we":[90],"present":[91],"3t-seq,":[92],"Snakemake":[94],"pipeline":[95],"differential":[98],"expression":[99,132,144],"genes,":[105],"TEs,":[106],"tRNA.":[108],"3t-seq":[109,166],"produces":[110],"an":[111,152],"accessible":[112],"report":[113],"easy-to-use":[115],"results":[116],"downstream":[118],"starting":[120],"raw":[122],"performing":[126],"quality":[127],"control,":[128],"genome":[129],"mapping,":[130],"gene":[131],"quantification,":[133],"statistical":[135],"testing.":[136],"It":[137,150],"implements":[138],"three":[139],"TEs":[143],"one":[146],"tRNA":[148],"genes.":[149],"provides":[151],"easy-to-configure":[153],"manage":[156],"dependencies":[158],"lets":[160],"user":[162],"focus":[163],"results.":[165],"released":[168],"under":[169],"MIT":[170],"license":[171],"at":[175],"https://github.com/boulardlab/3t-seq.":[176]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-03-13T16:22:10.518609","created_date":"2025-10-10T00:00:00"}