{"id":"https://openalex.org/W7225314449","doi":"https://doi.org/10.5281/zenodo.23970271","title":"Genomic organization of tRNA genes and distribution of tRNA charging and modification enzymes across Bacteria, Archaea and major eukaryotic lineages","display_name":"Genomic organization of tRNA genes and distribution of tRNA charging and modification enzymes across Bacteria, Archaea and major eukaryotic lineages","publication_year":2026,"publication_date":"2026-11-05","ids":{"openalex":"https://openalex.org/W7225314449","doi":"https://doi.org/10.5281/zenodo.23970271"},"language":"en","primary_location":{"id":"doi:10.5281/zenodo.23970271","doi":"https://doi.org/10.5281/zenodo.23970271","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.23970271","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"},"volume":null,"type":"dataset","is_traditional":false,"indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.5281/zenodo.23970271","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002883245","display_name":"Davis W. Cheng","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Cheng, Davis W.","raw_affiliation_strings":["Rocky Institute of Biotechnology"],"raw_orcid":"https://orcid.org/0009-0001-1306-8923","affiliations":[{"raw_affiliation_string":"Rocky Institute of Biotechnology","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5002883245"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9990000128746033,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9990000128746033,"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/T11482","display_name":"RNA modifications and cancer","score":0.0007999999797903001,"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":9.999999747378752e-05,"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/trna-genes","display_name":"tRNA genes","score":0.9660000205039978},{"id":"https://openalex.org/keywords/trna-modifying-enzymes","display_name":"tRNA modification enzymes","score":0.9829999804496765},{"id":"https://openalex.org/keywords/aminoacyl-trna-synthetase","display_name":"aminoacyl-tRNA synthetase","score":0.925000011920929},{"id":"https://openalex.org/keywords/bacteria","display_name":"bacteria","score":0.5450000166893005},{"id":"https://openalex.org/keywords/archaea","display_name":"archaea","score":1.0},{"id":"https://openalex.org/keywords/eukaryotic-lineages","display_name":"eukaryotic lineages","score":0.9449999928474426},{"id":"https://openalex.org/keywords/trna-introns","display_name":"tRNA introns","score":0.5189999938011169},{"id":"https://openalex.org/keywords/aimp2","display_name":"AIMP2","score":0.6510000228881836}],"concepts":[{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.9176999926567078},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7930999994277954},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.699999988079071},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6733999848365784},{"id":"https://openalex.org/C153957851","wikidata":"https://www.wikidata.org/wiki/Q201448","display_name":"Transfer RNA","level":4,"score":0.6473000049591064},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.61080002784729},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5597000122070312},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5073000192642212},{"id":"https://openalex.org/C550995028","wikidata":"https://www.wikidata.org/wiki/Q10872","display_name":"Archaea","level":3,"score":0.40540000796318054},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.34369999170303345},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.3163999915122986},{"id":"https://openalex.org/C34957205","wikidata":"https://www.wikidata.org/wiki/Q277338","display_name":"Pseudogene","level":4,"score":0.29670000076293945},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.29179999232292175},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.2863999903202057},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.2786000072956085},{"id":"https://openalex.org/C149034497","wikidata":"https://www.wikidata.org/wiki/Q1384835","display_name":"Expressed sequence tag","level":4,"score":0.2773999869823456},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.27709999680519104},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.2750000059604645},{"id":"https://openalex.org/C94795543","wikidata":"https://www.wikidata.org/wiki/Q3813754","display_name":"Human proteome project","level":4,"score":0.271699994802475},{"id":"https://openalex.org/C151810110","wikidata":"https://www.wikidata.org/wiki/Q7307074","display_name":"RefSeq","level":4,"score":0.26899999380111694},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.26600000262260437},{"id":"https://openalex.org/C5911399","wikidata":"https://www.wikidata.org/wiki/Q2278983","display_name":"Gene