{"id":"https://openalex.org/W3116325393","doi":"https://doi.org/10.1016/j.ocarto.2020.100131","title":"A bioinformatics approach to microRNA-sequencing analysis","display_name":"A bioinformatics approach to microRNA-sequencing analysis","publication_year":2020,"publication_date":"2020-12-19","ids":{"openalex":"https://openalex.org/W3116325393","doi":"https://doi.org/10.1016/j.ocarto.2020.100131","mag":"3116325393","pmid":"https://pubmed.ncbi.nlm.nih.gov/36475076","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/9718162"},"language":"en","primary_location":{"id":"doi:10.1016/j.ocarto.2020.100131","doi":"https://doi.org/10.1016/j.ocarto.2020.100131","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.ocarto.2020.100131","pdf_url":"https://www.sciencedirect.com/science/article/pii/S266591312030131X/pdf","source":{"id":"https://openalex.org/S4210208012","display_name":"Osteoarthritis and Cartilage Open","issn_l":"2665-9131","issn":["2665-9131"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","doyens","jufo-1","ki-jl-1","norway-1"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Osteoarthritis and Cartilage Open","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.sciencedirect.com/science/article/pii/S266591312030131X/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081412728","display_name":"Pratibha Potla","orcid":"https://orcid.org/0000-0002-3000-6820","observed_orcids":["https://orcid.org/0000-0002-3000-6820"]},"institutions":[{"id":"https://openalex.org/I1325899441","display_name":"University Health Network","ror":"https://ror.org/042xt5161","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441"]},{"id":"https://openalex.org/I4388446386","display_name":"Krembil Research Institute","ror":"https://ror.org/01f6jys10","country_code":"CA","type":"facility","lineage":["https://openalex.org/I1325899441","https://openalex.org/I2799337515","https://openalex.org/I4388446386"]},{"id":"https://openalex.org/I4388891853","display_name":"Schroeder Arthritis Institute","ror":"https://ror.org/03ex4ek60","country_code":"CA","type":"facility","lineage":["https://openalex.org/I1325899441","https://openalex.org/I2799337515","https://openalex.org/I4388446386","https://openalex.org/I4388891853"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Pratibha Potla","raw_affiliation_strings":["Krembil Research Institute, University Health Network, Toronto, Ontario, Canada","Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada"],"raw_orcid":"https://orcid.org/0000-0002-3000-6820","affiliations":[{"raw_affiliation_string":"Krembil Research Institute, University Health Network, Toronto, Ontario, Canada","institution_ids":["https://openalex.org/I1325899441","https://openalex.org/I4388446386"]},{"raw_affiliation_string":"Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada","institution_ids":["https://openalex.org/I1325899441","https://openalex.org/I4388891853"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070760357","display_name":"Shabana Amanda Ali","orcid":"https://orcid.org/0000-0002-4339-9467","observed_orcids":["https://orcid.org/0000-0002-4339-9467"]},"institutions":[{"id":"https://openalex.org/I154057602","display_name":"Henry Ford Health","ror":"https://ror.org/02kwnkm68","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I154057602"]},{"id":"https://openalex.org/I2803043754","display_name":"Henry Ford Hospital","ror":"https://ror.org/0193sb042","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I154057602","https://openalex.org/I2803043754"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Shabana Amanda Ali","raw_affiliation_strings":["Bone and Joint Center, Department of Orthopaedic Surgery, Henry Ford Health System, Detroit, MI, USA"],"raw_orcid":"https://orcid.org/0000-0002-4339-9467","affiliations":[{"raw_affiliation_string":"Bone and Joint Center, Department of Orthopaedic Surgery, Henry Ford Health System, Detroit, MI, USA","institution_ids":["https://openalex.org/I154057602","https://openalex.org/I2803043754"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066040148","display_name":"Mohit Kapoor","orcid":"https://orcid.org/0000-0001-7994-110X","observed_orcids":["https://orcid.org/0000-0001-7994-110X","https://orcid.org/0000-0001-9877-0772","https://orcid.org/0000-0003-4138-3733"]},"institutions":[{"id":"https://openalex.org/I1325899441","display_name":"University Health Network","ror":"https://ror.org/042xt5161","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I4388446386","display_name":"Krembil Research Institute","ror":"https://ror.org/01f6jys10","country_code":"CA","type":"facility","lineage":["https://openalex.org/I1325899441","https://openalex.org/I2799337515","https://openalex.org/I4388446386"]},{"id":"https://openalex.org/I4388891853","display_name":"Schroeder Arthritis Institute","ror":"https://ror.org/03ex4ek60","country_code":"CA","type":"facility","lineage":["https://openalex.org/I1325899441","https://openalex.org/I2799337515","https://openalex.org/I4388446386","https://openalex.org/I4388891853"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Mohit Kapoor","raw_affiliation_strings":["Department