{"id":"https://openalex.org/W3112369941","doi":"https://doi.org/10.1093/bib/bbaa346","title":"Encyclopedia of tools for the analysis of miRNA isoforms","display_name":"Encyclopedia of tools for the analysis of miRNA isoforms","publication_year":2020,"publication_date":"2020-11-23","ids":{"openalex":"https://openalex.org/W3112369941","doi":"https://doi.org/10.1093/bib/bbaa346","mag":"3112369941","pmid":"https://pubmed.ncbi.nlm.nih.gov/33313643"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaa346","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa346","pdf_url":null,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040200834","display_name":"Georges P Schmartz","orcid":"https://orcid.org/0000-0002-9627-9223"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Georges Pierre Schmartz","raw_affiliation_strings":["Saarland Center for Bioinformatics"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Saarland Center for Bioinformatics","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084504324","display_name":"Fabian Kern","orcid":"https://orcid.org/0000-0002-8223-3750"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Fabian Kern","raw_affiliation_strings":["Saarland Center for Bioinformatics"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Saarland Center for Bioinformatics","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075631508","display_name":"Tobias Fehlmann","orcid":"https://orcid.org/0000-0003-1967-2918"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Tobias Fehlmann","raw_affiliation_strings":["Saarland Center for Bioinformatics"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Saarland Center for Bioinformatics","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065419895","display_name":"Viktoria Wagner","orcid":"https://orcid.org/0000-0002-1957-0658"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Viktoria Wagner","raw_affiliation_strings":["Saarland Center for Bioinformatics"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Saarland Center for Bioinformatics","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050465824","display_name":"Bastian Fromm","orcid":"https://orcid.org/0000-0003-0352-3037"},"institutions":[{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]},{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Bastian Fromm","raw_affiliation_strings":["Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden","institution_ids":["https://openalex.org/I2800139495","https://openalex.org/I161593684"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020280119","display_name":"Andreas Keller","orcid":"https://orcid.org/0000-0002-5361-0895"},"institutions":[{"id":"https://openalex.org/I91712215","display_name":"Saarland University","ror":"https://ror.org/01jdpyv68","country_code":"DE","type":"education","lineage":["https://openalex.org/I91712215"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Andreas Keller","raw_affiliation_strings":["Saarland Center for Bioinformatics and Chair for Clinical Bioinformatics, Saarland University Building E2.1, 66123 Saarbr\u00fccken, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Saarland Center for Bioinformatics and Chair for Clinical Bioinformatics, Saarland University Building E2.1, 66123 Saarbr\u00fccken, Germany","institution_ids":["https://openalex.org/I91712215"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5020280119"],"corresponding_institution_ids":["https://openalex.org/I91712215"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.1606,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.45715101,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"22","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10062","display_name":"MicroRNA in disease regulation","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9988999962806702,"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":0.9987999796867371,"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/computer-science","display_name":"Computer science","score":0.641324520111084},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5213866829872131},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.4808407723903656},{"id":"https://openalex.org/keywords/range","display_name":"Range (aeronautics)","score":0.4778956174850464},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.45961683988571167},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43556201457977295},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2187192440032959},{"id":"https://openalex.org/keywords/systems-engineering","display_name":"Systems engineering","score":0.07913312315940857}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.641324520111084},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5213866829872131},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.4808407723903656},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.4778956174850464},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.45961683988571167},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43556201457977295},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2187192440032959},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.07913312315940857},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"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":"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":"D035683","descriptor_name":"MicroRNAs","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":