{"id":"https://openalex.org/W7140499957","doi":"https://doi.org/10.1371/journal.pcbi.1014114","title":"PymiRa: A rapid and accurate classification tool for small non-coding RNAs, including microRNAs","display_name":"PymiRa: A rapid and accurate classification tool for small non-coding RNAs, including microRNAs","publication_year":2026,"publication_date":"2026-03-26","ids":{"openalex":"https://openalex.org/W7140499957","doi":"https://doi.org/10.1371/journal.pcbi.1014114","pmid":"https://pubmed.ncbi.nlm.nih.gov/41886518"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1014114","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1014114","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1014114","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5092699354","display_name":"Zachary G. L. Scurlock","orcid":null},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Zachary G. L. Scurlock","raw_affiliation_strings":["Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom"],"raw_orcid":"https://orcid.org/0009-0003-8063-0167","affiliations":[{"raw_affiliation_string":"Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065916505","display_name":"Cinzia G. Scarpini","orcid":"https://orcid.org/0000-0003-4730-5197"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Cinzia G. Scarpini","raw_affiliation_strings":["Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5130630734","display_name":"Nicholas Coleman","orcid":null},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I2802466933","display_name":"Cambridge University Hospitals NHS Foundation Trust","ror":"https://ror.org/04v54gj93","country_code":"GB","type":"funder","lineage":["https://openalex.org/I2802466933"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Nicholas Coleman","raw_affiliation_strings":["Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, United Kingdom","Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I2802466933"]},{"raw_affiliation_string":"Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066179071","display_name":"Matthew J. Murray","orcid":"https://orcid.org/0000-0002-7106-7283"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I2802466933","display_name":"Cambridge University Hospitals NHS Foundation Trust","ror":"https://ror.org/04v54gj93","country_code":"GB","type":"funder","lineage":["https://openalex.org/I2802466933"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Matthew J. Murray","raw_affiliation_strings":["Department of Paediatric Haematology and Oncology, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, United Kingdom","Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Paediatric Haematology and Oncology, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I2802466933"]},{"raw_affiliation_string":"Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052303040","display_name":"Anton J. Enright","orcid":"https://orcid.org/0000-0002-6090-3100"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Anton J. Enright","raw_affiliation_strings":["Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-6090-3100","affiliations":[{"raw_affiliation_string":"Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I241749"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.29851318,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"3","first_page":"e1014114","last_page":"e1014114"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.757099986076355,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.757099986076355,"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/T10062","display_name":"MicroRNA in disease regulation","score":0.155799999833107,"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":0.033399999141693115,"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":0.8446000218391418},{"id":"https://openalex.org/keywords/microrna","display_name":"microRNA","score":0.6312999725341797},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.39089998602867126},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.35850000381469727},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.353300005197525},{"id":"https://openalex.org/keywords/small-rna","display_name":"Small RNA","score":0.3449000120162964},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.33649998903274536},{"id":"https://openalex.org/keywords/host","display_name":"Host (biology)","score":0.3336000144481659},{"id":"https://openalex.org/keywords/deep-sequencing","display_name":"Deep sequencing","score":0.3203999996185303}],"concepts":[{"id":"https://openalex.org/C49305753","wikidata":"https://www.wikidata.org/wiki/Q6826947","display_name":"MiRBase","level":4,"score":0.8446000218391418},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.7070000171661377},{"id":"https://openalex.org/C145059251","wikidata":"https://www.wikidata.org/wiki/Q310899","display_name":"microRNA","level":3,"score":0.6312999725341797},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5139999985694885},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4754999876022339},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.39089998602867126},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.35850000381469727},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.353300005197525},{"id":"https://openalex.org/C2779341050","wikidata":"https://www.wikidata.org/wiki/Q24287527","display_name":"Small RNA","level":4,"score":0.3449000120162964},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.33649998903274536},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.3336000144481659},{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.3203999996185303},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.31380000710487366},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.30880001187324524},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3084999918937683},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.3001999855041504},{"id":"https://openalex.org/C2988867146","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Human disease","level":3,"score":0.3001999855041504},{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.2955999970436096},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.29420000314712524},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.29330000281333923},{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.289900004863739},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.2897000014781952},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.289000004529953},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.2867000102996826},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.2847000062465668},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.2766000032424927},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.2761000096797943},{"id":"https://openalex.org/C74318829","wikidata":"https://www.wikidata.org/wiki/Q36458","display_name":"Multicellular