{"id":"https://openalex.org/W4313423877","doi":"https://doi.org/10.1093/bib/bbac612","title":"Systematic benchmarking of statistical methods to assess differential expression of circular RNAs","display_name":"Systematic benchmarking of statistical methods to assess differential expression of circular RNAs","publication_year":2023,"publication_date":"2023-01-01","ids":{"openalex":"https://openalex.org/W4313423877","doi":"https://doi.org/10.1093/bib/bbac612","pmid":"https://pubmed.ncbi.nlm.nih.gov/36592056"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac612","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac612","pdf_url":"https://academic.oup.com/bib/article-pdf/24/1/bbac612/48783149/bbac612.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":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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/24/1/bbac612/48783149/bbac612.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085144508","display_name":"Alessia Buratin","orcid":"https://orcid.org/0000-0003-2461-750X"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alessia Buratin","raw_affiliation_strings":["Department of Molecular Medicine, University of Padova , Padova, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Medicine, University of Padova , Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054227897","display_name":"Stefania Bortoluzzi","orcid":"https://orcid.org/0000-0001-8240-3070"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Stefania Bortoluzzi","raw_affiliation_strings":["Department of Molecular Medicine, University of Padova , Padova, Italy"],"raw_orcid":"https://orcid.org/0000-0001-8240-3070","affiliations":[{"raw_affiliation_string":"Department of Molecular Medicine, University of Padova , Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088374805","display_name":"Enrico Gaffo","orcid":"https://orcid.org/0000-0001-6338-7677"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Enrico Gaffo","raw_affiliation_strings":["Department of Molecular Medicine, University of Padova , Padova, Italy"],"raw_orcid":"https://orcid.org/0000-0001-6338-7677","affiliations":[{"raw_affiliation_string":"Department of Molecular Medicine, University of Padova , Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5088374805"],"corresponding_institution_ids":["https://openalex.org/I138689650"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.8477,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.73012783,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"24","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11765","display_name":"Circular RNAs in diseases","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/T11765","display_name":"Circular RNAs in diseases","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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.996999979019165,"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":0.9944000244140625,"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/benchmarking","display_name":"Benchmarking","score":0.8931983709335327},{"id":"https://openalex.org/keywords/differential","display_name":"Differential (mechanical device)","score":0.5781049132347107},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5467469096183777},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.5341780185699463},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5056664943695068},{"id":"https://openalex.org/keywords/circular-rna","display_name":"Circular RNA","score":0.465162068605423},{"id":"https://openalex.org/keywords/statistical-analysis","display_name":"Statistical analysis","score":0.42306482791900635},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37492725253105164},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.312639057636261},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.22297480702400208},{"id":"https://openalex.org/keywords/microrna","display_name":"microRNA","score":0.19736754894256592},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1935960352420807},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16410017013549805},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1058037281036377},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08056837320327759}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.8931983709335327},{"id":"https://openalex.org/C93226319","wikidata":"https://www.wikidata.org/wiki/Q193137","display_name":"Differential (mechanical device)","level":2,"score":0.5781049132347107},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5467469096183777},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.5341780185699463},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5056664943695068},{"id":"https://openalex.org/C2775893923","wikidata":"https://www.wikidata.org/wiki/Q17113455","display_name":"Circular RNA","level":4,"score":0.465162068605423},{"id":"https://openalex.org/C2986587452","wikidata":"https://www.wikidata.org/wiki/Q938438","display_name":"Statistical