{"id":"https://openalex.org/W4415080401","doi":"https://doi.org/10.1093/bioinformatics/btaf570","title":"LimROTS: a hybrid method integrating empirical Bayes and reproducibility-optimized statistics for robust differential expression analysis","display_name":"LimROTS: a hybrid method integrating empirical Bayes and reproducibility-optimized statistics for robust differential expression analysis","publication_year":2025,"publication_date":"2025-10-10","ids":{"openalex":"https://openalex.org/W4415080401","doi":"https://doi.org/10.1093/bioinformatics/btaf570","pmid":"https://pubmed.ncbi.nlm.nih.gov/41075160"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf570","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf570","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btaf570","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5119956766","display_name":"Ali Mostafa Anwara","orcid":null},"institutions":[{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]},{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]},{"id":"https://openalex.org/I4210140120","display_name":"Turku Centre for Biotechnology","ror":"https://ror.org/0421ba211","country_code":"FI","type":"facility","lineage":["https://openalex.org/I4210140120"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Ali Mostafa Anwar","raw_affiliation_strings":["Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University , Turku 20520,","University of Turku and \u00c5bo Akademi University Turku Bioscience Centre, , 20520 Turku, Finland"],"affiliations":[{"raw_affiliation_string":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University , Turku 20520,","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I130217899","https://openalex.org/I4210140120"]},{"raw_affiliation_string":"University of Turku and \u00c5bo Akademi University Turku Bioscience Centre, , 20520 Turku, Finland","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I130217899","https://openalex.org/I4210140120"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115019279","display_name":"Akewak Jeba","orcid":"https://orcid.org/0009-0007-1347-7552"},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I16231767","display_name":"Turku University of Applied Sciences","ror":"https://ror.org/04s0yt949","country_code":"FI","type":"education","lineage":["https://openalex.org/I16231767"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Akewak Jeba","raw_affiliation_strings":["Department of Computing, Faculty of Technology, University of Turku , Turku 20014,","University of Turku Department of Computing, , Turku, Finland"],"affiliations":[{"raw_affiliation_string":"Department of Computing, Faculty of Technology, University of Turku , Turku 20014,","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":"University of Turku Department of Computing, , Turku, Finland","institution_ids":["https://openalex.org/I155660961","https://openalex.org/I16231767"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082648063","display_name":"Leo Lahti","orcid":"https://orcid.org/0000-0001-5537-637X"},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I16231767","display_name":"Turku University of Applied Sciences","ror":"https://ror.org/04s0yt949","country_code":"FI","type":"education","lineage":["https://openalex.org/I16231767"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Leo Lahti","raw_affiliation_strings":["Department of Computing, Faculty of Technology, University of Turku , Turku 20014,","University of Turku Department of Computing, , Turku, Finland"],"affiliations":[{"raw_affiliation_string":"Department of Computing, Faculty of Technology, University of Turku , Turku 20014,","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":"University of Turku Department of Computing, , Turku, Finland","institution_ids":["https://openalex.org/I155660961","https://openalex.org/I16231767"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063451537","display_name":"Eleanor T. Coffey","orcid":"https://orcid.org/0000-0002-9717-5610"},"institutions":[{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]},{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]},{"id":"https://openalex.org/I4210140120","display_name":"Turku Centre for Biotechnology","ror":"https://ror.org/0421ba211","country_code":"FI","type":"facility","lineage":["https://openalex.org/I4210140120"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Eleanor Coffey","raw_affiliation_strings":["Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University , Turku 20520,","University of Turku and \u00c5bo Akademi University Turku Bioscience Centre, , 20520 Turku, Finland"],"affiliations":[{"raw_affiliation_string":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University , Turku 20520,","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I130217899","https://openalex.org/I4210140120"]},{"raw_affiliation_string":"University of Turku and \u00c5bo Akademi University Turku Bioscience Centre, , 20520 Turku, Finland","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I130217899","https://openalex.org/I4210140120"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5119956766"],"corresponding_institution_ids":["https://openalex.org/I130217899","https://openalex.org/I183173800","https://openalex.org/I4210140120"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.26400952,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"12","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9940999746322632,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9940999746322632,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9847000241279602,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9779999852180481,"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/bayes-theorem","display_name":"Bayes' theorem","score":0.6029999852180481},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5716000199317932},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.5285000205039978},{"id":"https://openalex.org/keywords/differential","display_name":"Differential (mechanical