organism","level":3,"score":0.2678000032901764},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.25929999351501465},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.25029999017715454}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"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":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D058727","descriptor_name":"RNA, Small Untranslated","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D058727","descriptor_name":"RNA, Small Untranslated","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D058727","descriptor_name":"RNA, Small Untranslated","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D058727","descriptor_name":"RNA, Small Untranslated","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D058727","descriptor_name":"RNA, Small Untranslated","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D058727","descriptor_name":"RNA, Small Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D058727","descriptor_name":"RNA, Small Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D058727","descriptor_name":"RNA, Small Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D058727","descriptor_name":"RNA, Small Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D058727","descriptor_name":"RNA, Small Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D058727","descriptor_name":"RNA, Small Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D058727","descriptor_name":"RNA, Small Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1014114","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1014114","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:41886518","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41886518","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:aab159a998f7414db590f8bcffd601c4","is_oa":false,"landing_page_url":"https://doaj.org/article/aab159a998f7414db590f8bcffd601c4","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 22, Iss 3, p e1014114 (2026)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13020842","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13020842/","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":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:www.repository.cam.ac.uk:1810/400721","is_oa":true,"landing_page_url":"https://www.repository.cam.ac.uk/handle/1810/400721","pdf_url":null,"source":{"id":"https://openalex.org/S4306401777","display_name":"Apollo (University of Cambridge)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I241749","host_organization_name":"University of Cambridge","host_organization_lineage":["https://openalex.org/I241749"],"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":"Article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1014114","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1014114","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320314731","display_name":"UK Research and Innovation","ror":"https://ror.org/001aqnf71"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W1519433744","https://openalex.org/W2025449301","https://openalex.org/W2058832897","https://openalex.org/W2072155079","https://openalex.org/W2074216902","https://openalex.org/W2100465225","https://openalex.org/W2103441770","https://openalex.org/W2124985265","https://openalex.org/W2126270345","https://openalex.org/W2134526812","https://openalex.org/W2138207763","https://openalex.org/W2158322625","https://openalex.org/W2193739999","https://openalex.org/W2765401875","https://openalex.org/W2898440040","https://openalex.org/W2954057550","https://openalex.org/W3001041847","https://openalex.org/W3213380759","https://openalex.org/W4229083685","https://openalex.org/W4394999393","https://openalex.org/W4415651687"],"related_works":[],"abstract_inverted_index":{"Small":[0],"non-coding":[1],"RNAs":[2],"(sncRNA;":[3],"<":[4],"200":[5],"nucleotide":[6],"length)":[7],"are":[8],"of":[9,22,33,117,187,213,216],"increasing":[10],"research":[11],"interest":[12],"due":[13],"to":[14,72,89,110,132,154,182],"their":[15,44,224],"key":[16],"regulatory":[17],"roles":[18],"in":[19,57,70,219,226],"a":[20,30,86,95,118,124,161,172,188,209],"host":[21],"fundamental":[23],"biological":[24,211],"processes.":[25],"For":[26],"example,":[27],"microRNAs":[28],"(miRNAs),":[29],"specific":[31],"class":[32],"sncRNAs,":[34],"regulate":[35],"gene":[36],"expression":[37,218],"through":[38],"messenger":[39],"RNA":[40],"(mRNA)":[41],"interactions,":[42],"and":[43,74,143,164,223],"dysregulation":[45,225],"is":[46,52,160],"associated":[47],"with":[48,200],"disease.":[49],"Classifying":[50],"sncRNAs":[51],"an":[53,65,91],"important":[54],"bioinformatic":[55],"task":[56],"small":[58,189],"RNA-sequencing":[59,190],"pipelines.":[60],"Here":[61],"we":[62,134],"have":[63],"developed":[64],"aligner":[66,148,167,206],"called":[67],"PymiRa,":[68],"written":[69],"Python,":[71],"identify":[73],"quantify":[75],"miRNAs":[76,155],"from":[77,102],"FASTA/FASTQ":[78],"sequencing":[79],"files.":[80],"Unlike":[81],"other":[82],"approaches,":[83],"PymiRa":[84,147,159,192,205],"utilises":[85],"Burrows-Wheeler":[87,125],"algorithm":[88],"align":[90],"input":[92],"file":[93,100],"against":[94],"reference":[96],"hairpin":[97],"precursor":[98],"FASTA":[99],"derived":[101],"miRBase,":[103],"the":[104,114,146,214],"online":[105],"miRNA":[106],"registry,":[107],"permitting":[108],"up":[109],"two":[111],"mismatches":[112],"at":[113],"3'":[115,151],"end":[116],"read.":[119],"Previous":[120],"tools":[121],"used":[122],"either":[123],"genome":[126],"alignment":[127,131],"or":[128],"dynamic":[129],"programming":[130],"precursors;":[133],"demonstrate":[135],"that":[136,156],"combining":[137],"both":[138],"approaches":[139],"yields":[140],"improved":[141],"results":[142],"efficiency.":[144],"Importantly,":[145],"accounts":[149],"for":[150,174],"post-transcriptional":[152],"modifications":[153],"typically":[157],"occur.":[158],"fast,":[162],"accurate,":[163],"publicly":[165],"accessible":[166],"available":[168],"via":[169],"GitHub":[170],"and/or":[171],"webserver":[173],"sncRNA":[175,217],"identification,":[176],"including":[177,229],"miRNAs,":[178],"enabling":[179],"accurate":[180],"counts":[181],"be":[183],"produced":[184],"as":[185],"part":[186],"pipeline.":[191],"will":[193,207],"undergo":[194],"relevant":[195],"revisions":[196],"over":[197],"time":[198],"e.g.,":[199],"miRBase":[201],"version":[202],"updates.":[203],"The":[204],"facilitate":[208],"deeper":[210],"understanding":[212],"landscape":[215],"normal":[220],"physiological":[221],"conditions":[222],"disease":[227],"states,":[228],"cancer.":[230]},"counts_by_year":[],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2026-03-27T00:00:00"}