{"id":"https://openalex.org/W3122856869","doi":"https://doi.org/10.1093/bioinformatics/btab016","title":"IsoMiRmap: fast, deterministic and exhaustive mining of isomiRs from short RNA-seq datasets","display_name":"IsoMiRmap: fast, deterministic and exhaustive mining of isomiRs from short RNA-seq datasets","publication_year":2021,"publication_date":"2021-01-10","ids":{"openalex":"https://openalex.org/W3122856869","doi":"https://doi.org/10.1093/bioinformatics/btab016","mag":"3122856869","pmid":"https://pubmed.ncbi.nlm.nih.gov/33471076"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab016","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab016","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/13/1828/39835834/btab016.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","license_id":"https://openalex.org/licenses/cc-by","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/37/13/1828/39835834/btab016.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016044802","display_name":"Phillipe Loher","orcid":"https://orcid.org/0000-0003-1302-9016"},"institutions":[{"id":"https://openalex.org/I149251103","display_name":"Thomas Jefferson University","ror":"https://ror.org/00ysqcn41","country_code":"US","type":"education","lineage":["https://openalex.org/I149251103"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Phillipe Loher","raw_affiliation_strings":["Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University , Philadelphia, PA 19107, USA"],"affiliations":[{"raw_affiliation_string":"Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University , Philadelphia, PA 19107, USA","institution_ids":["https://openalex.org/I149251103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061175529","display_name":"Nestoras Karathanasis","orcid":"https://orcid.org/0000-0003-4119-0851"},"institutions":[{"id":"https://openalex.org/I149251103","display_name":"Thomas Jefferson University","ror":"https://ror.org/00ysqcn41","country_code":"US","type":"education","lineage":["https://openalex.org/I149251103"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nestoras Karathanasis","raw_affiliation_strings":["Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University , Philadelphia, PA 19107, USA"],"affiliations":[{"raw_affiliation_string":"Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University , Philadelphia, PA 19107, USA","institution_ids":["https://openalex.org/I149251103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047890254","display_name":"Eric Londin","orcid":"https://orcid.org/0000-0003-4331-6366"},"institutions":[{"id":"https://openalex.org/I149251103","display_name":"Thomas Jefferson University","ror":"https://ror.org/00ysqcn41","country_code":"US","type":"education","lineage":["https://openalex.org/I149251103"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric Londin","raw_affiliation_strings":["Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University , Philadelphia, PA 19107, USA"],"affiliations":[{"raw_affiliation_string":"Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University , Philadelphia, PA 19107, USA","institution_ids":["https://openalex.org/I149251103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040154285","display_name":"Paul F. Bray","orcid":"https://orcid.org/0000-0002-8672-3183"},"institutions":[{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul F. Bray","raw_affiliation_strings":["Department of Internal Medicine, University of Utah , Salt Lake City, UT 84112, USA"],"affiliations":[{"raw_affiliation_string":"Department of Internal Medicine, University of Utah , Salt Lake City, UT 84112, USA","institution_ids":["https://openalex.org/I223532165"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085061389","display_name":"Venetia Pliatsika","orcid":"https://orcid.org/0009-0000-7462-6688"},"institutions":[{"id":"https://openalex.org/I149251103","display_name":"Thomas Jefferson University","ror":"https://ror.org/00ysqcn41","country_code":"US","type":"education","lineage":["https://openalex.org/I149251103"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Venetia Pliatsika","raw_affiliation_strings":["Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University , Philadelphia, PA 19107, USA"],"affiliations":[{"raw_affiliation_string":"Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University , Philadelphia, PA 19107, USA","institution_ids":["https://openalex.org/I149251103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023165177","display_name":"Aristeidis G. Telonis","orcid":"https://orcid.org/0000-0003-1575-2769"},"institutions":[{"id":"https://openalex.org/I145608581","display_name":"University of Miami","ror":"https://ror.org/02dgjyy92","country_code":"US","type":"education","lineage":["https://openalex.org/I145608581"]},{"id":"https://openalex.org/I149251103","display_name":"Thomas Jefferson University","ror":"https://ror.org/00ysqcn41","country_code":"US","type":"education","lineage":["https://openalex.org/I149251103"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aristeidis G. Telonis","raw_affiliation_strings":["Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University , Philadelphia, PA 19107, USA","Department of Human Genetics, Miller School of Medicine, University of Miami , Miami, FL 33136, USA"],"affiliations":[{"raw_affiliation_string":"Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University , Philadelphia, PA 19107, USA","institution_ids":["https://openalex.org/I149251103"]},{"raw_affiliation_string":"Department of Human Genetics, Miller School of Medicine, University of Miami , Miami, FL 33136, USA","institution_ids":["https://openalex.org/I145608581"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054046136","display_name":"Isidore Rigoutsos","orcid":"https://orcid.org/0000-0003-1529-8631"},"institutions":[{"id":"https://openalex.org/I149251103","display_name":"Thomas Jefferson University","ror":"https://ror.org/00ysqcn41","country_code":"US","type":"education","lineage":["https://openalex.org/I149251103"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Isidore Rigoutsos","raw_affiliation_strings":["Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University , Philadelphia, PA 19107, USA"],"affiliations":[{"raw_affiliation_string":"Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University , Philadelphia, PA 