{"id":"https://openalex.org/W4414625608","doi":"https://doi.org/10.1093/bib/bbaf515","title":"IMATAC imputes single-cell ATAC-seq data by deep hierarchical network with denoising autoencoder","display_name":"IMATAC imputes single-cell ATAC-seq data by deep hierarchical network with denoising autoencoder","publication_year":2025,"publication_date":"2025-08-31","ids":{"openalex":"https://openalex.org/W4414625608","doi":"https://doi.org/10.1093/bib/bbaf515","pmid":"https://pubmed.ncbi.nlm.nih.gov/41021262"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf515","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf515","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf515/64427494/bbaf515.pdf","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","license_id":"https://openalex.org/licenses/cc-by","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://academic.oup.com/bib/article-pdf/26/5/bbaf515/64427494/bbaf515.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100695374","display_name":"Li Yao","orcid":"https://orcid.org/0000-0002-6263-5832"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yao Li","raw_affiliation_strings":["Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University , No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049 ,","Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University, No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University , No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University, No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078674561","display_name":"Hongqiang Lv","orcid":"https://orcid.org/0000-0001-5061-4762"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hongqiang Lyu","raw_affiliation_strings":["Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University , No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049 ,","Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University, No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049, China"],"raw_orcid":"https://orcid.org/0000-0001-5061-4762","affiliations":[{"raw_affiliation_string":"Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University , No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University, No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100329677","display_name":"Kexin Li","orcid":"https://orcid.org/0000-0003-3854-1710"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kexin Li","raw_affiliation_strings":["Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University , No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049 ,","Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University, No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University , No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University, No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100390842","display_name":"Yuan Liu","orcid":"https://orcid.org/0000-0002-0682-6167"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuan Liu","raw_affiliation_strings":["Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University , No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049 ,","Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University, No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University , No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University, No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030452688","display_name":"Xinman Zhang","orcid":"https://orcid.org/0000-0001-7436-8113"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xinman Zhang","raw_affiliation_strings":["Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University , No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049 ,","Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University, No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University , No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University, No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100349462","display_name":"Ze Liu","orcid":"https://orcid.org/0000-0002-9044-139X"},"institutions":[{"id":"https://openalex.org/I4210088176","display_name":"North West Agriculture and Forestry University","ror":null,"country_code":"CN","type":null,"lineage":["https://openalex.org/I4210088176"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ze Liu","raw_affiliation_strings":["College of Water Resources and Architectural Engineering, Northwest A&F University , No. 3 Taicheng Road, Yangling District, Xianyang, Shaanxi 712100 ,","College of Water Resources and Architectural Engineering, Northwest A&F University, No. 3 Taicheng Road, Yangling District, Xianyang, Shaanxi 712100, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Water Resources and Architectural Engineering, Northwest A&F University , No. 3 Taicheng Road, Yangling District, Xianyang, Shaanxi 712100 ,","institution_ids":["https://openalex.org/I4210088176"]},{"raw_affiliation_string":"College of Water Resources and Architectural Engineering, Northwest A&F University, No. 3 Taicheng Road, Yangling District, Xianyang, Shaanxi 712100, China","institution_ids":["https://openalex.org/I4210088176"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Pengcheng Jing","orcid":null},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Pengcheng Jing","raw_affiliation_strings":["Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University , No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049 ,","Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University, No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University , No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University, No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066175556","display_name":"Peng Han","orcid":"https://orcid.org/0000-0003-0996-6103"},"institutions":[{"id":"https://openalex.org/I4210121771","display_name":"First Affiliated Hospital of Xi'an Jiaotong