analysis","level":2,"score":0.42306482791900635},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37492725253105164},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.312639057636261},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.22297480702400208},{"id":"https://openalex.org/C145059251","wikidata":"https://www.wikidata.org/wiki/Q310899","display_name":"microRNA","level":3,"score":0.19736754894256592},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1935960352420807},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16410017013549805},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1058037281036377},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08056837320327759},{"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/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C146978453","wikidata":"https://www.wikidata.org/wiki/Q3798668","display_name":"Aerospace engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D019985","descriptor_name":"Benchmarking","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbac612","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac612","pdf_url":"https://academic.oup.com/bib/article-pdf/24/1/bbac612/48783149/bbac612.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36592056","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36592056","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:9851295","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9851295","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9851295/pdf/bbac612.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"},{"id":"pmh:oai:www.research.unipd.it:11577/3468572","is_oa":true,"landing_page_url":"https://hdl.handle.net/11577/3468572","pdf_url":"https://www.research.unipd.it/bitstream/11577/3468572/2/bbac612.pdf","source":{"id":"https://openalex.org/S4377196283","display_name":"Research Padua  Archive (University of Padua)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138689650","host_organization_name":"University of Padua","host_organization_lineage":["https://openalex.org/I138689650"],"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":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bib/bbac612","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac612","pdf_url":"https://academic.oup.com/bib/article-pdf/24/1/bbac612/48783149/bbac612.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.49000000953674316,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G1614245106","display_name":null,"funder_award_id":"#20052","funder_id":"https://openalex.org/F4320323054","funder_display_name":"Associazione Italiana per la Ricerca sul Cancro"},{"id":"https://openalex.org/G4052829840","display_name":null,"funder_award_id":"#2017PPS2X4_003","funder_id":"https://openalex.org/F4320321873","funder_display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca"},{"id":"https://openalex.org/G7598815235","display_name":null,"funder_award_id":"20052","funder_id":"https://openalex.org/F4320323054","funder_display_name":"Associazione Italiana per la Ricerca sul Cancro"}],"funders":[{"id":"https://openalex.org/F4320321873","display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca","ror":"https://ror.org/0166hxq48"},{"id":"https://openalex.org/F4320323054","display_name":"Associazione Italiana per la Ricerca sul Cancro","ror":"https://ror.org/02g2x7380"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4313423877.pdf"},"referenced_works_count":107,"referenced_works":["https://openalex.org/W1962167333","https://openalex.org/W1966716734","https://openalex.org/W1976526581","https://openalex.org/W1984883254","https://openalex.org/W2020541351","https://openalex.org/W2021880506","https://openalex.org/W2026006003","https://openalex.org/W2058358568","https://openalex.org/W2058835062","https://openalex.org/W2069089843","https://openalex.org/W2070494252","https://openalex.org/W2074414424","https://openalex.org/W2098734857","https://openalex.org/W2107038793","https://openalex.org/W2110065044","https://openalex.org/W2112058982","https://openalex.org/W2114104545","https://openalex.org/W2116041602","https://openalex.org/W2123579165","https://openalex.org/W2127274965","https://openalex.org/W2137526110","https://openalex.org/W2138207763","https://openalex.org/W2142165994","https://openalex.org/W2143689381","https://openalex.org/W2146512944","https://openalex.org/W2156631105","https://openalex.org/W2168864202","https://openalex.org/W2170962119","https://openalex.org/W2179438025","https://openalex.org/W2190545194","https://openalex.org/W2194134194","https://openalex.org/W2196247406","https://openalex.org/W2197124664","https://openalex.org/W2236822143","https://openalex.org/W2277352155","https://openalex.org/W2318878471","https://openalex.org/W2321872593","https://openalex.org/W2333507044","https://openalex.org/W2343956310","https://openalex.