{"id":"https://openalex.org/W7163696587","doi":"https://doi.org/10.1093/bib/bbag286","title":"scHILL: deciphering individual-level immune cell heterogeneity with single-cell RNA sequencing data","display_name":"scHILL: deciphering individual-level immune cell heterogeneity with single-cell RNA sequencing data","publication_year":2026,"publication_date":"2026-05-01","ids":{"openalex":"https://openalex.org/W7163696587","doi":"https://doi.org/10.1093/bib/bbag286","pmid":"https://pubmed.ncbi.nlm.nih.gov/42248580"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbag286","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag286","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/bbag286","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5138012718","display_name":"Yi Wang","orcid":"https://orcid.org/0009-0002-9397-0673"},"institutions":[{"id":"https://openalex.org/I2801577699","display_name":"Beijing Institute of Genomics","ror":"https://ror.org/049gn7z52","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]},{"id":"https://openalex.org/I4210118410","display_name":"Institut th\u00e9matique G\u00e9n\u00e9tique, g\u00e9nomique et bioinformatique","ror":"https://ror.org/01rfstj90","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488","https://openalex.org/I4210118410"]},{"id":"https://openalex.org/I4210164898","display_name":"Beijing Chaoyang Emergency Medical Center","ror":"https://ror.org/05anb7a53","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210164898"]},{"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","FR"],"is_corresponding":false,"raw_author_name":"Yi Wang","raw_affiliation_strings":["Beijing Institute of Genomics, Chinese Academy of Sciences , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","Beijing Key Laboratory of Intelligent Governance and Application of Biological Big Data, China National Center for Bioinformation , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","National Genomics Data Center, China National Center for Bioinformation , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","University of Chinese Academy of Sciences , No. 1 Yanqihu East Road, Huairou District, Beijing 101408 ,"],"raw_orcid":"https://orcid.org/0009-0002-9397-0673","affiliations":[{"raw_affiliation_string":"Beijing Institute of Genomics, Chinese Academy of Sciences , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","institution_ids":["https://openalex.org/I2801577699"]},{"raw_affiliation_string":"Beijing Key Laboratory of Intelligent Governance and Application of Biological Big Data, China National Center for Bioinformation , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","institution_ids":["https://openalex.org/I4210164898"]},{"raw_affiliation_string":"National Genomics Data Center, China National Center for Bioinformation , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","institution_ids":["https://openalex.org/I4210118410"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences , No. 1 Yanqihu East Road, Huairou District, Beijing 101408 ,","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065859286","display_name":"Hui Li","orcid":"https://orcid.org/0000-0001-9198-3951"},"institutions":[{"id":"https://openalex.org/I4210094879","display_name":"Shandong Institute of Automation","ror":"https://ror.org/00qdtba35","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210094879","https://openalex.org/I4210142748"]},{"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":"Hongyu Li","raw_affiliation_strings":["Institute of Automation, Chinese Academy of Sciences , 95 Zhongguancun East Road, Haidian District, Beijing 100190 ,","School of Advanced Interdisciplinary Sciences, University of Chinese Academy of Sciences , No. 1 Yanqihu East Road, Huairou District, Beijing 101408 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Automation, Chinese Academy of Sciences , 95 Zhongguancun East Road, Haidian District, Beijing 100190 ,","institution_ids":["https://openalex.org/I4210094879"]},{"raw_affiliation_string":"School of Advanced Interdisciplinary Sciences, University of Chinese Academy of Sciences , No. 1 Yanqihu East Road, Huairou District, Beijing 101408 ,","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100371846","display_name":"Lun Li","orcid":"https://orcid.org/0000-0003-3242-031X"},"institutions":[{"id":"https://openalex.org/I2801577699","display_name":"Beijing Institute of Genomics","ror":"https://ror.org/049gn7z52","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]},{"id":"https://openalex.org/I4210118410","display_name":"Institut th\u00e9matique G\u00e9n\u00e9tique, g\u00e9nomique et bioinformatique","ror":"https://ror.org/01rfstj90","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488","https://openalex.org/I4210118410"]},{"id":"https://openalex.org/I4210164898","display_name":"Beijing Chaoyang Emergency Medical Center","ror":"https://ror.org/05anb7a53","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210164898"]}],"countries":["CN","FR"],"is_corresponding":false,"raw_author_name":"Lun Li","raw_affiliation_strings":["Beijing Institute of Genomics, Chinese Academy of Sciences , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","Beijing Key Laboratory of Intelligent Governance and Application of Biological Big Data, China National Center for Bioinformation , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","National Genomics Data Center, China National Center for Bioinformation , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,"],"raw_orcid":"https://orcid.org/0000-0003-3242-031X","affiliations":[{"raw_affiliation_string":"Beijing Institute of Genomics, Chinese Academy of Sciences , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","institution_ids":["https://openalex.org/I2801577699"]},{"raw_affiliation_string":"Beijing Key