{"id":"https://openalex.org/W2985955412","doi":"https://doi.org/10.1093/bioinformatics/btz806","title":"Jasmine: a Java pipeline for isomiR characterization in miRNA-Seq data","display_name":"Jasmine: a Java pipeline for isomiR characterization in miRNA-Seq data","publication_year":2019,"publication_date":"2019-10-30","ids":{"openalex":"https://openalex.org/W2985955412","doi":"https://doi.org/10.1093/bioinformatics/btz806","mag":"2985955412","pmid":"https://pubmed.ncbi.nlm.nih.gov/31681943"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz806","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz806","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/6/1933/32915344/btz806.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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/bioinformatics/article-pdf/36/6/1933/32915344/btz806.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058923206","display_name":"Xiangfu Zhong","orcid":"https://orcid.org/0000-0002-1872-1186"},"institutions":[{"id":"https://openalex.org/I1281400175","display_name":"Oslo University Hospital","ror":"https://ror.org/00j9c2840","country_code":"NO","type":"healthcare","lineage":["https://openalex.org/I1281400175"]},{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Xiangfu Zhong","raw_affiliation_strings":["Department of Medical Genetics, Institute of Clinical Medicine, Oslo University Hospital , Oslo","Department of Medical Genetics, University of Oslo , Oslo"],"raw_orcid":"https://orcid.org/0000-0002-1872-1186","affiliations":[{"raw_affiliation_string":"Department of Medical Genetics, Institute of Clinical Medicine, Oslo University Hospital , Oslo","institution_ids":["https://openalex.org/I1281400175"]},{"raw_affiliation_string":"Department of Medical Genetics, University of Oslo , Oslo","institution_ids":["https://openalex.org/I184942183"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047538223","display_name":"Albert Pl\u00e0","orcid":"https://orcid.org/0000-0001-7527-2500"},"institutions":[{"id":"https://openalex.org/I1281400175","display_name":"Oslo University Hospital","ror":"https://ror.org/00j9c2840","country_code":"NO","type":"healthcare","lineage":["https://openalex.org/I1281400175"]},{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Albert Pla","raw_affiliation_strings":["Department of Medical Genetics, Institute of Clinical Medicine, Oslo University Hospital , Oslo","Department of Medical Genetics, University of Oslo , Oslo"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Genetics, Institute of Clinical Medicine, Oslo University Hospital , Oslo","institution_ids":["https://openalex.org/I1281400175"]},{"raw_affiliation_string":"Department of Medical Genetics, University of Oslo , Oslo","institution_ids":["https://openalex.org/I184942183"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085179008","display_name":"Simon Rayner","orcid":"https://orcid.org/0000-0001-8703-9140"},"institutions":[{"id":"https://openalex.org/I1281400175","display_name":"Oslo University Hospital","ror":"https://ror.org/00j9c2840","country_code":"NO","type":"healthcare","lineage":["https://openalex.org/I1281400175"]},{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":true,"raw_author_name":"Simon Rayner","raw_affiliation_strings":["Department of Medical Genetics, Institute of Clinical Medicine, Oslo University Hospital , Oslo","Department of Medical Genetics, University of Oslo , Oslo","Hybrid Technology Hub \u2013 Centre of Excellence, Institute of Basic Medical Sciences, University of Oslo , Oslo, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Genetics, Institute of Clinical Medicine, Oslo University Hospital , Oslo","institution_ids":["https://openalex.org/I1281400175"]},{"raw_affiliation_string":"Department of Medical Genetics, University of Oslo , Oslo","institution_ids":["https://openalex.org/I184942183"]},{"raw_affiliation_string":"Hybrid Technology Hub \u2013 Centre of Excellence, Institute of Basic Medical Sciences, University of Oslo , Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5085179008"],"corresponding_institution_ids":["https://openalex.org/I1281400175","https://openalex.org/I184942183"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.4636,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.58362738,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"36","issue":"6","first_page":"1933","last_page":"1936"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10062","display_name":"MicroRNA in disease regulation","score":0.9476000070571899,"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":0.9476000070571899,"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/T10604","display_name":"RNA Research and Splicing","score":0.028599999845027924,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.003800000064074993,"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/pipeline","display_name":"Pipeline (software)","score":0.7678884267807007},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.7281549572944641},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6438543200492859},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5320229530334473},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.47238826751708984},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.4287834167480469},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4235437214374542},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29686880111694336},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.220858633518219}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7678884267807007},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.7281549572944641},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6438543200492859},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5320229530334473},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.47238826751708984},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.4287834167480469},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4235437214374542},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29686880111694336},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.220858633518219},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btz806","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz806","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/6/1933/32915344/btz806.