19107, USA","institution_ids":["https://openalex.org/I149251103"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5054046136"],"corresponding_institution_ids":["https://openalex.org/I149251103"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.9239,"has_fulltext":true,"cited_by_count":33,"citation_normalized_percentile":{"value":0.85732499,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"37","issue":"13","first_page":"1828","last_page":"1838"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10062","display_name":"MicroRNA in disease regulation","score":1.0,"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":1.0,"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":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9995999932289124,"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/computational-biology","display_name":"Computational biology","score":0.5408336520195007},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.505465030670166},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.4747248888015747},{"id":"https://openalex.org/keywords/laptop","display_name":"Laptop","score":0.46353960037231445},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.4441632926464081},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3895483613014221},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.36888694763183594},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.35918107628822327},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.21099355816841125},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12288722395896912}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5408336520195007},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.505465030670166},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.4747248888015747},{"id":"https://openalex.org/C2780008327","wikidata":"https://www.wikidata.org/wiki/Q3962","display_name":"Laptop","level":2,"score":0.46353960037231445},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.4441632926464081},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3895483613014221},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.36888694763183594},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.35918107628822327},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.21099355816841125},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12288722395896912},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btab016","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab016","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/13/1828/39835834/btab016.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33471076","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33471076","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:jdc.jefferson.edu:tjucompmedctrfp-1038","is_oa":true,"landing_page_url":"https://jdc.jefferson.edu/tjucompmedctrfp/38","pdf_url":"https://jdc.jefferson.edu/tjucompmedctrfp/38","source":{"id":"https://openalex.org/S4210178181","display_name":"The Medicine Forum","issn_l":"2325-2863","issn":["2325-2863"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Computational Medicine Center Faculty Papers","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8317110","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8317110","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab016","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab016","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/13/1828/39835834/btab016.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","score":0.4000000059604645,"display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G8628452099","display_name":null,"funder_award_id":"R01 HL141424","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3122856869.pdf","grobid_xml":"https://content.openalex.org/works/W3122856869.grobid-xml"},"referenced_works_count":70,"referenced_works":["https://openalex.org/W144423133","https://openalex.org/W1454791104","https://openalex.org/W1528213115","https://openalex.org/W1545529171","https://openalex.org/W1569043156","https://openalex.org/W1967517087","https://openalex.org/W1974134624","https://openalex.org/W1997393600","https://openalex.org/W2002995168","https://openalex.org/W2003370854","https://openalex.org/W2018507242","https://openalex.org/W2022326327","https://openalex.org/W2025943989","https://openalex.org/W2030507502","https://openalex.org/W2036897871","https://openalex.org/W2040290488","https://openalex.org/W2043704189","https://openalex.org/W2044131517","https://openalex.org/W2063959996","https://openalex.org/W2072636314","https://openalex.org/W2077327925","https://openalex.org/W2082448279","https://openalex.org/W2102120094","https://openalex.org/W2104549677","https://openalex.org/W2117147211","https://openalex.org/W2119480083","https://openalex.org/W2122732537","https://openalex.org/W2124985265","https://openalex.org/W2147110592","https://openalex.org/W2152091242","https://openalex.org/W2154768752","https://openalex.org/W2155412493","https://openalex.org/W2162674813","https://openalex.org/W2179438025","https://openalex.org/W2180405650","https://openalex.org/W2185215643","https://openalex.org/W2262761490","https://openalex.org/W2296142998","https://openalex.org/W2341142076","https://openalex.org/W2558715006","https://openalex.org/W2588840062","https://openalex.org/W2589911306","https://openalex.org/W2592927924","https://openalex.org/W2597632520","https://openalex.org/W2605795556","https://openalex.org/W2735747624","https://openalex.org/W2748710555","https://openalex.org/W2757262038","https://openalex.org/W2769912973","https://openalex.org/W2774031974","https://openalex.org/W2797749213","https://openalex.org/W2889417790","https://openalex.org/W2898440040","https://openalex.org/W2907850543","https://openalex.org/W2912491890","https://openalex.org/W2921268559","https://openalex.org/W2948399858","https://openalex.org/W2956847096","https://openalex.org/W2957041352","https://openalex.org/W2970503289","https://openalex.org/W2996823043","https://openalex.org/W3008420094","https://openalex.org/W3015624200","https://openalex.org/W3029661147","https://openalex.org/W3083205881","https://openalex.org/W4212941976","https://openalex.org/W4243624632","https://openalex.org/W4247730125","https://openalex.org/W6736307199","https://openalex.org/W6772290092"],"related_works":["https://openalex.org/W2045444909","https://openalex.org/W3153292769","https://openalex.org/W1516398359","https://openalex.org/W1901656956","https://openalex.org/W4239210160","https://openalex.org/W2941659365","https://openalex.org/W2376300433","https://openalex.org/W4242605858","https://openalex.org/W2132912433","https://openalex.org/W1971332228"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":2}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