Laboratory of Intelligent Governance and Application of Biological Big Data, China National Center for Bioinformation , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","institution_ids":["https://openalex.org/I4210164898"]},{"raw_affiliation_string":"National Genomics Data Center, China National Center for Bioinformation , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","institution_ids":["https://openalex.org/I4210118410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039280701","display_name":"Yongrong Cao","orcid":"https://orcid.org/0000-0001-8533-3864"},"institutions":[{"id":"https://openalex.org/I2801577699","display_name":"Beijing Institute of Genomics","ror":"https://ror.org/049gn7z52","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]},{"id":"https://openalex.org/I4210118410","display_name":"Institut th\u00e9matique G\u00e9n\u00e9tique, g\u00e9nomique et bioinformatique","ror":"https://ror.org/01rfstj90","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488","https://openalex.org/I4210118410"]},{"id":"https://openalex.org/I4210164898","display_name":"Beijing Chaoyang Emergency Medical Center","ror":"https://ror.org/05anb7a53","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210164898"]},{"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","FR"],"is_corresponding":false,"raw_author_name":"Yongrong Cao","raw_affiliation_strings":["Beijing Institute of Genomics, Chinese Academy of Sciences , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","Beijing Key Laboratory of Intelligent Governance and Application of Biological Big Data, China National Center for Bioinformation , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","National Genomics Data Center, China National Center for Bioinformation , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","University of Chinese Academy of Sciences , No. 1 Yanqihu East Road, Huairou District, Beijing 101408 ,"],"raw_orcid":"https://orcid.org/0000-0001-8533-3864","affiliations":[{"raw_affiliation_string":"Beijing Institute of Genomics, Chinese Academy of Sciences , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","institution_ids":["https://openalex.org/I2801577699"]},{"raw_affiliation_string":"Beijing Key Laboratory of Intelligent Governance and Application of Biological Big Data, China National Center for Bioinformation , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","institution_ids":["https://openalex.org/I4210164898"]},{"raw_affiliation_string":"National Genomics Data Center, China National Center for Bioinformation , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","institution_ids":["https://openalex.org/I4210118410"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences , No. 1 Yanqihu East Road, Huairou District, Beijing 101408 ,","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063455525","display_name":"Zhijian Duan","orcid":null},"institutions":[{"id":"https://openalex.org/I2801577699","display_name":"Beijing Institute of Genomics","ror":"https://ror.org/049gn7z52","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]},{"id":"https://openalex.org/I4210118410","display_name":"Institut th\u00e9matique G\u00e9n\u00e9tique, g\u00e9nomique et bioinformatique","ror":"https://ror.org/01rfstj90","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488","https://openalex.org/I4210118410"]},{"id":"https://openalex.org/I4210164898","display_name":"Beijing Chaoyang Emergency Medical Center","ror":"https://ror.org/05anb7a53","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210164898"]},{"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","FR"],"is_corresponding":false,"raw_author_name":"Zhijian Duan","raw_affiliation_strings":["Beijing Institute of Genomics, Chinese Academy of Sciences , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","Beijing Key Laboratory of Intelligent Governance and Application of Biological Big Data, China National Center for Bioinformation , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","National Genomics Data Center, China National Center for Bioinformation , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","University of Chinese Academy of Sciences , No. 1 Yanqihu East Road, Huairou District, Beijing 101408 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Institute of Genomics, Chinese Academy of Sciences , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","institution_ids":["https://openalex.org/I2801577699"]},{"raw_affiliation_string":"Beijing Key Laboratory of Intelligent Governance and Application of Biological Big Data, China National Center for Bioinformation , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","institution_ids":["https://openalex.org/I4210164898"]},{"raw_affiliation_string":"National Genomics Data Center, China National Center for Bioinformation , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","institution_ids":["https://openalex.org/I4210118410"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences , No. 1 Yanqihu East Road, Huairou District, Beijing 101408 ,","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5109518703","display_name":"S Song","orcid":null},"institutions":[{"id":"https://openalex.org/I2801577699","display_name":"Beijing Institute of Genomics","ror":"https://ror.org/049gn7z52","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]},{"id":"https://openalex.org/I4210118410","display_name":"Institut th\u00e9matique G\u00e9n\u00e9tique, g\u00e9nomique et bioinformatique","ror":"https://ror.org/01rfstj90","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488","https://openalex.org/I4210118410"]},{"id":"https://openalex.org/I4210164898","display_name":"Beijing Chaoyang Emergency Medical