University","ror":"https://ror.org/02tbvhh96","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210121771"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Peng Han","raw_affiliation_strings":["Department of Otorhinolaryngology\u2014Head and Neck Surgery, The First Affiliated Hospital, Xi'an Jiaotong University , No. 277 West Yanta Road, Yanta District, Xi'an, Shaanxi 710061 ,","Department of Otorhinolaryngology-Head and Neck Surgery, The First Affiliated Hospital, Xi'an Jiaotong University, No. 277 West Yanta Road, Yanta District, Xi'an, Shaanxi 710061, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Otorhinolaryngology\u2014Head and Neck Surgery, The First Affiliated Hospital, Xi'an Jiaotong University , No. 277 West Yanta Road, Yanta District, Xi'an, Shaanxi 710061 ,","institution_ids":["https://openalex.org/I4210121771"]},{"raw_affiliation_string":"Department of Otorhinolaryngology-Head and Neck Surgery, The First Affiliated Hospital, Xi'an Jiaotong University, No. 277 West Yanta Road, Yanta District, Xi'an, Shaanxi 710061, China","institution_ids":["https://openalex.org/I4210121771"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.19817905,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"26","issue":"5","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":0.9975000023841858,"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":0.9975000023841858,"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":0.961899995803833,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/dropout","display_name":"Dropout (neural networks)","score":0.6748999953269958},{"id":"https://openalex.org/keywords/autoencoder","display_name":"Autoencoder","score":0.6438000202178955},{"id":"https://openalex.org/keywords/imputation","display_name":"Imputation (statistics)","score":0.6345000267028809},{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.49900001287460327},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4562999904155731},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.43220001459121704},{"id":"https://openalex.org/keywords/noise-reduction","display_name":"Noise reduction","score":0.38600000739097595},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.38429999351501465},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.37560001015663147}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7188000082969666},{"id":"https://openalex.org/C2776145597","wikidata":"https://www.wikidata.org/wiki/Q25339462","display_name":"Dropout (neural networks)","level":2,"score":0.6748999953269958},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.6438000202178955},{"id":"https://openalex.org/C58041806","wikidata":"https://www.wikidata.org/wiki/Q1660484","display_name":"Imputation (statistics)","level":3,"score":0.6345000267028809},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.628000020980835},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.49900001287460327},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4562999904155731},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.43220001459121704},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.42879998683929443},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.41440001130104065},{"id":"https://openalex.org/C163294075","wikidata":"https://www.wikidata.org/wiki/Q581861","display_name":"Noise reduction","level":2,"score":0.38600000739097595},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.38429999351501465},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.37560001015663147},{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.367900013923645},{"id":"https://openalex.org/C160920958","wikidata":"https://www.wikidata.org/wiki/Q7662746","display_name":"Synthetic data","level":2,"score":0.3562000095844269},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.3345000147819519},{"id":"https://openalex.org/C193415008","wikidata":"https://www.wikidata.org/wiki/Q639681","display_name":"Network architecture","level":2,"score":0.31439998745918274},{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.30489999055862427},{"id":"https://openalex.org/C83546350","wikidata":"https://www.wikidata.org/wiki/Q1139051","display_name":"Regression","level":2,"score":0.28929999470710754},{"id":"https://openalex.org/C144986985","wikidata":"https://www.wikidata.org/wiki/Q871236","display_name":"Hierarchical database model","level":2,"score":0.28700000047683716},{"id":"https://openalex.org/C2776207758","wikidata":"https://www.wikidata.org/wiki/Q5303302","display_name":"Downstream (manufacturing)","level":2,"score":0.2800999879837036},{"id":"https://openalex.org/C37616216","wikidata":"https://www.wikidata.org/wiki/Q3218363","display_name":"Lasso (programming language)","level":2,"score":0.2766000032424927},{"id":"https://openalex.org/C75553542","wikidata":"https://www.wikidata.org/wiki/Q178161","display_name":"A priori and a posteriori","level":2,"score":0.2700999975204468},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.26809999346733093},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.2524000108242035}],"mesh":[{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"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":"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":"D000465","descriptor_name":"Algorithms","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":"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":"D019295","descriptor_name":"Computational