family","level":4,"score":0.26499998569488525},{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.2639999985694885}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.5281/zenodo.23970271","doi":"https://doi.org/10.5281/zenodo.23970271","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.23970271","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"},{"id":"doi:10.5281/zenodo.23970272","doi":"https://doi.org/10.5281/zenodo.23970272","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.23970272","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"}],"best_oa_location":{"id":"doi:10.5281/zenodo.23970271","doi":"https://doi.org/10.5281/zenodo.23970271","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.23970271","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2223836536","https://openalex.org/W2036649644","https://openalex.org/W4246658119","https://openalex.org/W7140026519","https://openalex.org/W2072091744","https://openalex.org/W7071834170","https://openalex.org/W1992773451","https://openalex.org/W2074299224","https://openalex.org/W2062967359","https://openalex.org/W1971824376"],"abstract_inverted_index":{"This":[0],"dataset":[1],"contains":[2],"the":[3,13,46,67,174,205,253,256,259,265],"data":[4,220],"tables,":[5],"analysis":[6,142,186,260],"scripts,":[7],"figures":[8],"and":[9,20,25,31,51,64,70,112,114,131,152,166,187,191,231,244,262],"supplementary":[10],"tables":[11],"for":[12,159,173,184,255],"manuscript":[14],"\u201cGenomic":[15],"organization":[16],"of":[17,22,48,92,120,148],"tRNA":[18,23,42,49,76,98],"genes":[19,85],"distribution":[21],"charging":[24,50],"modification":[26,52],"enzymes":[27,130],"across":[28,55],"Bacteria,":[29,56],"Archaea":[30],"major":[32],"eukaryotic":[33,163],"lineages\u201d":[34],"(D.W.":[35],"Cheng,":[36],"version":[37],"12).":[38],"The":[39,140],"study":[40],"compares":[41],"gene":[43,77,100],"repertoires":[44],"with":[45,66],"distributions":[47],"enzyme":[53],"families":[54],"Archaea,":[57],"fungi,":[58],"non-flowering":[59],"green":[60],"plants,":[61],"flowering":[62],"plants":[63],"animals,":[65],"human":[68],"genome":[69],"proteome":[71,154],"as":[72],"references.":[73],"Contents:":[74],"High-confidence":[75],"predictions":[78],"parsed":[79],"from":[80,86],"GtRNAdb":[81,229],"Release":[82],"22:":[83],"439,964":[84],"4,852":[87],"genomes.":[88],"A":[89,199],"one-assembly-per-species":[90],"selection":[91],"2,125":[93,175],"species":[94],"was":[95],"used.":[96],"Per-genome":[97],"metrics:":[99],"number,":[101],"anticodon":[102],"richness,":[103],"copies":[104],"per":[105,155],"anticodon,":[106],"introns,":[107],"adjacent-gene":[108],"proximity,":[109],"A34":[110],"anticodons,":[111],"Ile2-CAU":[113],"Ile-UAU":[115],"genes.":[116],"Presence":[117],"or":[118,215],"absence":[119],"31":[121],"InterPro":[122,245],"protein-family":[123,200],"markers":[124],"(aminoacyl-tRNA":[125],"synthetases,":[126],"amidotransferase":[127],"subunits,":[128],"wobble-modification":[129],"AIMP2)":[132],"in":[133],"22,134":[134],"UniProt":[135,240],"reference":[136],"proteomes":[137],"(release":[138],"2026_03).":[139],"18,612-proteome":[141],"set":[143],"has":[144],"a":[145],"BUSCO":[146],"completeness":[147],"at":[149],"least":[150],"90%":[151],"one":[153],"species.":[156],"Co-detection":[157],"counts":[158],"alternative":[160],"charging-enzyme":[161],"families,":[162],"lineage":[164,266],"assignments":[165],"figure":[167],"source":[168],"data.":[169],"NCBI":[170],"Taxonomy":[171],"lineages":[172],"genomes,":[176],"rebuilt":[177],"on":[178,264],"5":[179],"November":[180],"2026.":[181],"Python":[182],"scripts":[183],"parsing,":[185],"figures.":[188],"Figures":[189],"1\u20135":[190],"Supplementary":[192],"Tables":[193],"S1\u2013S8.":[194],"All":[195,218],"comparisons":[196],"are":[197,221],"descriptive.":[198],"marker":[201],"hit":[202],"shows":[203],"that":[204],"family":[206],"is":[207],"present;":[208],"it":[209],"does":[210],"not":[211],"show":[212],"pathway":[213],"activity":[214],"cellular":[216],"location.":[217],"input":[219],"public.":[222],"When":[223],"reusing":[224],"them,":[225],"please":[226],"also":[227],"cite":[228],"(Chan":[230,236],"Lowe":[232],"2016),":[233],"tRNAscan-SE":[234],"2.0":[235],"et":[237,247],"al.":[238,248],"2021),":[239],"(UniProt":[241],"Consortium":[242],"2025)":[243],"(Blum":[246],"2025).":[249],"See":[250],"README.md":[251],"inside":[252],"archive":[254],"file":[257],"list,":[258],"pipeline":[261],"notes":[263],"table.":[267]},"counts_by_year":[],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2026-11-06T00:00:00"}