Center","ror":"https://ror.org/05anb7a53","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210164898"]},{"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","FR"],"is_corresponding":true,"raw_author_name":"Shuhui Song","raw_affiliation_strings":["Beijing Institute of Genomics, Chinese Academy of Sciences , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","Beijing Key Laboratory of Intelligent Governance and Application of Biological Big Data, China National Center for Bioinformation , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","National Genomics Data Center, China National Center for Bioinformation , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","University of Chinese Academy of Sciences , No. 1 Yanqihu East Road, Huairou District, Beijing 101408 ,"],"raw_orcid":"https://orcid.org/0000-0003-2409-8770","affiliations":[{"raw_affiliation_string":"Beijing Institute of Genomics, Chinese Academy of Sciences , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","institution_ids":["https://openalex.org/I2801577699"]},{"raw_affiliation_string":"Beijing Key Laboratory of Intelligent Governance and Application of Biological Big Data, China National Center for Bioinformation , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","institution_ids":["https://openalex.org/I4210164898"]},{"raw_affiliation_string":"National Genomics Data Center, China National Center for Bioinformation , No. 1 Beichen West Road, Chaoyang District, Beijing 100101 ,","institution_ids":["https://openalex.org/I4210118410"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences , No. 1 Yanqihu East Road, Huairou District, Beijing 101408 ,","institution_ids":["https://openalex.org/I4210165038"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5109518703"],"corresponding_institution_ids":["https://openalex.org/I2801577699","https://openalex.org/I4210118410","https://openalex.org/I4210164898","https://openalex.org/I4210165038"],"apc_list":{"value":3885,"currency":"USD","value_usd":3885},"apc_paid":{"value":3885,"currency":"USD","value_usd":3885},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.50915262,"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":0.998199999332428,"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":0.998199999332428,"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":0.00019999999494757503,"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/T13410","display_name":"Immune responses and vaccinations","score":0.00019999999494757503,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/decipher","display_name":"DECIPHER","score":0.7387999892234802},{"id":"https://openalex.org/keywords/autoencoder","display_name":"Autoencoder","score":0.5156000256538391},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.4099000096321106},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.4050999879837036},{"id":"https://openalex.org/keywords/genetic-heterogeneity","display_name":"Genetic heterogeneity","score":0.3977999985218048},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.3749000132083893},{"id":"https://openalex.org/keywords/single-cell-sequencing","display_name":"Single cell sequencing","score":0.3668000102043152}],"concepts":[{"id":"https://openalex.org/C164614171","wikidata":"https://www.wikidata.org/wiki/Q5204775","display_name":"DECIPHER","level":2,"score":0.7387999892234802},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5541999936103821},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.5156000256538391},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46050000190734863},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.451200008392334},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.4099000096321106},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.4050999879837036},{"id":"https://openalex.org/C64618202","wikidata":"https://www.wikidata.org/wiki/Q3733697","display_name":"Genetic heterogeneity","level":4,"score":0.3977999985218048},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.3749000132083893},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37130001187324524},{"id":"https://openalex.org/C174749747","wikidata":"https://www.wikidata.org/wiki/Q15917269","display_name":"Single cell sequencing","level":5,"score":0.3668000102043152},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.35519999265670776},{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.3190999925136566},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.3027999997138977},{"id":"https://openalex.org/C3018252375","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune recognition","level":3,"score":0.2919999957084656},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.28700000047683716},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2840000092983246},{"id":"https://openalex.org/C163763905","wikidata":"https://www.wikidata.org/wiki/Q17075943","display_name":"Precision medicine","level":2,"score":0.2761000096797943},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.27160000801086426}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D000098421","descriptor_name":"Multilayer Perceptrons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098421","descriptor_name":"Multilayer Perceptrons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098421","descriptor_name":"Multilayer Perceptrons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098421","descriptor_name":"Multilayer Perceptrons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098446","descriptor_name":"Autoencoder","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098446","descriptor_name":"Autoencoder","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098446","descriptor_name":"Autoencoder","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098446","descriptor_name":"Autoencoder","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001327","descriptor_name":"Autoimmune Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001327","descriptor_name":"Autoimmune Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001327","descriptor_name":"Autoimmune Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001327","descriptor_name":"Autoimmune Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001327","descriptor_name":"Autoimmune