Biology","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}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbaf515","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf515","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf515/64427494/bbaf515.pdf","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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41021262","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41021262","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:11288896","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12478030","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12478030","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12478030/","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf515","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf515","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf515/64427494/bbaf515.pdf","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","license_id":"https://openalex.org/licenses/cc-by","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/G6324912543","display_name":null,"funder_award_id":"xzy012022087","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G6864691011","display_name":null,"funder_award_id":"82571316","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8147005953","display_name":null,"funder_award_id":"2024JC-YBMS-783","funder_id":"https://openalex.org/F4320324173","funder_display_name":"Natural Science Foundation of Shaanxi Province"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320324173","display_name":"Natural Science Foundation of Shaanxi Province","ror":null},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4414625608.pdf"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W1492083415","https://openalex.org/W1547736903","https://openalex.org/W1602702667","https://openalex.org/W1705168361","https://openalex.org/W1915157371","https://openalex.org/W1972532453","https://openalex.org/W1979594866","https://openalex.org/W2015416439","https://openalex.org/W2029773193","https://openalex.org/W2092390808","https://openalex.org/W2096105973","https://openalex.org/W2102619694","https://openalex.org/W2111274140","https://openalex.org/W2117757143","https://openalex.org/W2121607820","https://openalex.org/W2133557974","https://openalex.org/W2155249898","https://openalex.org/W2170830174","https://openalex.org/W2172557341","https://openalex.org/W2343364134","https://openalex.org/W2605406102","https://openalex.org/W2747166117","https://openalex.org/W2792693509","https://openalex.org/W2801527818","https://openalex.org/W2805619986","https://openalex.org/W2900012522","https://openalex.org/W2911555896","https://openalex.org/W2951054376","https://openalex.org/W2951217100","https://openalex.org/W2977512847","https://openalex.org/W2979464975","https://openalex.org/W2980495984","https://openalex.org/W2988716798","https://openalex.org/W2989061519","https://openalex.org/W3017348419","https://openalex.org/W3020430716","https://openalex.org/W3106846504","https://openalex.org/W3129111826","https://openalex.org/W3182470536","https://openalex.org/W3183528829","https://openalex.org/W3208967609","https://openalex.org/W3210657952","https://openalex.org/W3210860076","https://openalex.org/W4205559708","https://openalex.org/W4220680295","https://openalex.org/W4225108987","https://openalex.org/W4226185665","https://openalex.org/W4379599555","https://openalex.org/W4385269564","https://openalex.org/W4389628854","https://openalex.org/W4392044395","https://openalex.org/W4392899359","https://openalex.org/W4396878042","https://openalex.org/W4399746447","https://openalex.org/W4403007541"],"related_works":[],"abstract_inverted_index":{"Single-cell":[0],"ATAC-seq":[1],"(scATAC-seq)":[2],"technology":[3],"allows":[4],"the":[5,17,33,78,118,131,152,158,161,165,176,187,204,217,235],"interrogation":[6],"of":[7,10,27,35,80,167,178,219],"chromatin":[8,25],"accessibility":[9],"individual":[11],"cells.":[12],"Dropout":[13],"events":[14],"occur":[15],"while":[16],"sequencing":[18],"data":[19,40,52,76,88,134],"signals":[20],"at":[21,98],"some":[22],"bona":[23],"fide":[24],"sites":[26],"individuals":[28],"are":[29,227,241],"not":[30],"captured,":[31],"and":[32,59,108,173,202,212,229],"curse":[34],"these":[36],"dropouts":[37],"in":[38,77,224],"scATAC-seq":[39,51,75,87,121,133],"inevitably":[41],"hinders":[42],"downstream":[43,205],"analysis.":[44],"It":[45],"remains":[46],"a":[47,66,90,94,141,168,183],"challenge":[48],"to":[49,54,116,127,129,146,150],"impute":[50],"due":[53],"its":[55],"high":[56],"dimensionality,":[57],"sparsity,":[58],"near-binarization":[60],"properties.":[61],"Herein,":[62],"we":[63],"propose":[64],"IMATAC,":[65],"deep":[67,95],"hierarchical":[68,96],"network":[69,85,222],"with":[70,164,186],"denoising":[71,142],"autoencoder":[72],"for":[73,105,111],"imputing":[74],"form":[79],"peak":[81],"by":[82,93,182],"cell.":[83],"The":[84,191],"embeds":[86],"into":[89],"latent":[91],"space":[92],"architecture":[97],"two":[99],"different":[100],"levels,":[101],"including":[102,207],"bottom":[103],"level":[104,110],"local":[106],"details":[107],"top":[109],"global":[112],"information,":[113],"that":[114,194],"helps":[115],"characterize":[117],"high-dimensional":[119],"sparse":[120],"data.":[122],"Besides,":[123,216],"it":[124,232],"is":[125,180],"encouraged":[126],"learn":[128],"reconstruct":[130],"original":[132],"from":[135,238],"an":[136,148],"artificially":[137],"corrupted":[138],"version":[139],"through":[140],"autoencoder,":[143],"so":[144],"as":[145],"acquire":[147],"ability":[149],"recover":[151],"missing":[153],"values":[154],"primarily":[155],"relying":[156],"on":[157],"cells":[159],"under":[160],"same":[162],"population":[163],"help":[166],"parallel":[169],"multi-classifier.":[170],"Using":[171],"simulated":[172],"experimental":[174],"data,":[175],"performance":[177],"IMATAC":[179,226],"demonstrated":[181],"comparative":[184],"analysis":[185],"other":[188],"competing":[189],"methods.":[190],"results":[192],"suggest":[193],"our":[195,225],"method":[196],"can":[197,233],"achieve":[198],"lower":[199],"imputation":[200],"errors,":[201],"benefit":[203],"analysis,":[206,211],"heterogeneous":[208],"clustering,":[209],"differential":[210],"regulatory":[213],"element":[214],"discovery.":[215],"contributions":[218],"several":[220],"important":[221],"modules":[223],"investigated,":[228],"how":[230],"well":[231],"separate":[234],"dropout":[236],"zeros":[237,240],"biological":[239],"discussed.":[242]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}