org/W2464424326","https://openalex.org/W2466314544","https://openalex.org/W2531297636","https://openalex.org/W2599812844","https://openalex.org/W2616187748","https://openalex.org/W2617446144","https://openalex.org/W2621124619","https://openalex.org/W2761803678","https://openalex.org/W2783644856","https://openalex.org/W2788908087","https://openalex.org/W2791184452","https://openalex.org/W2792647356","https://openalex.org/W2793635274","https://openalex.org/W2799273685","https://openalex.org/W2805888371","https://openalex.org/W2884003833","https://openalex.org/W2889138197","https://openalex.org/W2904375316","https://openalex.org/W2925033480","https://openalex.org/W2949084500","https://openalex.org/W2950464315","https://openalex.org/W2951624434","https://openalex.org/W2952526240","https://openalex.org/W2954342385","https://openalex.org/W2964382959","https://openalex.org/W2979791414","https://openalex.org/W2980800610","https://openalex.org/W2996796392","https://openalex.org/W2997280954","https://openalex.org/W2999146435","https://openalex.org/W3007722513","https://openalex.org/W3008929648","https://openalex.org/W3021278324","https://openalex.org/W3046991322","https://openalex.org/W3078790022","https://openalex.org/W3092209757","https://openalex.org/W3092663751","https://openalex.org/W3093781399","https://openalex.org/W3106120778","https://openalex.org/W3107932947","https://openalex.org/W3111378927","https://openalex.org/W3119269459","https://openalex.org/W3127021593","https://openalex.org/W3131007245","https://openalex.org/W3163951899","https://openalex.org/W3164692211","https://openalex.org/W3186687754","https://openalex.org/W3201667851","https://openalex.org/W3208194349","https://openalex.org/W3211014030","https://openalex.org/W4200074879","https://openalex.org/W4210661597","https://openalex.org/W4225981439","https://openalex.org/W4226434402","https://openalex.org/W4241872665","https://openalex.org/W4280488394","https://openalex.org/W4280638470","https://openalex.org/W4281568005","https://openalex.org/W4285239760","https://openalex.org/W4297397521","https://openalex.org/W4309908811","https://openalex.org/W6678907343","https://openalex.org/W6689944646","https://openalex.org/W6719957963","https://openalex.org/W6749509199","https://openalex.org/W6784856094","https://openalex.org/W6801399799","https://openalex.org/W6838720223"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699","https://openalex.org/W1993948687","https://openalex.org/W2000169967","https://openalex.org/W2112883198"],"abstract_inverted_index":{"Circular":[0],"RNAs":[1],"(circRNAs)":[2],"are":[3],"covalently":[4],"closed":[5],"transcripts":[6],"involved":[7],"in":[8,161],"critical":[9],"regulatory":[10],"axes,":[11],"cancer":[12],"pathways":[13],"and":[14,57,77,116,153],"disease":[15],"mechanisms.":[16],"CircRNA":[17,144],"expression":[18,34,47,145,170],"measured":[19],"with":[20,90,127,171],"RNA-seq":[21,55,131,172],"has":[22],"particular":[23],"characteristics":[24],"that":[25],"might":[26],"hamper":[27],"the":[28,87,96,128,140,163],"performance":[29,99,136],"of":[30,67,142,151],"standard":[31],"biostatistical":[32],"differential":[33,169],"assessment":[35],"methods":[36],"(DEMs).":[37],"We":[38],"compared":[39],"38":[40],"DEM":[41,152,154],"pipelines":[42],"configured":[43],"to":[44,166],"fit":[45],"circRNA":[46,168],"data's":[48],"statistical":[49],"properties,":[50],"including":[51],"bulk":[52,130],"RNA-seq,":[53],"single-cell":[54],"(scRNA-seq)":[56],"metagenomics":[58],"DEMs.":[59],"The":[60],"DEMs":[61,123],"performed":[62],"poorly":[63],"on":[64],"data":[65,103],"sets":[66,104],"typical":[68],"size.":[69],"Widely":[70],"used":[71],"DEMs,":[72],"such":[73],"as":[74,106,108],"DESeq2,":[75],"edgeR":[76],"Limma-Voom,":[78],"gave":[79],"scarce":[80],"results,":[81],"unreliable":[82],"predictions":[83],"or":[84],"even":[85],"contravened":[86],"expected":[88],"behaviour":[89],"some":[91],"parameter":[92],"configurations.":[93],"Limma-Voom":[94],"achieved":[95],"most":[97],"consistent":[98],"throughout":[100],"different":[101],"benchmark":[102],"and,":[105],"well":[107],"SAMseq,":[109],"reasonably":[110],"balanced":[111],"false":[112],"discovery":[113],"rate":[114],"(FDR)":[115],"recall":[117],"rate.":[118],"Interestingly,":[119],"a":[120],"few":[121],"scRNA-seq":[122],"obtained":[124],"results":[125],"comparable":[126],"best-performing":[129],"tools.":[132],"Almost":[133],"all":[134],"DEMs'":[135],"improved":[137],"when":[138],"increasing":[139],"number":[141],"replicates.":[143],"studies":[146],"require":[147],"careful":[148],"design,":[149],"choice":[150],"configuration.":[155],"This":[156],"analysis":[157],"can":[158],"guide":[159],"scientists":[160],"selecting":[162],"appropriate":[164],"tools":[165],"investigate":[167],"experiments.":[173]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1}],"updated_date":"2026-06-21T07:57:09.225873","created_date":"2025-10-10T00:00:00"}