Diseases","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D001327","descriptor_name":"Autoimmune Diseases","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D001327","descriptor_name":"Autoimmune Diseases","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D001327","descriptor_name":"Autoimmune Diseases","qualifier_ui":"Q000276","qualifier_name":"immunology","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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","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":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbag286","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag286","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:42248580","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42248580","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:13273425","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13273425/","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/bbag286","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag286","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":[],"awards":[{"id":"https://openalex.org/G2079071458","display_name":null,"funder_award_id":"92374201","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":62,"referenced_works":["https://openalex.org/W1972029787","https://openalex.org/W1980313076","https://openalex.org/W1993396994","https://openalex.org/W1999435920","https://openalex.org/W1999587975","https://openalex.org/W2007268662","https://openalex.org/W2064304125","https://openalex.org/W2064999867","https://openalex.org/W2073688197","https://openalex.org/W2098919737","https://openalex.org/W2115783720","https://openalex.org/W2279588067","https://openalex.org/W2321809676","https://openalex.org/W2560758606","https://openalex.org/W2612519453","https://openalex.org/W2766676715","https://openalex.org/W2796450030","https://openalex.org/W2797120312","https://openalex.org/W2901481287","https://openalex.org/W2909242481","https://openalex.org/W2986810323","https://openalex.org/W3024643080","https://openalex.org/W3048884493","https://openalex.org/W3080503847","https://openalex.org/W3094502228","https://openalex.org/W3128961456","https://openalex.org/W3134078202","https://openalex.org/W3153732845","https://openalex.org/W3153912282","https://openalex.org/W3186314395","https://openalex.org/W3195806951","https://openalex.org/W3196665061","https://openalex.org/W3216893266","https://openalex.org/W4200289086","https://openalex.org/W4210826564","https://openalex.org/W4213441758","https://openalex.org/W4220939068","https://openalex.org/W4280598116","https://openalex.org/W4289335819","https://openalex.org/W4292229998","https://openalex.org/W4313156423","https://openalex.org/W4322718191","https://openalex.org/W4378838672","https://openalex.org/W4380089902","https://openalex.org/W4387569894","https://openalex.org/W4392168151","https://openalex.org/W4392393054","https://openalex.org/W4396780660","https://openalex.org/W4396888753","https://openalex.org/W4399387478","https://openalex.org/W4400239272","https://openalex.org/W4400916290","https://openalex.org/W4403174218","https://openalex.org/W4404658388","https://openalex.org/W4404793799","https://openalex.org/W4406410640","https://openalex.org/W4411534790","https://openalex.org/W4412397217","https://openalex.org/W4414281281","https://openalex.org/W4414778512","https://openalex.org/W7125280895","https://openalex.org/W7160708377"],"related_works":[],"abstract_inverted_index":{"Deep":[0],"learning":[1,82],"frameworks":[2],"have":[3,14],"been":[4],"developed":[5],"for":[6,100,140],"interpreting":[7,141],"single-cell":[8],"RNA":[9],"sequencing":[10],"(scRNA-seq)":[11],"data":[12,77],"and":[13,85,110,122,133],"demonstrated":[15],"excellent":[16],"performance":[17],"across":[18],"a":[19,45,49,54,98,137],"range":[20],"of":[21,90,108,150],"tasks.":[22],"However,":[23],"existing":[24,117],"methods":[25,118],"remain":[26],"limited":[27,91],"in":[28,119,128],"their":[29],"ability":[30],"to":[31,58,103],"characterize":[32],"heterogeneity":[33,61,66,127],"at":[34],"the":[35,88,105,147],"individual":[36,102],"level.":[37],"To":[38],"address":[39],"this":[40],"gap,":[41],"we":[42],"present":[43],"scHILL,":[44],"framework":[46,139],"that":[47],"integrates":[48],"masked":[50],"autoencoder":[51],"(MAE)":[52],"with":[53,76],"multilayer":[55],"perceptron":[56],"(MLP)":[57],"decipher":[59],"phenotypic":[60],"arises":[62],"from":[63],"immune":[64,125],"cell":[65,126],"among":[67],"individuals":[68],"under":[69],"specific":[70],"disease":[71],"conditions.":[72],"The":[73,94],"MAE,":[74],"pretrained":[75],"augmentation,":[78],"enables":[79],"self-supervised":[80],"feature":[81],"without":[83],"labels":[84],"effectively":[86],"mitigates":[87],"challenge":[89],"sample":[92],"size.":[93],"MLP":[95],"further":[96],"generates":[97],"score":[99],"each":[101],"quantify":[104],"functional":[106],"significance":[107],"cells":[109],"genes.":[111],"Across":[112],"multiple":[113],"datasets,":[114],"scHILL":[115,135],"outperforms":[116],"phenotype":[120],"prediction":[121],"reveals":[123],"individual-level":[124,142],"infectious":[129],"disease,":[130,132],"autoimmune":[131],"cancer.":[134],"provides":[136],"generalizable":[138],"scRNA-seq":[143],"data,":[144],"thereby":[145],"facilitating":[146],"future":[148],"realization":[149],"personalized":[151],"medicine.":[152]},"counts_by_year":[],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2026-06-06T00:00:00"}
