{"id":"https://openalex.org/W7225808760","doi":"https://doi.org/10.1093/nar/gkag1165","title":"oRNAment V2: an expanded database of putative RNA binding protein target sites in the transcriptomes of diverse model species.","display_name":"oRNAment V2: an expanded database of putative RNA binding protein target sites in the transcriptomes of diverse model species.","publication_year":2026,"publication_date":"2026-11-11","ids":{"openalex":"https://openalex.org/W7225808760","doi":"https://doi.org/10.1093/nar/gkag1165","pmid":"https://pubmed.ncbi.nlm.nih.gov/43010843"},"language":"en","primary_location":{"id":"pmid:43010843","doi":"https://doi.org/10.1093/nar/gkag1165","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/43010843","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"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5161422901","display_name":"Delong Zhou","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210158752","display_name":"Montreal Clinical Research Institute","ror":"https://ror.org/05m8pzq90","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210158752","https://openalex.org/I70931966"]},{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]},{"id":"https://openalex.org/I70931966","display_name":"Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0161xgx34","country_code":"CA","type":"education","lineage":["https://openalex.org/I70931966"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Delong Zhou","raw_affiliation_strings":["Montreal Clinical Research Institute (IRCM), Montr\u00e9al, QC H2W 1R7, Canada","Division of Clinical and Translational Research, McGill University, Montr\u00e9al, QC H4A 3J1, Canada","Department of Biochemistry and Molecular Medicine, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, QC H3C 3J7, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Montreal Clinical Research Institute (IRCM), Montr\u00e9al, QC H2W 1R7, Canada","institution_ids":["https://openalex.org/I4210158752"]},{"raw_affiliation_string":"Division of Clinical and Translational Research, McGill University, Montr\u00e9al, QC H4A 3J1, Canada","institution_ids":["https://openalex.org/I5023651"]},{"raw_affiliation_string":"Department of Biochemistry and Molecular Medicine, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, QC H3C 3J7, Canada","institution_ids":["https://openalex.org/I70931966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091742946","display_name":"Shaimae I. Elhajjajy","orcid":"https://orcid.org/0000-0002-7497-5519","observed_orcids":["https://orcid.org/0000-0002-7497-5519"]},"institutions":[{"id":"https://openalex.org/I4210158752","display_name":"Montreal Clinical Research Institute","ror":"https://ror.org/05m8pzq90","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210158752","https://openalex.org/I70931966"]},{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Shaimae I Elhajjajy","raw_affiliation_strings":["Montreal Clinical Research Institute (IRCM), Montr\u00e9al, QC H2W 1R7, Canada","Division of Clinical and Translational Research, McGill University, Montr\u00e9al, QC H4A 3J1, Canada","School of Computer Science, McGill University, Montr\u00e9al, QC H3A 2A7, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Montreal Clinical Research Institute (IRCM), Montr\u00e9al, QC H2W 1R7, Canada","institution_ids":["https://openalex.org/I4210158752"]},{"raw_affiliation_string":"Division of Clinical and Translational Research, McGill University, Montr\u00e9al, QC H4A 3J1, Canada","institution_ids":["https://openalex.org/I5023651"]},{"raw_affiliation_string":"School of Computer Science, McGill University, Montr\u00e9al, QC H3A 2A7, Canada","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061698042","display_name":"Gabrielle Deschamps-Francoeur","orcid":"https://orcid.org/0000-0001-7129-960X","observed_orcids":["https://orcid.org/0000-0001-7129-960X"]},"institutions":[{"id":"https://openalex.org/I4210158752","display_name":"Montreal Clinical Research Institute","ror":"https://ror.org/05m8pzq90","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210158752","https://openalex.org/I70931966"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Gabrielle Deschamps-Francoeur","raw_affiliation_strings":["Montreal Clinical Research Institute (IRCM), Montr\u00e9al, QC H2W 1R7, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Montreal Clinical Research Institute (IRCM), Montr\u00e9al, QC H2W 1R7, Canada","institution_ids":["https://openalex.org/I4210158752"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5160103486","display_name":"Marie