{"id":"https://openalex.org/W3182470536","doi":"https://doi.org/10.1093/bioinformatics/btab303","title":"SAILER: scalable and accurate invariant representation learning for single-cell ATAC-seq processing and integration","display_name":"SAILER: scalable and accurate invariant representation learning for single-cell ATAC-seq processing and integration","publication_year":2021,"publication_date":"2021-04-26","ids":{"openalex":"https://openalex.org/W3182470536","doi":"https://doi.org/10.1093/bioinformatics/btab303","mag":"3182470536","pmid":"https://pubmed.ncbi.nlm.nih.gov/34252968"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab303","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab303","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/Supplement_1/i317/39620122/btab303.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/37/Supplement_1/i317/39620122/btab303.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032238772","display_name":"Yingxin Cao","orcid":"https://orcid.org/0000-0002-2769-9056"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yingxin Cao","raw_affiliation_strings":["Center for Complex Biological Systems, University of California , Irvine, CA 92697, USA","Department of Computer Science, University of California , Irvine, CA 92697, USA","NSF-Simons Center for Multiscale Cell Fate Research, University of California , Irvine, CA 92697, USA"],"affiliations":[{"raw_affiliation_string":"Center for Complex Biological Systems, University of California , Irvine, CA 92697, USA","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"Department of Computer Science, University of California , Irvine, CA 92697, USA","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"NSF-Simons Center for Multiscale Cell Fate Research, University of California , Irvine, CA 92697, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062656355","display_name":"Laiyi Fu","orcid":"https://orcid.org/0000-0001-9086-3982"},"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"]},{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Laiyi Fu","raw_affiliation_strings":["Department of Computer Science, University of California , Irvine, CA 92697, USA","Systems Engineering Institute, School of Electronic and Information Engineering, Xi\u2019an Jiaotong University , Xi\u2019an, Shannxi 710049, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California , Irvine, CA 92697, USA","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"Systems Engineering Institute, School of Electronic and Information Engineering, Xi\u2019an Jiaotong University , Xi\u2019an, Shannxi 710049, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045089479","display_name":"Jie Wu","orcid":"https://orcid.org/0000-0003-2759-5879"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jie Wu","raw_affiliation_strings":["Department of Biological Chemistry, University of California , Irvine, CA 92697, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biological Chemistry, University of California , Irvine, CA 92697, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074144985","display_name":"Qinke Peng","orcid":"https://orcid.org/0000-0002-5448-8529"},"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":"Qinke Peng","raw_affiliation_strings":["Systems Engineering Institute, School of Electronic and Information Engineering, Xi\u2019an Jiaotong University , Xi\u2019an, Shannxi 710049, China"],"affiliations":[{"raw_affiliation_string":"Systems Engineering Institute, School of Electronic and Information Engineering, Xi\u2019an Jiaotong University , Xi\u2019an, Shannxi 710049, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076311980","display_name":"Qing Nie","orcid":"https://orcid.org/0000-0002-8804-3368"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qing Nie","raw_affiliation_strings":["Center for Complex Biological Systems, University of California , Irvine, CA 92697, USA","Department of Mathematics, University of California , Irvine, CA 92697, USA","NSF-Simons Center for Multiscale Cell Fate Research, University of California , Irvine, CA 92697, USA"],"affiliations":[{"raw_affiliation_string":"Center for Complex Biological Systems, University of California , Irvine, CA 92697, USA","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"Department of Mathematics, University of California , Irvine, CA 92697, USA","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"NSF-Simons Center for Multiscale Cell Fate Research, University of California , Irvine, CA 92697, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033555140","display_name":"Jing Zhang","orcid":"https://orcid.org/0000-0002-2624-9029"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jing Zhang","raw_affiliation_strings":["Department of Computer Science, University of California , Irvine, CA 92697, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California , Irvine, CA 92697, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084618257","display_name":"Xiaohui Xie","orcid":"https://orcid.org/0000-0002-5479-6345"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaohui Xie","raw_affiliation_strings":["Department of Computer Science, University of California , Irvine, CA 92697, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California , Irvine, CA 92697, USA","institution_ids":["https://openalex.org/I204250578"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5032238772"],"corresponding_institution_ids":["https://openalex.org/I204250578"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.1361,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.77483579,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"37","issue":"Supplement_1","first_page":"i317","last_page":"i326"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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":1.0,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9954000115394592,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.992900013923645,"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/computer-science","display_name":"Computer science","score":0.6589608192443848},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.45964646339416504},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.45824286341667175},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.45458921790122986},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.38866516947746277},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.12374651432037354},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09892448782920837}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6589608192443848},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.45964646339416504},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.45824286341667175},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.45458921790122986},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.38866516947746277},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.12374651432037354},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09892448782920837}],"mesh":[{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019895","descriptor_name":"Transposases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019895","descriptor_name":"Transposases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019895","descriptor_name":"Transposases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btab303","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab303","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/Supplement_1/i317/39620122/btab303.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34252968","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34252968","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt58m9k5gd","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/58m9k5gd","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, vol 37, iss Supplement_1","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8275346","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8275346","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab303","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab303","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/Supplement_1/i317/39620122/btab303.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5664410856","display_name":null,"funder_award_id":"DMS-1763272","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6170557363","display_name":null,"funder_award_id":"U54-CA217378","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G747440273","display_name":null,"funder_award_id":"K01 MH123896","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"},{"id":"https://openalex.org/G986754019","display_name":null,"funder_award_id":"594598","funder_id":"https://openalex.org/F4320306164","funder_display_name":"Simons Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306164","display_name":"Simons Foundation","ror":"https://ror.org/01cmst727"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337346","display_name":"National Institute of Mental Health","ror":"https://ror.org/04xeg9z08"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3182470536.pdf","grobid_xml":"https://content.openalex.org/works/W3182470536.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1492083415","https://openalex.org/W1531821806","https://openalex.org/W1602702667","https://openalex.org/W2092390808","https://openalex.org/W2092939357","https://openalex.org/W2106827861","https://openalex.org/W2117756735","https://openalex.org/W2131681506","https://openalex.org/W2133557974","https://openalex.org/W2187089797","https://openalex.org/W2612519453","https://openalex.org/W2750049634","https://openalex.org/W2805619986","https://openalex.org/W2887694579","https://openalex.org/W2887910040","https://openalex.org/W2899477140","https://openalex.org/W2911555896","https://openalex.org/W2922020904","https://openalex.org/W2934716754","https://openalex.org/W2951054376","https://openalex.org/W2963926704","https://openalex.org/W2965985232","https://openalex.org/W2979464975","https://openalex.org/W2984472267","https://openalex.org/W2989061519","https://openalex.org/W3005039546","https://openalex.org/W3012788672","https://openalex.org/W3099559583","https://openalex.org/W3099768174","https://openalex.org/W3112390879","https://openalex.org/W3120225135","https://openalex.org/W3124819020","https://openalex.org/W3131634425","https://openalex.org/W3133082627","https://openalex.org/W4213108508","https://openalex.org/W6755490972"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2389214306","https://openalex.org/W4396696052","https://openalex.org/W3151146928"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":4}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
