{"id":"https://openalex.org/W4391005566","doi":"https://doi.org/10.1093/bib/bbad515","title":"sRNAfrag: a pipeline and suite of tools to analyze fragmentation in small RNA sequencing data","display_name":"sRNAfrag: a pipeline and suite of tools to analyze fragmentation in small RNA sequencing data","publication_year":2023,"publication_date":"2023-11-22","ids":{"openalex":"https://openalex.org/W4391005566","doi":"https://doi.org/10.1093/bib/bbad515","pmid":"https://pubmed.ncbi.nlm.nih.gov/38243693"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad515","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad515","pdf_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad515/56207009/bbad515.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad515/56207009/bbad515.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089555217","display_name":"K. Nakatsu","orcid":"https://orcid.org/0000-0002-7956-2270"},"institutions":[{"id":"https://openalex.org/I117965899","display_name":"University of Hawai\u02bbi at M\u0101noa","ror":"https://ror.org/01wspgy28","country_code":"US","type":"education","lineage":["https://openalex.org/I117965899"]},{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ken Nakatsu","raw_affiliation_strings":["Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine , 651 Ilalo St, 96813, Hawaii , United States of America","Emory College of Arts and Sciences, Emory University , 201 Dowman Dr, 30322, Georgia , United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine , 651 Ilalo St, 96813, Hawaii , United States of America","institution_ids":["https://openalex.org/I117965899"]},{"raw_affiliation_string":"Emory College of Arts and Sciences, Emory University , 201 Dowman Dr, 30322, Georgia , United States of America","institution_ids":["https://openalex.org/I150468666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075017895","display_name":"Mayumi Jijiwa","orcid":"https://orcid.org/0000-0003-1596-856X"},"institutions":[{"id":"https://openalex.org/I117965899","display_name":"University of Hawai\u02bbi at M\u0101noa","ror":"https://ror.org/01wspgy28","country_code":"US","type":"education","lineage":["https://openalex.org/I117965899"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mayumi Jijiwa","raw_affiliation_strings":["Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine , 651 Ilalo St, 96813, Hawaii , United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine , 651 Ilalo St, 96813, Hawaii , United States of America","institution_ids":["https://openalex.org/I117965899"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030130280","display_name":"Vedbar S. Khadka","orcid":"https://orcid.org/0000-0002-8652-2904"},"institutions":[{"id":"https://openalex.org/I117965899","display_name":"University of Hawai\u02bbi at M\u0101noa","ror":"https://ror.org/01wspgy28","country_code":"US","type":"education","lineage":["https://openalex.org/I117965899"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vedbar Khadka","raw_affiliation_strings":["Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine , 651 Ilalo St, 96813, Hawaii , United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine , 651 Ilalo St, 96813, Hawaii , United States of America","institution_ids":["https://openalex.org/I117965899"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113811481","display_name":"Masaki Nasu","orcid":null},"institutions":[{"id":"https://openalex.org/I117965899","display_name":"University of Hawai\u02bbi at M\u0101noa","ror":"https://ror.org/01wspgy28","country_code":"US","type":"education","lineage":["https://openalex.org/I117965899"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Masaki Nasu","raw_affiliation_strings":["Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine , 651 Ilalo St, 96813, Hawaii , United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine , 651 Ilalo St, 96813, Hawaii , United States of America","institution_ids":["https://openalex.org/I117965899"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042435594","display_name":"Youping Deng","orcid":"https://orcid.org/0000-0002-5951-8213"},"institutions":[{"id":"https://openalex.org/I117965899","display_name":"University of Hawai\u02bbi at M\u0101noa","ror":"https://ror.org/01wspgy28","country_code":"US","type":"education","lineage":["https://openalex.org/I117965899"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Youping Deng","raw_affiliation_strings":["Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine , 651 Ilalo St, 96813, Hawaii , United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine , 651 Ilalo St, 96813, Hawaii , United States of America","institution_ids":["https://openalex.org/I117965899"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5042435594"],"corresponding_institution_ids":["https://openalex.org/I117965899"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.2782,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.52258017,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"25","issue":"1","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":0.9998999834060669,"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":0.9998999834060669,"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":0.9990000128746033,"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/T10604","display_name":"RNA Research and Splicing","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/suite","display_name":"Suite","score":0.8267866373062134},{"id":"https://openalex.org/keywords/fragmentation","display_name":"Fragmentation (computing)","score":0.6965651512145996},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6792358160018921},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5843619704246521},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.49860596656799316},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4792037904262543},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4293896555900574},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24966925382614136},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.17320474982261658},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17148390412330627},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11946296691894531},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.10126042366027832},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.09755799174308777},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.05340951681137085}],"concepts":[{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.8267866373062134},{"id":"https://openalex.org/C191015642","wikidata":"https://www.wikidata.org/wiki/Q1132459","display_name":"Fragmentation (computing)","level":2,"score":0.6965651512145996},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6792358160018921},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5843619704246521},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.49860596656799316},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4792037904262543},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4293896555900574},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24966925382614136},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.17320474982261658},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17148390412330627},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11946296691894531},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.10126042366027832},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.09755799174308777},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.05340951681137085},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"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":"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":"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":"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":"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":"D020537","descriptor_name":"RNA, Small Nucleolar","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020537","descriptor_name":"RNA, Small Nucleolar","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020537","descriptor_name":"RNA, Small Nucleolar","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020537","descriptor_name":"RNA, Small Nucleolar","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020537","descriptor_name":"RNA, Small Nucleolar","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020537","descriptor_name":"RNA, Small Nucleolar","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020537","descriptor_name":"RNA, Small Nucleolar","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020537","descriptor_name":"RNA, Small Nucleolar","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020537","descriptor_name":"RNA, Small Nucleolar","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020537","descriptor_name":"RNA, Small Nucleolar","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020537","descriptor_name":"RNA, Small Nucleolar","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"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":"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":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbad515","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad515","pdf_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad515/56207009/bbad515.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38243693","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38243693","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:10796253","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10796253","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10796253/pdf/bbad515.pdf","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbad515","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad515","pdf_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad515/56207009/bbad515.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.6899999976158142}],"awards":[{"id":"https://openalex.org/G1046289072","display_name":null,"funder_award_id":"U54 GM138062","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G1446977215","display_name":null,"funder_award_id":"P30 CA 071789","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G155562842","display_name":null,"funder_award_id":"R01 CA230514","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G1840313264","display_name":null,"funder_award_id":"P20GM 103466","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1939176559","display_name":null,"funder_award_id":"P30GM114737","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2280392065","display_name":null,"funder_award_id":"U54 HG013243","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G2282300103","display_name":null,"funder_award_id":"P20GM 103466","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2912100404","display_name":null,"funder_award_id":"P20 GM139753","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3120514273","display_name":null,"funder_award_id":"P30CA071789","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G3538213265","display_name":null,"funder_award_id":"P30 GM114737","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G493811095","display_name":"CC* Data Storage: KoaStore: A High Performance and Flexible Research Storage Resource","funder_award_id":"2232862","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5355444672","display_name":null,"funder_award_id":"R01CA223490","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G538116012","display_name":null,"funder_award_id":"U54MD007601","funder_id":"https://openalex.org/F4320337534","funder_display_name":"National Institute on Minority Health and Health Disparities"},{"id":"https://openalex.org/G6556881659","display_name":null,"funder_award_id":"U54GM138062","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7802449969","display_name":null,"funder_award_id":"P20GM139753","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G784175012","display_name":null,"funder_award_id":"R01CA230514","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8316543636","display_name":null,"funder_award_id":"U54HG013243","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8644125217","display_name":"CC* Compute: Koa - A High Performance and Flexible Research Computing Resource","funder_award_id":"2201428","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G971811331","display_name":null,"funder_award_id":"R01 