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31681943","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31681943","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7703784","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7703784","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:www.duo.uio.no:10852/77809","is_oa":true,"landing_page_url":"http://hdl.handle.net/10852/77809","pdf_url":null,"source":{"id":"https://openalex.org/S4306401717","display_name":"Duo Research Archive (University of Oslo)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184942183","host_organization_name":"University of Oslo","host_organization_lineage":["https://openalex.org/I184942183"],"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":"1367-4803","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz806","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz806","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/6/1933/32915344/btz806.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5963893655","display_name":null,"funder_award_id":"274715","funder_id":"https://openalex.org/F4320323299","funder_display_name":"Norges Forskningsr\u00e5d"},{"id":"https://openalex.org/G7373723384","display_name":null,"funder_award_id":"2016122","funder_id":"https://openalex.org/F4320335102","funder_display_name":"Helse S\u00f8r-\u00d8st RHF"}],"funders":[{"id":"https://openalex.org/F4320323299","display_name":"Norges Forskningsr\u00e5d","ror":"https://ror.org/00epmv149"},{"id":"https://openalex.org/F4320335102","display_name":"Helse S\u00f8r-\u00d8st RHF","ror":"https://ror.org/02qx2s478"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2985955412.pdf"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W2004791359","https://openalex.org/W2036897871","https://openalex.org/W2089055162","https://openalex.org/W2100465225","https://openalex.org/W2124985265","https://openalex.org/W2131271579","https://openalex.org/W2335715691","https://openalex.org/W2432815617","https://openalex.org/W2496634721","https://openalex.org/W2742823509","https://openalex.org/W2898440040","https://openalex.org/W2956146155","https://openalex.org/W4211064852","https://openalex.org/W6765110879"],"related_works":["https://openalex.org/W2749690376","https://openalex.org/W2786317006","https://openalex.org/W4367724653","https://openalex.org/W2788563018","https://openalex.org/W3037187668","https://openalex.org/W2997587123","https://openalex.org/W4281673905","https://openalex.org/W3206385231","https://openalex.org/W1566482460","https://openalex.org/W3118256810"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1],"existence":[2],"of":[3,6,60,72,84,132],"complex":[4],"subpopulations":[5],"miRNA":[7],"isoforms,":[8],"or":[9,121],"isomiRs,":[10],"is":[11,41,108,150],"well":[12],"established.":[13],"While":[14],"many":[15],"tools":[16],"exist":[17],"for":[18,44,51,103],"investigating":[19],"isomiR":[20,61,105,133],"populations,":[21],"they":[22,26],"differ":[23],"in":[24,64,118,124,142,152],"how":[25],"characterize":[27],"an":[28,81],"isomiR,":[29],"making":[30],"it":[31],"difficult":[32],"to":[33,80,127],"compare":[34],"results":[35],"across":[36],"different":[37],"tools.":[38],"Thus,":[39,135],"there":[40],"a":[42,45,55,95,100,109,129,143],"need":[43],"more":[46,66,73],"comprehensive":[47],"and":[48,78,154,156],"systematic":[49],"standard":[50,56,144],"defining":[52],"isomiRs.":[53],"Such":[54],"would":[57],"allow":[58],"investigation":[59],"population":[62],"structure":[63,139],"progressively":[65],"refined":[67],"sub-populations,":[68],"permitting":[69],"the":[70,85],"identification":[71],"subtle":[74],"changes":[75],"between":[76],"conditions":[77],"leading":[79],"improved":[82],"understanding":[83],"processes":[86],"that":[87,98,112],"generate":[88],"these":[89],"differences.":[90],"RESULTS:":[91],"We":[92],"developed":[93],"Jasmine,":[94],"software":[96],"tool":[97],"incorporates":[99],"hierarchal":[101],"framework":[102],"characterizing":[104],"populations.":[106,134],"Jasmine":[107,136,149],"Java":[110,153],"application":[111],"can":[113,137],"process":[114],"raw":[115],"read":[116],"data":[117,165],"fastq/fasta":[119],"format,":[120],"mapped":[122],"reads":[123],"SAM":[125],"format":[126],"produce":[128],"detailed":[130],"characterization":[131],"reveal":[138],"not":[140],"apparent":[141],"miRNA-Seq":[145],"analysis":[146],"pipeline.":[147],"AVAILABILITY:":[148],"implemented":[151],"R":[155],"freely":[157],"available":[158,167],"at":[159,168],"bitbucket":[160],"https://bitbucket.org/bipous/jasmine/src/master/.":[161],"SUPPLEMENTARY":[162],"INFORMATION:":[163],"Supplementary":[164],"are":[166],"Bioinformatics":[169],"online.":[170]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":4}],"updated_date":"2026-05-22T06:13:13.366637","created_date":"2025-10-10T00:00:00"}
