{"id":"https://openalex.org/W2077327925","doi":"https://doi.org/10.1093/nar/gkt1181","title":"miRBase: annotating high confidence microRNAs using deep sequencing data","display_name":"miRBase: annotating high confidence microRNAs using deep sequencing data","publication_year":2013,"publication_date":"2013-11-25","ids":{"openalex":"https://openalex.org/W2077327925","doi":"https://doi.org/10.1093/nar/gkt1181","mag":"2077327925","pmid":"https://pubmed.ncbi.nlm.nih.gov/24275495"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkt1181","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkt1181","pdf_url":"https://academic.oup.com/nar/article-pdf/42/D1/D68/3618976/gkt1181.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","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/nar/article-pdf/42/D1/D68/3618976/gkt1181.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085511144","display_name":"Ana Kozomara","orcid":null},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ana Kozomara","raw_affiliation_strings":["Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK","Faculty of Life Sciences; University of Manchester; Manchester M13 9PT UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK","institution_ids":["https://openalex.org/I28407311"]},{"raw_affiliation_string":"Faculty of Life Sciences; University of Manchester; Manchester M13 9PT UK","institution_ids":["https://openalex.org/I28407311"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001502247","display_name":"Sam Griffiths\u2010Jones","orcid":"https://orcid.org/0000-0001-6043-807X"},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Sam Griffiths-Jones","raw_affiliation_strings":["Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK","Faculty of Life Sciences; University of Manchester; Manchester M13 9PT UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK","institution_ids":["https://openalex.org/I28407311"]},{"raw_affiliation_string":"Faculty of Life Sciences; University of Manchester; Manchester M13 9PT UK","institution_ids":["https://openalex.org/I28407311"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5001502247"],"corresponding_institution_ids":["https://openalex.org/I28407311"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":130.1286,"has_fulltext":true,"cited_by_count":5225,"citation_normalized_percentile":{"value":0.99987533,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"42","issue":"D1","first_page":"D68","last_page":"D73"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10062","display_name":"MicroRNA in disease regulation","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10062","display_name":"MicroRNA in disease regulation","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.9980999827384949,"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/mirbase","display_name":"MiRBase","score":0.9924408793449402},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7025947570800781},{"id":"https://openalex.org/keywords/microrna","display_name":"microRNA","score":0.6060433983802795},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.4199148416519165},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3861615061759949},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.30187854170799255},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07397070527076721}],"concepts":[{"id":"https://openalex.org/C49305753","wikidata":"https://www.wikidata.org/wiki/Q6826947","display_name":"MiRBase","level":4,"score":0.9924408793449402},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7025947570800781},{"id":"https://openalex.org/C145059251","wikidata":"https://www.wikidata.org/wiki/Q310899","display_name":"microRNA","level":3,"score":0.6060433983802795},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.4199148416519165},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3861615061759949},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.30187854170799255},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07397070527076721}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gkt1181","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkt1181","pdf_url":"https://academic.oup.com/nar/article-pdf/42/D1/D68/3618976/gkt1181.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:24275495","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24275495","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:pure.atira.dk:openaire/e7a8dc94-23a2-433d-ba79-e3538301e27c","is_oa":true,"landing_page_url":"https://research.manchester.ac.uk/en/publications/e7a8dc94-23a2-433d-ba79-e3538301e27c","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"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":"Kozomara, A & Griffiths-Jones, S 2014, 'MiRBase: Annotating high confidence microRNAs using deep sequencing data', Nucleic acids research., vol. 42, no. 1, pp. D68-D73. https://doi.org/10.1093/nar/gkt1181","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:europepmc.org:2943239","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3965103","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:pure.atira.dk:publications/e7a8dc94-23a2-433d-ba79-e3538301e27c","is_oa":true,"landing_page_url":"https://www.research.manchester.ac.uk/portal/en/publications/mirbase-annotating-high-confidence-micrornas-using-deep-sequencing-data(e7a8dc94-23a2-433d-ba79-e3538301e27c).html","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"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":"Kozomara, A & Griffiths-Jones, S 2014, 'MiRBase: Annotating high confidence microRNAs using deep sequencing data', Nucleic acids research., vol. 42, no. 1, pp. D68-D73. https://doi.org/10.1093/nar/gkt1181","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/nar/gkt1181","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkt1181","pdf_url":"https://academic.oup.com/nar/article-pdf/42/D1/D68/3618976/gkt1181.