CA223490","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G992900636","display_name":null,"funder_award_id":"U54MD007601","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320311887","display_name":"Washington and Lee University","ror":"https://ror.org/05r9xgf14"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337534","display_name":"National Institute on Minority Health and Health Disparities","ror":"https://ror.org/0493hgw16"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4391005566.pdf"},"referenced_works_count":69,"referenced_works":["https://openalex.org/W776567260","https://openalex.org/W1485571925","https://openalex.org/W1978560967","https://openalex.org/W1980900189","https://openalex.org/W1989035822","https://openalex.org/W1997874688","https://openalex.org/W2010775154","https://openalex.org/W2026566929","https://openalex.org/W2038310925","https://openalex.org/W2039357236","https://openalex.org/W2049245111","https://openalex.org/W2061989469","https://openalex.org/W2066429806","https://openalex.org/W2072636314","https://openalex.org/W2086561953","https://openalex.org/W2095968788","https://openalex.org/W2102619694","https://openalex.org/W2108070864","https://openalex.org/W2108234281","https://openalex.org/W2117338524","https://openalex.org/W2121196786","https://openalex.org/W2124985265","https://openalex.org/W2138207763","https://openalex.org/W2151435150","https://openalex.org/W2159506512","https://openalex.org/W2173732482","https://openalex.org/W2179438025","https://openalex.org/W2263582186","https://openalex.org/W2589911306","https://openalex.org/W2726005250","https://openalex.org/W2737196618","https://openalex.org/W2769912973","https://openalex.org/W2898440040","https://openalex.org/W2899798803","https://openalex.org/W2919470997","https://openalex.org/W2922969171","https://openalex.org/W2936702203","https://openalex.org/W2952109315","https://openalex.org/W2979751848","https://openalex.org/W3002494882","https://openalex.org/W3003059409","https://openalex.org/W3005149796","https://openalex.org/W3021239624","https://openalex.org/W3038494215","https://openalex.org/W3082961051","https://openalex.org/W3088521497","https://openalex.org/W3093127543","https://openalex.org/W3127140457","https://openalex.org/W3134329288","https://openalex.org/W3139977424","https://openalex.org/W3148088922","https://openalex.org/W3203422069","https://openalex.org/W3206717311","https://openalex.org/W3207591281","https://openalex.org/W4200083425","https://openalex.org/W4205502736","https://openalex.org/W4220794133","https://openalex.org/W4225278419","https://openalex.org/W4226070127","https://openalex.org/W4281732087","https://openalex.org/W4285900028","https://openalex.org/W4308882298","https://openalex.org/W4312125373","https://openalex.org/W4312158493","https://openalex.org/W4376134949","https://openalex.org/W6628922508","https://openalex.org/W6803767736","https://openalex.org/W6846861470","https://openalex.org/W6853039905"],"related_works":["https://openalex.org/W4231704780","https://openalex.org/W2083794993","https://openalex.org/W352609212","https://openalex.org/W4200340037","https://openalex.org/W1511772879","https://openalex.org/W4379115841","https://openalex.org/W608917066","https://openalex.org/W4283652261","https://openalex.org/W585424826","https://openalex.org/W564602992"],"abstract_inverted_index":{"Fragments":[0],"derived":[1],"from":[2],"small":[3,7,37,192,207,217],"RNAs":[4,9],"such":[5,63],"as":[6,64,198],"nucleolar":[8,193],"are":[10],"biologically":[11,60],"relevant":[12],"but":[13],"remain":[14],"poorly":[15],"understood.":[16],"To":[17],"address":[18],"this":[19],"gap,":[20],"we":[21,115],"developed":[22],"sRNAfrag,":[23],"a":[24,46,51,75,103,161,199,212],"modular":[25],"and":[26,34,66,138,173,182,210],"interoperable":[27],"tool":[28,44],"designed":[29],"to":[30,81,132,191,215],"standardize":[31],"the":[32,94,111,143,169],"quantification":[33],"analysis":[35],"of":[36,48,59,85,125,206],"RNA":[38,67,208,218],"fragmentation":[39,140],"across":[40,70],"various":[41],"biotypes.":[42],"The":[43],"outputs":[45],"set":[47],"tables":[49],"forming":[50],"relational":[52,112],"database,":[53],"allowing":[54],"for":[55,155,202],"an":[56,130],"in-depth":[57],"exploration":[58],"complex":[61],"events":[62,121],"multi-mapping":[65],"fragment":[68,119],"stability":[69],"different":[71],"cell":[72,184],"types.":[73],"In":[74],"benchmark":[76],"test,":[77],"sRNAfrag":[78,196],"was":[79],"able":[80],"identify":[82],"established":[83],"loci":[84],"mature":[86],"microRNAs":[87],"solely":[88],"based":[89],"on":[90],"sequencing":[91],"data.":[92],"Furthermore,":[93],"5'":[95],"seed":[96],"sequence":[97],"could":[98],"be":[99],"rediscovered":[100],"by":[101,177],"utilizing":[102],"visualization":[104],"approach":[105],"primarily":[106],"applied":[107,190],"in":[108],"multi-sequence-alignments.":[109],"Utilizing":[110],"database":[113],"outputs,":[114],"detected":[116],"1411":[117],"snoRNA":[118],"conservation":[120],"between":[122],"two":[123],"out":[124],"four":[126],"eukaryotic":[127],"species,":[128],"providing":[129],"opportunity":[131],"explore":[133],"motifs":[134],"through":[135],"evolutionary":[136],"time":[137],"conserved":[139],"patterns.":[141],"Additionally,":[142],"tool's":[144],"interoperability":[145],"with":[146],"other":[147],"bioinformatics":[148],"tools":[149],"like":[150],"ViennaRNA":[151],"amplifies":[152],"its":[153],"utility":[154],"customized":[156],"analyses.":[157],"We":[158],"also":[159],"introduce":[160],"novel":[162],"loci-level":[163],"variance-score":[164],"which":[165],"provides":[166],"insights":[167],"into":[168],"noise":[170],"around":[171],"peaks":[172],"demonstrates":[174],"biological":[175],"relevance":[176],"distinctly":[178],"separating":[179],"breast":[180],"cancer":[181],"neuroblastoma":[183],"lines":[185],"after":[186],"dimension":[187],"reduction":[188],"when":[189],"RNAs.":[194],"Overall,":[195],"serves":[197],"versatile":[200],"foundation":[201,214],"advancing":[203],"our":[204],"understanding":[205],"fragments":[209],"offers":[211],"functional":[213],"further":[216],"research.":[219],"Availability:":[220],"https://github.com/kenminsoo/sRNAfrag.":[221]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
