{"id":"https://openalex.org/W4410061395","doi":"https://doi.org/10.1016/j.crmeth.2026.101417","title":"Dissecting serum polyclonal antibody escape to SARS-CoV-2 variants by deep mutational learning","display_name":"Dissecting serum polyclonal antibody escape to SARS-CoV-2 variants by deep mutational learning","publication_year":2026,"publication_date":"2026-04-23","ids":{"openalex":"https://openalex.org/W4410061395","doi":"https://doi.org/10.1016/j.crmeth.2026.101417","pmid":"https://pubmed.ncbi.nlm.nih.gov/42030951"},"language":"en","primary_location":{"id":"doi:10.1016/j.crmeth.2026.101417","doi":"https://doi.org/10.1016/j.crmeth.2026.101417","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.crmeth.2026.101417","pdf_url":null,"source":{"id":"https://openalex.org/S4210214705","display_name":"Cell Reports Methods","issn_l":"2667-2375","issn":["2667-2375"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","poland-20"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Cell Reports Methods","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1016/j.crmeth.2026.101417","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5039015867","display_name":"Danielle Shlesinger","orcid":"https://orcid.org/0000-0001-9719-1023","observed_orcids":["https://orcid.org/0000-0001-9719-1023"]},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Danielle Shlesinger","raw_affiliation_strings":["Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"],"raw_orcid":"https://orcid.org/0000-0001-9719-1023","affiliations":[{"raw_affiliation_string":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5097578741","display_name":"Viktor Sad\u00edlek","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Viktor Sadilek","raw_affiliation_strings":["Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064134308","display_name":"Mason Minot","orcid":"https://orcid.org/0000-0003-0225-9107","observed_orcids":["https://orcid.org/0000-0003-0225-9107"]},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Mason Minot","raw_affiliation_strings":["Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089721817","display_name":"Evangelos Stamkopoulos","orcid":"https://orcid.org/0000-0002-0646-1364","observed_orcids":["https://orcid.org/0000-0002-0646-1364"]},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Evangelos Stamkopoulos","raw_affiliation_strings":["Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004144216","display_name":"Thomas Bikias","orcid":"https://orcid.org/0009-0003-5678-4350","observed_orcids":["https://orcid.org/0009-0003-5678-4350"]},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Thomas Bikias","raw_affiliation_strings":["Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103573125","display_name":"Raphael Kuhn","orcid":"https://orcid.org/0000-0002-4068-2048","observed_orcids":["https://orcid.org/0000-0002-4068-2048"]},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Raphael Kuhn","raw_affiliation_strings":["Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042596314","display_name":"Andreas Agrafiotis","orcid":"https://orcid.org/0000-0003-0797-4695","observed_orcids":["https://orcid.org/0000-0003-0797-4695"]},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Andreas Agrafiotis","raw_affiliation_strings":["Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032713145","display_name":"Joseph M. Taft","orcid":"https://orcid.org/0000-0003-1345-6122","observed_orcids":["https://orcid.org/0000-0003-1345-6122"]},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Joseph M. Taft","raw_affiliation_strings":["Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067719585","display_name":"Alexander Yermanos","orcid":"https://orcid.org/0000-0001-6238-0588","observed_orcids":["https://orcid.org/0000-0001-6238-0588"]},"institutions":[{"id":"https://openalex.org/I3018483916","display_name":"University Medical Center Utrecht","ror":"https://ror.org/0575yy874","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I3018483916"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH","NL"],"is_corresponding":true,"raw_author_name":"Alexander Yermanos","raw_affiliation_strings":["Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands; Botnar Institute of Immune Engineering, Basel, Switzerland. Electronic address: yermanos@umcutrecht.nl"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands; Botnar Institute of Immune Engineering, Basel, Switzerland. Electronic address: yermanos@umcutrecht.nl","institution_ids":["https://openalex.org/I3018483916","https://openalex.org/I35440088"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072818273","display_name":"Sai