Sandler","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Marie Sandler","raw_affiliation_strings":["School of Computer Science, McGill University, Montr\u00e9al, QC H3A 2A7, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, McGill University, Montr\u00e9al, QC H3A 2A7, Canada","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5161473221","display_name":"Maroua Ait El Baz","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210158752","display_name":"Montreal Clinical Research Institute","ror":"https://ror.org/05m8pzq90","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210158752","https://openalex.org/I70931966"]},{"id":"https://openalex.org/I70931966","display_name":"Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0161xgx34","country_code":"CA","type":"education","lineage":["https://openalex.org/I70931966"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Maroua Ait El Baz","raw_affiliation_strings":["Montreal Clinical Research Institute (IRCM), Montr\u00e9al, QC H2W 1R7, Canada","Department of Biochemistry and Molecular Medicine, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, QC H3C 3J7, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Montreal Clinical Research Institute (IRCM), Montr\u00e9al, QC H2W 1R7, Canada","institution_ids":["https://openalex.org/I4210158752"]},{"raw_affiliation_string":"Department of Biochemistry and Molecular Medicine, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, QC H3C 3J7, Canada","institution_ids":["https://openalex.org/I70931966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065720651","display_name":"Mathieu Blanchette","orcid":"https://orcid.org/0000-0002-9555-860X","observed_orcids":["https://orcid.org/0000-0002-9555-860X"]},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Mathieu Blanchette","raw_affiliation_strings":["School of Computer Science, McGill University, Montr\u00e9al, QC H3A 2A7, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, McGill University, Montr\u00e9al, QC H3A 2A7, Canada","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018570031","display_name":"\u00c9ric L\u00e9cuyer","orcid":"https://orcid.org/0000-0002-4383-342X","observed_orcids":["https://orcid.org/0000-0002-4383-342X"]},"institutions":[{"id":"https://openalex.org/I4210158752","display_name":"Montreal Clinical Research Institute","ror":"https://ror.org/05m8pzq90","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210158752","https://openalex.org/I70931966"]},{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]},{"id":"https://openalex.org/I70931966","display_name":"Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0161xgx34","country_code":"CA","type":"education","lineage":["https://openalex.org/I70931966"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Eric L\u00e9cuyer","raw_affiliation_strings":["Montreal Clinical Research Institute (IRCM), Montr\u00e9al, QC H2W 1R7, Canada","Division of Clinical and Translational Research, McGill University, Montr\u00e9al, QC H4A 3J1, Canada","Department of Biochemistry and Molecular Medicine, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, QC H3C 3J7, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Montreal Clinical Research Institute (IRCM), Montr\u00e9al, QC H2W 1R7, Canada","institution_ids":["https://openalex.org/I4210158752"]},{"raw_affiliation_string":"Division of Clinical and Translational Research, McGill University, Montr\u00e9al, QC H4A 3J1, Canada","institution_ids":["https://openalex.org/I5023651"]},{"raw_affiliation_string":"Department of Biochemistry and Molecular Medicine, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, QC H3C 3J7, Canada","institution_ids":["https://openalex.org/I70931966"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"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/T10604","display_name":"RNA Research and Splicing","score":0.9976000189781189,"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/T10604","display_name":"RNA Research and Splicing","score":0.9976000189781189,"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":0.0005000000237487257,"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":0.00039999998989515007,"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":[],"concepts":[{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.7458000183105469},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6575000286102295},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6179999709129333},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.5393000245094299},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5250999927520752},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5006999969482422},{"id":"https://openalex.org/C41282012","wikidata":"https://www.wikidata.org/wiki/Q3928341","display_name":"RNA-binding