of Surgery and Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada","Krembil Research Institute, University Health Network, Toronto, Ontario, Canada","Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Surgery and Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Krembil Research Institute, University Health Network, Toronto, Ontario, Canada","institution_ids":["https://openalex.org/I1325899441","https://openalex.org/I4388446386"]},{"raw_affiliation_string":"Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada","institution_ids":["https://openalex.org/I1325899441","https://openalex.org/I4388891853"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5066040148","https://openalex.org/A5070760357"],"corresponding_institution_ids":["https://openalex.org/I1325899441","https://openalex.org/I154057602","https://openalex.org/I185261750","https://openalex.org/I2803043754","https://openalex.org/I4388446386","https://openalex.org/I4388891853"],"apc_list":{"value":1400,"currency":"USD","value_usd":1400},"apc_paid":{"value":1400,"currency":"USD","value_usd":1400},"fwci":2.3584,"has_fulltext":true,"cited_by_count":77,"citation_normalized_percentile":{"value":0.90535468,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":88,"max":100},"biblio":{"volume":"3","issue":"1","first_page":"100131","last_page":"100131"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.5425000190734863,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.5425000190734863,"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/T10062","display_name":"MicroRNA in disease regulation","score":0.38260000944137573,"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/T10885","display_name":"Gene expression and cancer classification","score":0.023800000548362732,"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/mirna-sequencing","display_name":"miRNA sequencing","score":0.8169999718666077},{"id":"https://openalex.org/keywords/unique-molecular-identifiers","display_name":"unique molecular identifiers","score":0.7760000228881836},{"id":"https://openalex.org/keywords/sequencing-quality-assessment","display_name":"sequencing quality assessment","score":0.7129999995231628},{"id":"https://openalex.org/keywords/novel-mirna-discovery","display_name":"novel miRNA discovery","score":0.9900000095367432},{"id":"https://openalex.org/keywords/reproducibility","display_name":"reproducibility","score":0.9089999794960022}],"concepts":[{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5867593884468079},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5286380052566528},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5273566842079163},{"id":"https://openalex.org/C145059251","wikidata":"https://www.wikidata.org/wiki/Q310899","display_name":"microRNA","level":3,"score":0.48383083939552307},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46392425894737244},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4574337601661682},{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.45649898052215576},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.4321146607398987},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3604716658592224},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3522772789001465},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.144430011510849},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13202908635139465},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1081627905368805},{"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/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1016/j.ocarto.2020.100131","doi":"https://doi.org/10.1016/j.ocarto.2020.100131","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.ocarto.2020.100131","pdf_url":"https://www.sciencedirect.com/science/article/pii/S266591312030131X/pdf","source":{"id":"https://openalex.org/S4210208012","display_name":"Osteoarthritis and Cartilage Open","issn_l":"2665-9131","issn":["2665-9131"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","doyens","jufo-1","ki-jl-1","norway-1"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Osteoarthritis and Cartilage Open","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9718162","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9718162","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,"listed_in":[],"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-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Osteoarthr Cartil Open","raw_type":"Text"},{"id":"pmid:36475076","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36475076","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,"listed_in":[],"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":"Osteoarthritis and cartilage open","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:0486d27945a24ed5807cca46d71bcfe7","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/0486d27945a24ed5807cca46d71bcfe7","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Osteoarthritis and Cartilage Open, Vol 3, Iss 1, Pp 