{"id":"https://openalex.org/W7161235564","doi":"https://doi.org/10.1093/bib/bbag223","title":"scMarkerGene: an interpretable neural network framework for cell-type-specific marker gene discovery","display_name":"scMarkerGene: an interpretable neural network framework for cell-type-specific marker gene discovery","publication_year":2026,"publication_date":"2026-04-21","ids":{"openalex":"https://openalex.org/W7161235564","doi":"https://doi.org/10.1093/bib/bbag223","pmid":"https://pubmed.ncbi.nlm.nih.gov/42139163"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbag223","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag223","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"gold","oa_url":"https://doi.org/10.1093/bib/bbag223","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100377745","display_name":"Junhua Zhang","orcid":"https://orcid.org/0000-0002-8936-3822"},"institutions":[{"id":"https://openalex.org/I2802148028","display_name":"Guangzhou Institutes of Biomedicine and Health","ror":"https://ror.org/02c31t502","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2802148028"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jingkai Zhang","raw_affiliation_strings":["Center for Biomedical Digital Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomedical Digital Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","institution_ids":["https://openalex.org/I2802148028"]},{"raw_affiliation_string":"Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","institution_ids":["https://openalex.org/I2802148028"]},{"raw_affiliation_string":"Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","institution_ids":["https://openalex.org/I2802148028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049400509","display_name":"Si Hoi Kou","orcid":"https://orcid.org/0000-0002-0109-1835"},"institutions":[{"id":"https://openalex.org/I2802148028","display_name":"Guangzhou Institutes of Biomedicine and Health","ror":"https://ror.org/02c31t502","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2802148028"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Si Hoi Kou","raw_affiliation_strings":["Center for Biomedical Digital Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomedical Digital Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","institution_ids":["https://openalex.org/I2802148028"]},{"raw_affiliation_string":"Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","institution_ids":["https://openalex.org/I2802148028"]},{"raw_affiliation_string":"Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","institution_ids":["https://openalex.org/I2802148028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102641152","display_name":"Jiulu Zhao","orcid":null},"institutions":[{"id":"https://openalex.org/I2802148028","display_name":"Guangzhou Institutes of Biomedicine and Health","ror":"https://ror.org/02c31t502","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2802148028"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiulu Zhao","raw_affiliation_strings":["Center for Biomedical Digital Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","University of Chinese Academy of Sciences , No. 1, Yanqi Lake East Road, Huairou District, Beijing 100049 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomedical Digital Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","institution_ids":["https://openalex.org/I2802148028"]},{"raw_affiliation_string":"Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","institution_ids":["https://openalex.org/I2802148028"]},{"raw_affiliation_string":"Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","institution_ids":["https://openalex.org/I2802148028"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences , No. 1, Yanqi Lake East Road, Huairou District, Beijing 100049 ,","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041607266","display_name":"Li X","orcid":"https://orcid.org/0000-0002-5981-2762"},"institutions":[{"id":"https://openalex.org/I2802148028","display_name":"Guangzhou Institutes of Biomedicine and Health","ror":"https://ror.org/02c31t502","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2802148028"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaomin Li","raw_affiliation_strings":["Center for Biomedical Digital Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","University of Chinese Academy of Sciences , No. 1, Yanqi Lake East Road, Huairou District, Beijing 100049 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomedical Digital Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","institution_ids":["https://openalex.org/I2802148028"]},{"raw_affiliation_string":"Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","institution_ids":["https://openalex.org/I2802148028"]},{"raw_affiliation_string":"Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","institution_ids":["https://openalex.org/I2802148028"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences , No. 1, Yanqi Lake East Road, Huairou District, Beijing 100049 ,","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031386345","display_name":"Y ZHAO","orcid":null},"institutions":[{"id":"https://openalex.org/I2802148028","display_name":"Guangzhou Institutes of Biomedicine and Health","ror":"https://ror.org/02c31t502","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2802148028"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yongbing Zhao","raw_affiliation_strings":["Center for Biomedical Digital Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","University of Chinese Academy of Sciences , No. 1, Yanqi Lake East Road, Huairou District, Beijing 100049 ,"],"raw_orcid":"https://orcid.org/0000-0002-9917-7425","affiliations":[{"raw_affiliation_string":"Center for Biomedical Digital Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","institution_ids":["https://openalex.org/I2802148028"]},{"raw_affiliation_string":"Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","institution_ids":["https://openalex.org/I2802148028"]},{"raw_affiliation_string":"Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou 510530 ,","institution_ids":["https://openalex.org/I2802148028"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences , No. 1, Yanqi Lake East Road, Huairou District, Beijing 100049 ,","institution_ids":["https://openalex.org/I4210165038"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5031386345"],"corresponding_institution_ids":["https://openalex.org/I2802148028","https://openalex.org/I4210165038"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.53318207,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"3","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":0.9983999729156494,"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":0.9983999729156494,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.000699999975040555,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":9.999999747378752e-05,"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/annotation","display_name":"Annotation","score":0.6229000091552734},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.5412999987602234},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.49950000643730164},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4738999903202057},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.45890000462532043},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.429500013589859},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.4203000068664551},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.41620001196861267}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6488999724388123},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6229000091552734},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5953999757766724},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.5412999987602234},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.49950000643730164},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4738999903202057},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.45890000462532043},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.429500013589859},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.4203000068664551},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.41620001196861267},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40639999508857727},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.40560001134872437},{"id":"https://openalex.org/C2984842247","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep neural networks","level":3,"score":0.4050999879837036},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.39430001378059387},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.3709999918937683},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.32739999890327454},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.3050999939441681},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.2872999906539917},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.28459998965263367},{"id":"https://openalex.org/C2776145597","wikidata":"https://www.wikidata.org/wiki/Q25339462","display_name":"Dropout (neural networks)","level":2,"score":0.2761000096797943},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.27300000190734863},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.2687000036239624},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.26739999651908875}],"mesh":[{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","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":"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":"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":"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","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":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","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},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbag223","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag223","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:42139163","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42139163","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":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13178462","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13178462/","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,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbag223","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag223","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6114141345024109,"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities"}],"awards":[{"id":"https://openalex.org/G1604232312","display_name":null,"funder_award_id":"2023B1212060050","funder_id":"https://openalex.org/F4320335795","funder_display_name":"Science and Technology Planning Project of Guangdong Province"},{"id":"https://openalex.org/G1992682476","display_name":null,"funder_award_id":"2024YFA1802300","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G2223093553","display_name":null,"funder_award_id":"2023QN10X323","funder_id":"https://openalex.org/F4320335795","funder_display_name":"Science and Technology Planning Project of Guangdong Province"},{"id":"https://openalex.org/G3817518962","display_name":null,"funder_award_id":"2023B1212120009","funder_id":"https://openalex.org/F4320335795","funder_display_name":"Science and Technology Planning Project of Guangdong Province"},{"id":"https://openalex.org/G7742062529","display_name":null,"funder_award_id":"2023ZT10Y154","funder_id":"https://openalex.org/F4320335795","funder_display_name":"Science and Technology Planning Project of Guangdong Province"}],"funders":[{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320335795","display_name":"Science and Technology Planning Project of Guangdong Province","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W1979283544","https://openalex.org/W1984883254","https://openalex.org/W2177432730","https://openalex.org/W2747545374","https://openalex.org/W2771542157","https://openalex.org/W2800392236","https://openalex.org/W2938221109","https://openalex.org/W2949177718","https://openalex.org/W2949676527","https://openalex.org/W2997831639","https://openalex.org/W3009370296","https://openalex.org/W3109243443","https://openalex.org/W3121168830","https://openalex.org/W3131383906","https://openalex.org/W3159762970","https://openalex.org/W3205489570","https://openalex.org/W4200613928","https://openalex.org/W4210587306","https://openalex.org/W4239026366","https://openalex.org/W4283704002","https://openalex.org/W4289527383","https://openalex.org/W4290648831","https://openalex.org/W4319773543","https://openalex.org/W4384523448","https://openalex.org/W4386208756","https://openalex.org/W4387495568","https://openalex.org/W4387806108","https://openalex.org/W4391819608","https://openalex.org/W4391931733","https://openalex.org/W4401455176","https://openalex.org/W4403729668","https://openalex.org/W4404014264","https://openalex.org/W4411272877"],"related_works":[],"abstract_inverted_index":{"In":[0],"single-cell":[1,151],"transcriptomics,":[2],"the":[3],"accurate":[4],"identification":[5],"of":[6],"cell-type-specific":[7],"marker":[8,55,139],"genes":[9],"is":[10,168],"fundamental":[11],"for":[12,54,150,157],"understanding":[13],"cellular":[14],"heterogeneity.":[15],"However,":[16],"existing":[17],"approaches":[18],"often":[19],"rely":[20],"on":[21,71,124],"arbitrary":[22],"thresholds":[23],"and":[24,34,93,107,127,136,147,163],"clustering":[25],"heuristics,":[26],"making":[27],"them":[28],"sensitive":[29],"to":[30,36,97,159],"noise,":[31,99],"annotation":[32,105],"bias,":[33],"prone":[35],"capturing":[37],"highly":[38],"expressed":[39],"rather":[40],"than":[41],"truly":[42],"specific":[43],"genes.":[44,140],"Here,":[45],"we":[46],"present":[47],"scMarkerGene,":[48],"an":[49,144],"interpretable":[50,148],"neural":[51,75],"network":[52,76],"framework":[53,149],"gene":[56],"discovery.":[57],"scMarkerGene":[58,88,114,142],"constructs":[59],"a":[60,83],"Contribution":[61],"Score":[62],"(CS)":[63],"matrix":[64],"that":[65],"quantitatively":[66],"measures":[67],"each":[68],"gene's":[69],"influence":[70],"cell-type":[72],"discrimination,":[73],"transforming":[74],"predictions":[77],"into":[78],"gene-level":[79],"importance":[80],"signals.":[81],"Through":[82],"downstream":[84],"specificity":[85],"filtering":[86],"process,":[87],"robustly":[89],"captures":[90],"cell-type-distinguishing":[91],"features":[92],"demonstrates":[94],"strong":[95],"robustness":[96],"dropout":[98],"diverse":[100],"cell":[101],"population":[102],"sizes,":[103],"varying":[104],"resolutions,":[106],"heterogeneous":[108],"sequencing":[109],"technologies.":[110],"We":[111],"comprehensively":[112],"validated":[113],"across":[115],"scRNA-seq":[116],"datasets":[117],"from":[118],"multiple":[119],"species,":[120],"as":[121,123],"well":[122],"spatial":[125],"transcriptomics":[126],"discretized":[128],"pseudotime":[129],"data,":[130],"where":[131],"it":[132],"effectively":[133],"identified":[134],"dynamic":[135],"spatially":[137],"resolved":[138],"Collectively,":[141],"provides":[143],"efficient,":[145],"accurate,":[146],"transcriptomic":[152],"analysis,":[153],"with":[154],"broad":[155],"potential":[156],"extension":[158],"multi-omics":[160],"data":[161],"integration":[162],"interpretation.":[164],"The":[165],"source":[166],"code":[167],"available":[169],"at":[170],"https://scmarkergene.zhaopage.com/.":[171]},"counts_by_year":[],"updated_date":"2026-07-18T07:39:51.176621","created_date":"2026-05-16T00:00:00"}