protein","level":4,"score":0.4478999972343445},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4180999994277954},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.40389999747276306},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.40070000290870667},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.3425999879837036},{"id":"https://openalex.org/C51639874","wikidata":"https://www.wikidata.org/wiki/Q167149","display_name":"Plasma protein binding","level":2,"score":0.34060001373291016},{"id":"https://openalex.org/C2781148417","wikidata":"https://www.wikidata.org/wiki/Q5533486","display_name":"Genome browser","level":5,"score":0.3005000054836273},{"id":"https://openalex.org/C94966510","wikidata":"https://www.wikidata.org/wiki/Q2252764","display_name":"DNA-binding protein","level":4,"score":0.2944999933242798},{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.2782000005245209},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.2754000127315521},{"id":"https://openalex.org/C21786251","wikidata":"https://www.wikidata.org/wiki/Q14886350","display_name":"RNA editing","level":4,"score":0.27219998836517334},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.2694999873638153},{"id":"https://openalex.org/C553089730","wikidata":"https://www.wikidata.org/wiki/Q4914021","display_name":"Binding protein","level":3,"score":0.2662000060081482},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.25699999928474426}],"mesh":[],"locations_count":1,"locations":[{"id":"pmid:43010843","doi":"https://doi.org/10.1093/nar/gkag1165","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/43010843","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"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"RNA":[0,11,194],"binding":[1,40,51,67,119,136,154],"proteins":[2],"(RBPs)":[3],"modulate":[4],"the":[5,99,122,157,193],"expression,":[6],"form,":[7],"and":[8,34,71,77,98,126,144,165,171,176],"fate":[9],"of":[10,21,38,48,64,94,101,112,124,131,135,141],"transcripts":[12],"throughout":[13],"their":[14],"lifecycle,":[15],"thereby":[16],"serving":[17],"as":[18],"essential":[19],"regulators":[20],"gene":[22],"expression.":[23],"Despite":[24],"impactful":[25],"high-throughput":[26],"experimental":[27],"advances":[28],"that":[29],"have":[30],"enabled":[31],"in":[32,35,75],"vitro":[33],"vivo":[36],"identification":[37],"RBP":[39,50,66,118,153],"sites,":[41],"few":[42],"resources":[43],"provide":[44,185],"a":[45,62,86,110],"comprehensive":[46],"catalog":[47],"potential":[49],"sites":[52,68,120],"transcriptome-wide.":[53],"To":[54],"address":[55],"this":[56],"limitation,":[57],"we":[58,82],"previously":[59],"developed":[60],"oRNAment,":[61],"database":[63],"putative":[65,117,152],"across":[69,121],"coding":[70],"non-coding":[72],"transcriptome":[73],"regions":[74],"human":[76,125],"four":[78],"model":[79],"species.":[80,128],"Here,":[81],"present":[83],"oRNAment":[84,106,132,181,196],"V2,":[85],"significantly":[87],"enhanced":[88],"resource,":[89],"with":[90,146],"an":[91,186],"expanded":[92],"collection":[93],"RBPs,":[95],"motifs,":[96],"species,":[97],"addition":[100],"intronic":[102],"sequences.":[103],"The":[104],"updated":[105],"resource":[107,188],"now":[108],"predicts":[109],"total":[111],"3":[113],"808":[114],"264":[115],"959":[116],"transcriptomes":[123],"14":[127],"Novel":[129],"features":[130],"include":[133],"predictions":[134],"site":[137],"evolutionary":[138],"age,":[139],"annotations":[140],"CLIP":[142],"support,":[143],"visualizations":[145],"UCSC":[147],"track":[148],"hubs":[149],"for":[150],"all":[151],"sites.":[155],"On":[156],"front":[158],"end,":[159],"oRNAment's":[160],"web":[161],"interface":[162],"enhances":[163],"functionality":[164],"usability":[166],"by":[167,192],"providing":[168],"improved":[169],"search":[170],"filtering":[172],"functions,":[173],"download":[174],"options,":[175],"visualizations.":[177],"With":[178],"its":[179],"expansion,":[180],"V2":[182,197],"continues":[183],"to":[184,189],"important":[187],"support":[190],"research":[191],"community.":[195],"is":[198],"available":[199],"at":[200],"https://rnabiology.ircm.qc.ca/oRNAmentv2.":[201]},"counts_by_year":[],"updated_date":"2026-11-12T12:28:57.059296","created_date":"2026-11-12T00:00:00"}