100131- (2021)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1016/j.ocarto.2020.100131","doi":"https://doi.org/10.1016/j.ocarto.2020.100131","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.ocarto.2020.100131","pdf_url":"https://www.sciencedirect.com/science/article/pii/S266591312030131X/pdf","source":{"id":"https://openalex.org/S4210208012","display_name":"Osteoarthritis and Cartilage Open","issn_l":"2665-9131","issn":["2665-9131"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","doyens","jufo-1","ki-jl-1","norway-1"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Osteoarthritis and Cartilage Open","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.4000000059604645}],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322353","display_name":"Krembil Foundation","ror":"https://ror.org/037svw098"},{"id":"https://openalex.org/F4320334506","display_name":"Canadian Institutes of Health Research","ror":"https://ror.org/01gavpb45"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3116325393.pdf","grobid_xml":"https://content.openalex.org/works/W3116325393.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W144423133","https://openalex.org/W1558516755","https://openalex.org/W1981509058","https://openalex.org/W1984621241","https://openalex.org/W1993165035","https://openalex.org/W2070571588","https://openalex.org/W2092784580","https://openalex.org/W2105679485","https://openalex.org/W2115093090","https://openalex.org/W2130305733","https://openalex.org/W2138270253","https://openalex.org/W2147416962","https://openalex.org/W2289678372","https://openalex.org/W2576734941","https://openalex.org/W2762638728","https://openalex.org/W2776332611","https://openalex.org/W2801006204","https://openalex.org/W2806388412","https://openalex.org/W2889417790","https://openalex.org/W2939859838","https://openalex.org/W2945288061","https://openalex.org/W2949145460","https://openalex.org/W2951912016","https://openalex.org/W2952109315","https://openalex.org/W2981692913","https://openalex.org/W2995111932","https://openalex.org/W3021393188","https://openalex.org/W3031351022","https://openalex.org/W3045016448","https://openalex.org/W3045647287","https://openalex.org/W7098838276"],"related_works":["https://openalex.org/W1993165035","https://openalex.org/W4213438624","https://openalex.org/W1976355615","https://openalex.org/W7099391235","https://openalex.org/W2947781194","https://openalex.org/W4310184746","https://openalex.org/W2791364237","https://openalex.org/W2771984578","https://openalex.org/W2056703789","https://openalex.org/W2597544746"],"abstract_inverted_index":{"The":[0],"rapid":[1],"expansion":[2],"of":[3,13,87,144,170,174,185],"Next":[4],"Generation":[5],"Sequencing":[6],"(NGS)":[7],"data":[8,114,147],"availability":[9],"has":[10],"made":[11],"exploration":[12],"appropriate":[14],"bioinformatics":[15,89,126,172],"analysis":[16,43],"pipelines":[17],"a":[18,45,123],"timely":[19],"issue.":[20],"Since":[21],"there":[22,33,68],"are":[23,81],"multiple":[24],"tools":[25],"and":[26,47,78,108,115,157,168],"combinations":[27],"thereof":[28],"to":[29,39,66,76,104,165,182],"analyze":[30],"any":[31,179],"dataset,":[32],"can":[34],"be":[35],"uncertainty":[36],"in":[37,44,188],"how":[38],"best":[40],"perform":[41],"an":[42],"robust":[46],"reproducible":[48],"manner.":[49],"This":[50,118,161],"is":[51,163],"especially":[52],"true":[53],"for":[54,153],"newer":[55],"omics":[56],"applications,":[57],"such":[58,93],"as":[59,94],"miRNomics,":[60],"or":[61],"microRNA-sequencing":[62],"(miRNA-sequencing).":[63],"As":[64],"compared":[65],"transcriptomics,":[67],"have":[69],"been":[70],"far":[71],"fewer":[72],"miRNA-sequencing":[73,113,132,175],"studies":[74],"performed":[75],"date,":[77],"those":[79],"that":[80,128],"reported":[82],"seldom":[83],"provide":[84],"detailed":[85,186],"description":[86],"the":[88,106,171,189],"analysis,":[90,176],"including":[91],"aspects":[92],"Unique":[95],"Molecular":[96],"Identifiers":[97],"(UMIs).":[98],"In":[99],"this":[100],"article,":[101],"we":[102],"attempt":[103],"fill":[105],"gap":[107],"help":[109],"researchers":[110],"understand":[111],"their":[112],"its":[116],"analysis.":[117],"article":[119],"will":[120],"specifically":[121],"discuss":[122],"customizable":[124],"miRNA":[125,154,159],"pipeline":[127],"was":[129],"developed":[130],"using":[131],"datasets":[133],"generated":[134],"from":[135],"human":[136],"osteoarthritis":[137],"plasma":[138],"samples.":[139],"We":[140],"describe":[141],"quality":[142],"assessment":[143],"raw":[145],"sequencing":[146],"files,":[148],"reference-based":[149],"alignment,":[150],"counts":[151],"generation":[152],"expression":[155],"levels,":[156],"novel":[158],"discovery.":[160],"report":[162],"expected":[164],"improve":[166],"clarity":[167],"reproducibility":[169],"portion":[173],"applicable":[177],"across":[178],"sample":[180],"type,":[181],"promote":[183],"sharing":[184],"protocols":[187],"NGS":[190],"field.":[191]},"counts_by_year":[{"year":2026,"cited_by_count":12},{"year":2025,"cited_by_count":15},{"year":2024,"cited_by_count":16},{"year":2023,"cited_by_count":11},{"year":2022,"cited_by_count":20},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":1}],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2021-01-05T00:00:00"}