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4276085033","display_name":"miRBase: microRNA gene nomenclature sequences and targets","funder_award_id":"BB/G022623/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G8804256067","display_name":null,"funder_award_id":"BB/G022623/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320320240","display_name":"Research Councils UK","ror":"https://ror.org/00dq2kk65"},{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2077327925.pdf","grobid_xml":"https://content.openalex.org/works/W2077327925.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W1974220890","https://openalex.org/W2009658305","https://openalex.org/W2017426710","https://openalex.org/W2018219462","https://openalex.org/W2026581189","https://openalex.org/W2040676413","https://openalex.org/W2049836150","https://openalex.org/W2053078446","https://openalex.org/W2061664626","https://openalex.org/W2064060400","https://openalex.org/W2070571588","https://openalex.org/W2072155079","https://openalex.org/W2074624286","https://openalex.org/W2098422994","https://openalex.org/W2107713715","https://openalex.org/W2111001535","https://openalex.org/W2112192177","https://openalex.org/W2116824254","https://openalex.org/W2118258530","https://openalex.org/W2120141270","https://openalex.org/W2131475898","https://openalex.org/W2137257434","https://openalex.org/W2147495091","https://openalex.org/W2149385968","https://openalex.org/W2151889113","https://openalex.org/W2164286670","https://openalex.org/W2165446840"],"related_works":["https://openalex.org/W2367016030","https://openalex.org/W2088415316","https://openalex.org/W2134097555","https://openalex.org/W2743228635","https://openalex.org/W941572292","https://openalex.org/W2725073276","https://openalex.org/W1479910578","https://openalex.org/W2332870555","https://openalex.org/W2002128513","https://openalex.org/W2116661471"],"abstract_inverted_index":{"We":[0,126,158],"describe":[1,94,108,160],"an":[2],"update":[3],"of":[4,39,41,47,67,73,82,97,113,121,133,140],"the":[5,9,45,65,80,83,98,109,138,152,166,171],"miRBase":[6,16,99,124,134,167],"database":[7,100],"(http://www.mirbase.org/),":[8],"primary":[10],"microRNA":[11,24,35,74,84,146,154,172],"sequence":[12,85],"repository.":[13],"The":[14,37,143],"latest":[15],"release":[17],"(v20,":[18],"June":[19],"2013)":[20],"contains":[21],"24":[22],"521":[23],"loci":[25],"from":[26],"206":[27],"species,":[28],"processed":[29],"to":[30,54,101,118,123,169,174],"produce":[31],"30":[32],"424":[33],"mature":[34],"products.":[36],"rate":[38],"deposition":[40],"novel":[42],"microRNAs":[43],"and":[44,70,77,111,176,179],"number":[46],"researchers":[48],"involved":[49],"in":[50],"their":[51],"discovery":[52],"continue":[53],"increase,":[55],"driven":[56],"largely":[57],"by":[58],"small":[59],"RNA":[60],"deep":[61,114],"sequencing":[62,115],"experiments.":[63],"In":[64,105],"face":[66],"these":[68],"increases,":[69],"a":[71,89,129],"range":[72],"annotation":[75],"methods":[76],"criteria,":[78],"maintaining":[79],"quality":[81],"data":[86,116,147],"set":[87,148],"is":[88,149],"significant":[90],"challenge.":[91],"Here,":[92],"we":[93,107],"recent":[95],"developments":[96],"address":[102],"this":[103],"issue.":[104],"particular,":[106],"collation":[110],"use":[112],"sets":[117],"assign":[119],"levels":[120],"confidence":[122,131,145],"entries.":[125],"now":[127],"provide":[128],"high":[130,144],"subset":[132],"entries,":[135],"based":[136],"on":[137,165],"pattern":[139],"mapped":[141],"reads.":[142],"available":[150],"alongside":[151],"complete":[153],"collection":[155],"at":[156],"http://www.mirbase.org/.":[157],"also":[159],"embedding":[161],"microRNA-specific":[162],"Wikipedia":[163],"pages":[164],"website":[168],"encourage":[170],"community":[173],"contribute":[175],"share":[177],"textual":[178],"functional":[180],"information.":[181]},"counts_by_year":[{"year":2026,"cited_by_count":58},{"year":2025,"cited_by_count":159},{"year":2024,"cited_by_count":253},{"year":2023,"cited_by_count":228},{"year":2022,"cited_by_count":305},{"year":2021,"cited_by_count":393},{"year":2020,"cited_by_count":495},{"year":2019,"cited_by_count":620},{"year":2018,"cited_by_count":745},{"year":2017,"cited_by_count":670},{"year":2016,"cited_by_count":581},{"year":2015,"cited_by_count":514},{"year":2014,"cited_by_count":192},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":3}],"updated_date":"2026-08-04T08:18:43.703281","created_date":"2025-10-10T00:00:00"}