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbaa346","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa346","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33313643","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33313643","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":63,"referenced_works":["https://openalex.org/W1454791104","https://openalex.org/W1545529171","https://openalex.org/W1560889834","https://openalex.org/W1973401140","https://openalex.org/W1997393600","https://openalex.org/W2004791359","https://openalex.org/W2005388332","https://openalex.org/W2022326327","https://openalex.org/W2040290488","https://openalex.org/W2053078446","https://openalex.org/W2075996757","https://openalex.org/W2089055162","https://openalex.org/W2100465225","https://openalex.org/W2106077004","https://openalex.org/W2109923675","https://openalex.org/W2112192177","https://openalex.org/W2119942258","https://openalex.org/W2122866775","https://openalex.org/W2123265753","https://openalex.org/W2130305733","https://openalex.org/W2216943200","https://openalex.org/W2279137520","https://openalex.org/W2288482887","https://openalex.org/W2312825490","https://openalex.org/W2326425295","https://openalex.org/W2335715691","https://openalex.org/W2371020134","https://openalex.org/W2391969373","https://openalex.org/W2530460077","https://openalex.org/W2587667774","https://openalex.org/W2588840062","https://openalex.org/W2592927924","https://openalex.org/W2597544746","https://openalex.org/W2601736435","https://openalex.org/W2735747624","https://openalex.org/W2743511563","https://openalex.org/W2757262038","https://openalex.org/W2778968255","https://openalex.org/W2806293562","https://openalex.org/W2807316340","https://openalex.org/W2810144884","https://openalex.org/W2889417790","https://openalex.org/W2891392248","https://openalex.org/W2897967970","https://openalex.org/W2898440040","https://openalex.org/W2907850543","https://openalex.org/W2919470997","https://openalex.org/W2945288061","https://openalex.org/W2947781194","https://openalex.org/W2951626485","https://openalex.org/W2966451150","https://openalex.org/W2970503289","https://openalex.org/W2979975313","https://openalex.org/W2985955412","https://openalex.org/W2987567173","https://openalex.org/W2993429139","https://openalex.org/W3009983268","https://openalex.org/W3017213930","https://openalex.org/W3022324779","https://openalex.org/W4211064852","https://openalex.org/W4243624632","https://openalex.org/W6735847198","https://openalex.org/W6766716985"],"related_works":["https://openalex.org/W2012531322","https://openalex.org/W2402761219","https://openalex.org/W2785900585","https://openalex.org/W2353730437","https://openalex.org/W2490303674","https://openalex.org/W2609066826","https://openalex.org/W2810752900","https://openalex.org/W2365677836","https://openalex.org/W2531295127","https://openalex.org/W3186538219"],"abstract_inverted_index":{"RNA":[0],"sequencing":[1,203],"data":[2,163,204],"sets":[3,205],"rapidly":[4],"increase":[5],"in":[6,120,233],"quantity.":[7],"For":[8],"microRNAs":[9],"(miRNAs),":[10],"frequently":[11],"dozens":[12],"to":[13,44,112],"hundreds":[14],"of":[15,24,30,41,51,55,57,67,73,90,115,128,133,142,148,160,169,176,183,214,228,238],"billion":[16],"reads":[17],"are":[18,33,145,172],"generated":[19],"per":[20],"study.":[21],"The":[22,53],"quantification":[23],"annotated":[25],"miRNAs":[26,32,58],"and":[27,64,99,104,122,178,232],"the":[28,38,49,71,88,116,125,129,134,158,170,186,212,226,236,239],"prediction":[29],"new":[31],"leading":[34],"computational":[35,68,85],"tasks.":[36],"Now,":[37],"increased":[39],"depth":[40],"coverage":[42],"allows":[43],"gain":[45],"deeper":[46],"insights":[47,210],"into":[48,211],"variability":[50],"miRNAs.":[52],"analysis":[54,72,89,159,174,180,230],"isoforms":[56],"(isomiRs)":[59],"is":[60,181],"a":[61,65,106,139,149,222],"trending":[62],"topic,":[63],"range":[66,109,141],"tools":[69,117,136,153,171,175,189,208,231],"for":[70,87,138,157,165,194,206,243],"isomiRs":[74],"has":[75],"been":[76,155,192],"developed.":[77],"We":[78],"provide":[79,220],"an":[80],"overview":[81,224],"on":[82,200,225],"27":[83],"available":[84],"solutions":[86,101],"isomiRs.":[91],"These":[92],"include":[93],"both":[94],"stand-alone":[95],"programs":[96],"(17":[97],"tools)":[98,103],"web-based":[100],"(10":[102],"span":[105],"publication":[107],"time":[108],"from":[110],"2010":[111],"2020.":[113],"Seven":[114],"were":[118],"published":[119],"2019":[121],"2020,":[123],"confirming":[124],"rising":[126],"importance":[127],"topic.":[130],"While":[131,167],"most":[132,240],"analyzed":[135],"work":[137],"broad":[140],"organisms":[143],"or":[144,164],"completely":[146],"independent":[147],"reference":[150],"organism,":[151],"several":[152],"have":[154,190],"tailored":[156],"human":[161],"miRNA":[162],"plants.":[166],"14":[168],"general":[173],"miRNAs,":[177],"isomiR":[179,195,229],"one":[182],"their":[184,244],"features,":[185],"remaining":[187],"13":[188],"specifically":[191],"developed":[193],"analysis.":[196],"A":[197],"direct":[198],"comparison":[199],"20":[201],"deep":[202],"selected":[207],"provides":[209],"heterogeneity":[213],"results.":[215],"With":[216],"our":[217],"work,":[218],"we":[219],"users":[221],"comprehensive":[223],"landscape":[227],"that":[234],"support":[235],"selection":[237],"appropriate":[241],"tool":[242],"respective":[245],"research":[246],"task.":[247]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