device)","score":0.4657000005245209},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.37770000100135803},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.37599998712539673}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7304999828338623},{"id":"https://openalex.org/C207201462","wikidata":"https://www.wikidata.org/wiki/Q182505","display_name":"Bayes' theorem","level":3,"score":0.6029999852180481},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5716000199317932},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.536899983882904},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.5285000205039978},{"id":"https://openalex.org/C93226319","wikidata":"https://www.wikidata.org/wiki/Q193137","display_name":"Differential (mechanical device)","level":2,"score":0.4657000005245209},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.37770000100135803},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.37599998712539673},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3531999886035919},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.32359999418258667},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3149999976158142},{"id":"https://openalex.org/C2986587452","wikidata":"https://www.wikidata.org/wiki/Q938438","display_name":"Statistical analysis","level":2,"score":0.3046000003814697},{"id":"https://openalex.org/C67226441","wikidata":"https://www.wikidata.org/wiki/Q1665389","display_name":"Robust statistics","level":3,"score":0.2971000075340271},{"id":"https://openalex.org/C120936955","wikidata":"https://www.wikidata.org/wiki/Q2155640","display_name":"Empirical research","level":2,"score":0.2930000126361847},{"id":"https://openalex.org/C3020402766","wikidata":"https://www.wikidata.org/wiki/Q104376712","display_name":"Prior information","level":2,"score":0.26420000195503235},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.26409998536109924},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.26330000162124634}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","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":"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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaf570","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf570","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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:41075160","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41075160","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:pure.atira.dk:publications/ea63bd8b-dd53-4370-a80e-824f3e991bf3","is_oa":true,"landing_page_url":"https://research.abo.fi/en/publications/ea63bd8b-dd53-4370-a80e-824f3e991bf3","pdf_url":null,"source":{"id":"https://openalex.org/S4406923060","display_name":"\u00c5bo Akademi University Research Portal","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Youssef, A, Jeba, A, Lahti, L & Coffey, E 2025, 'LimROTS: a hybrid method integrating empirical Bayes and reproducibility-optimized statistics for robust differential expression analysis', Bioinformatics, vol. 41, no. 12, btaf570. https://doi.org/10.1093/bioinformatics/btaf570","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:www.utupub.fi:10024/196052","is_oa":false,"landing_page_url":"https://www.utupub.fi/handle/10024/196052","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf570","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf570","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":[],"awards":[{"id":"https://openalex.org/G4855324266","display_name":"Unified computational solutions to disentangle biological interactions in multi-omics data","funder_award_id":"952914","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8318064016","display_name":null,"funder_award_id":"Horizon","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320306136","display_name":"Michael J. Fox Foundation for Parkinson's Research","ror":"https://ror.org/03arq3225"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":53,"referenced_works":["https://openalex.org/W1257453011","https://openalex.org/W1758524554","https://openalex.org/W1973094248","https://openalex.org/W2008344560","https://openalex.org/W2017418037","https://openalex.org/W2079752406","https://openalex.org/W2081098333","https://openalex.org/W2093017030","https://openalex.org/W2105381419","https://openalex.org/W2114165700","https://openalex.org/W2146512944","https://openalex.org/W2147700150","https://openalex.org/W2161980312","https://openalex.org/W2169353806","https://openalex.org/W2170776626","https://openalex.org/W2170962119","https://openalex.org/W2221358813","https://openalex.org/W2278988761","https://openalex.org/W2563754444","https://openalex.org/W2603189578","https://openalex.org/W2607310450","https://openalex.org/W2617446144","https://openalex.org/W2766172487","https://openalex.org/W2787897791","https://openalex.org/W2798133595","https://openalex.org/W2991106430","https://openalex.org/W3010753112","https://openalex.org/W3012843216","https://openalex.org/W3015916968","https://openalex.org/W3034554053","https://openalex.org/W3081814543","https://openalex.org/W3120998555","https://openalex.org/W3123680469","https://openalex.org/W3145969289","https://openalex.org/W3183806972","https://openalex.org/W3192804007","https://openalex.org/W3196705307","https://openalex.org/W4210499727","https://openalex.org/W4220990424","https://openalex.org/W4225545880","https://openalex.org/W4281877108","https://openalex.org/W4290861579","https://openalex.org/W4291885337","https://openalex.org/W4294107304","https://openalex.org/W4312065586","https://openalex.org/W4313577308","https://openalex.org/W4377294656","https://openalex.org/W4393926514","https://openalex.org/W4396781347","https://openalex.org/W4403378209","https://openalex.org/W4403405900","https://openalex.org/W4404628441","https://openalex.org/W6921475931"],"related_works":[],"abstract_inverted_index":{"LimROTS":[0],"has":[1],"been":[2],"implemented":[3],"as":[4],"an":[5],"R/Bioconductor":[6],"package,":[7],"available":[8,19],"at":[9],"https://doi.org/doi:10.18129/B9.bioc.LimROTS.":[10],"Additionally,":[11],"the":[12],"code":[13],"used":[14],"in":[15,20],"this":[16],"study":[17],"is":[18],"GitHub":[21],"repository":[22],"https://github.com/AliYoussef96/LimROTSmanuscript.":[23]},"counts_by_year":[],"updated_date":"2026-04-03T22:45:19.894376","created_date":"2025-10-12T00:00:00"}
