{"id":"https://openalex.org/W7127338439","doi":"https://doi.org/10.1093/bioinformatics/btag051","title":"Inference of marker genes of subtle cell state changes via iLR: iterative logistic regression","display_name":"Inference of marker genes of subtle cell state changes via iLR: iterative logistic regression","publication_year":2026,"publication_date":"2026-01-28","ids":{"openalex":"https://openalex.org/W7127338439","doi":"https://doi.org/10.1093/bioinformatics/btag051","pmid":"https://pubmed.ncbi.nlm.nih.gov/41627891"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag051","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag051","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/btag051","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5124920792","display_name":"Yingtong Liu","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Yingtong Liu","raw_affiliation_strings":["Department of Quantitative and Computational Biology, Dornsife College of Letters, Arts and Sciences, University of Southern California , Los Angeles, CA 90089,"],"affiliations":[{"raw_affiliation_string":"Department of Quantitative and Computational Biology, Dornsife College of Letters, Arts and Sciences, University of Southern California , Los Angeles, CA 90089,","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089169410","display_name":"Aaron G. Baugh","orcid":"https://orcid.org/0000-0001-8763-509X"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I4210117038","display_name":"USC Norris Comprehensive Cancer Center","ror":"https://ror.org/01nmyfr60","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2800154431","https://openalex.org/I4210117038"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aaron G Baugh","raw_affiliation_strings":["Division of Medical Oncology, Department of Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California , Los Angeles, CA 90033,"],"affiliations":[{"raw_affiliation_string":"Division of Medical Oncology, Department of Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California , Los Angeles, CA 90033,","institution_ids":["https://openalex.org/I1174212","https://openalex.org/I4210117038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036018104","display_name":"Evanthia T. Roussos Torres","orcid":"https://orcid.org/0000-0002-0740-5102"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]},{"id":"https://openalex.org/I4210117038","display_name":"USC Norris Comprehensive Cancer Center","ror":"https://ror.org/01nmyfr60","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2800154431","https://openalex.org/I4210117038"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Evanthia T Roussos Torres","raw_affiliation_strings":["Division of Medical Oncology, Department of Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California , Los Angeles, CA 90033,"],"affiliations":[{"raw_affiliation_string":"Division of Medical Oncology, Department of Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California , Los Angeles, CA 90033,","institution_ids":["https://openalex.org/I1174212","https://openalex.org/I4210117038"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5124960197","display_name":"Adam L MacLean","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Adam L MacLean","raw_affiliation_strings":["Department of Quantitative and Computational Biology, Dornsife College of Letters, Arts and Sciences, University of Southern California , Los Angeles, CA 90089,"],"affiliations":[{"raw_affiliation_string":"Department of Quantitative and Computational Biology, Dornsife College of Letters, Arts and Sciences, University of Southern California , Los Angeles, CA 90089,","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5124920792"],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.35421327,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9969000220298767,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9969000220298767,"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/T11297","display_name":"Ferroptosis and cancer prognosis","score":0.00019999999494757503,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12610","display_name":"RNA regulation and disease","score":0.00019999999494757503,"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/inference","display_name":"Inference","score":0.7487999796867371},{"id":"https://openalex.org/keywords/logistic-regression","display_name":"Logistic regression","score":0.6671000123023987},{"id":"https://openalex.org/keywords/regression","display_name":"Regression","score":0.46939998865127563},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4587000012397766},{"id":"https://openalex.org/keywords/state","display_name":"State (computer science)","score":0.4535999894142151},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3562999963760376}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7487999796867371},{"id":"https://openalex.org/C151956035","wikidata":"https://www.wikidata.org/wiki/Q1132755","display_name":"Logistic regression","level":2,"score":0.6671000123023987},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.593999981880188},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4851999878883362},{"id":"https://openalex.org/C83546350","wikidata":"https://www.wikidata.org/wiki/Q1139051","display_name":"Regression","level":2,"score":0.46939998865127563},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4587000012397766},{"id":"https://openalex.org/C48103436","wikidata":"https://www.wikidata.org/wiki/Q599031","display_name":"State (computer science)","level":2,"score":0.4535999894142151},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4140999913215637},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3562999963760376},{"id":"https://openalex.org/C152877465","wikidata":"https://www.wikidata.org/wiki/Q208042","display_name":"Regression analysis","level":2,"score":0.32659998536109924},{"id":"https://openalex.org/C159694833","wikidata":"https://www.wikidata.org/wiki/Q2321565","display_name":"Iterative method","level":2,"score":0.3005000054836273},{"id":"https://openalex.org/C134261354","wikidata":"https://www.wikidata.org/wiki/Q938438","display_name":"Statistical inference","level":2,"score":0.2985000014305115},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.29019999504089355},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2840999960899353},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2752000093460083},{"id":"https://openalex.org/C49781872","wikidata":"https://www.wikidata.org/wiki/Q1045555","display_name":"Maximum likelihood","level":2,"score":0.2703000009059906},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2685999870300293},{"id":"https://openalex.org/C48921125","wikidata":"https://www.wikidata.org/wiki/Q10861030","display_name":"Linear regression","level":2,"score":0.25540000200271606}],"mesh":[{"descriptor_ui":"D000067877","descriptor_name":"Autism Spectrum Disorder","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000067877","descriptor_name":"Autism Spectrum Disorder","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000067877","descriptor_name":"Autism Spectrum Disorder","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005819","descriptor_name":"Genetic Markers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005819","descriptor_name":"Genetic Markers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005819","descriptor_name":"Genetic Markers","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":"D016015","descriptor_name":"Logistic Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016015","descriptor_name":"Logistic Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016015","descriptor_name":"Logistic Models","qualifier_ui":null,"qualifier_name":null,"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btag051","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag051","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:41627891","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41627891","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:pubmedcentral.nih.gov:12925251","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12925251/","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/btag051","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag051","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":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":66,"referenced_works":["https://openalex.org/W1527265103","https://openalex.org/W1968032893","https://openalex.org/W1993004730","https://openalex.org/W1994663540","https://openalex.org/W2046345187","https://openalex.org/W2081104044","https://openalex.org/W2114104545","https://openalex.org/W2117247812","https://openalex.org/W2152239989","https://openalex.org/W2168950294","https://openalex.org/W2332579289","https://openalex.org/W2585344729","https://openalex.org/W2654158031","https://openalex.org/W2800392236","https://openalex.org/W2897028592","https://openalex.org/W2901677030","https://openalex.org/W2901878811","https://openalex.org/W2903950532","https://openalex.org/W2914286378","https://openalex.org/W2937177974","https://openalex.org/W2946016273","https://openalex.org/W2949067670","https://openalex.org/W2959034083","https://openalex.org/W2964315448","https://openalex.org/W3094585864","https://openalex.org/W3109243443","https://openalex.org/W3120557481","https://openalex.org/W3130705868","https://openalex.org/W3131383906","https://openalex.org/W3132492725","https://openalex.org/W3132661792","https://openalex.org/W3160758604","https://openalex.org/W3166550340","https://openalex.org/W4200369270","https://openalex.org/W4214603532","https://openalex.org/W4214876469","https://openalex.org/W4252684946","https://openalex.org/W4282914396","https://openalex.org/W4290648831","https://openalex.org/W4296804050","https://openalex.org/W4308834893","https://openalex.org/W4309944312","https://openalex.org/W4317811051","https://openalex.org/W4319591822","https://openalex.org/W4322489923","https://openalex.org/W4361301386","https://openalex.org/W4385544378","https://openalex.org/W4387661643","https://openalex.org/W4389229708","https://openalex.org/W4391814503","https://openalex.org/W4392167979","https://openalex.org/W4392376413","https://openalex.org/W4392982836","https://openalex.org/W4396741830","https://openalex.org/W4398250247","https://openalex.org/W4399213494","https://openalex.org/W4402874796","https://openalex.org/W4404051878","https://openalex.org/W4405315138","https://openalex.org/W4405357279","https://openalex.org/W4407956796","https://openalex.org/W4409660862","https://openalex.org/W4410075135","https://openalex.org/W4414959343","https://openalex.org/W4416149780","https://openalex.org/W4416185399"],"related_works":[],"abstract_inverted_index":{"iLR":[0],"is":[1],"freely":[2],"available":[3],"at":[4],"GitHub":[5],"https://github.com/maclean-lab/iLR":[6],"and":[7],"Zenodo":[8],"https://zenodo.org/records/17728797.":[9]},"counts_by_year":[],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2026-02-04T00:00:00"}