T. Reddy","orcid":"https://orcid.org/0000-0002-9177-0857","observed_orcids":["https://orcid.org/0000-0002-9177-0857","https://orcid.org/0000-0003-0751-7814","https://orcid.org/0000-0003-2959-9531"]},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Sai.T. Reddy","raw_affiliation_strings":["Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Botnar Institute of Immune Engineering, Basel, Switzerland. Electronic address: sai.reddy@ethz.ch"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Botnar Institute of Immune Engineering, Basel, Switzerland. Electronic address: sai.reddy@ethz.ch","institution_ids":["https://openalex.org/I35440088"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5067719585","https://openalex.org/A5072818273"],"corresponding_institution_ids":["https://openalex.org/I3018483916","https://openalex.org/I35440088"],"apc_list":{"value":4824,"currency":"USD","value_usd":4824},"apc_paid":{"value":4824,"currency":"USD","value_usd":4824},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.00222519,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"6","issue":"6","first_page":"101417","last_page":"101417"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10118","display_name":"SARS-CoV-2 and COVID-19 Research","score":0.9955999851226807,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10118","display_name":"SARS-CoV-2 and COVID-19 Research","score":0.9955999851226807,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.0027000000700354576,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.00019999999494757503,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/sars-cov-2","display_name":"SARS-CoV-2","score":0.9179999828338623},{"id":"https://openalex.org/keywords/immune-evasion","display_name":"immune evasion","score":0.5740000009536743},{"id":"https://openalex.org/keywords/receptor-binding-domain","display_name":"receptor binding domain","score":0.8640000224113464},{"id":"https://openalex.org/keywords/deep-mutational-scanning","display_name":"deep mutational scanning","score":0.9369999766349792},{"id":"https://openalex.org/keywords/covid-19-vaccination","display_name":"COVID-19 vaccination","score":0.6710000038146973},{"id":"https://openalex.org/keywords/vaccine-design","display_name":"vaccine design","score":0.5429999828338623},{"id":"https://openalex.org/keywords/viral-evolution","display_name":"viral evolution","score":0.5680000185966492},{"id":"https://openalex.org/keywords/antibody-binding","display_name":"antibody binding","score":0.43299999833106995},{"id":"https://openalex.org/keywords/epitope-targeting","display_name":"epitope targeting","score":0.7049999833106995}],"concepts":[{"id":"https://openalex.org/C956191","wikidata":"https://www.wikidata.org/wiki/Q930144","display_name":"Polyclonal antibodies","level":3,"score":0.9035888910293579},{"id":"https://openalex.org/C3007834351","wikidata":"https://www.wikidata.org/wiki/Q82069695","display_name":"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)","level":5,"score":0.7142838835716248},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.6502443552017212},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.6256520748138428},{"id":"https://openalex.org/C3008058167","wikidata":"https://www.wikidata.org/wiki/Q84263196","display_name":"Coronavirus disease 2019 (COVID-19)","level":4,"score":0.598689615726471},{"id":"https://openalex.org/C3018558359","wikidata":"https://www.wikidata.org/wiki/Q1660157","display_name":"Immune escape","level":3,"score":0.5523668527603149},{"id":"https://openalex.org/C3006700255","wikidata":"https://www.wikidata.org/wiki/Q81068910","display_name":"2019-20 coronavirus outbreak","level":3,"score":0.4932960867881775},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4076384902000427},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.32629725337028503},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.2253318727016449},{"id":"https://openalex.org/C524204448","wikidata":"https://www.wikidata.org/wiki/Q788926","display_name":"Infectious disease (medical specialty)","level":3,"score":0.07888177037239075},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.07198020815849304},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.0},{"id":"https://openalex.org/C116675565","wikidata":"https://www.wikidata.org/wiki/Q3241045","display_name":"Outbreak","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000085962","descriptor_name":"Angiotensin-Converting Enzyme 2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000085962","descriptor_name":"Angiotensin-Converting Enzyme 2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000085962","descriptor_name":"Angiotensin-Converting Enzyme 2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000085962","descriptor_name":"Angiotensin-Converting Enzyme 2","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000085962","descriptor_name":"Angiotensin-Converting Enzyme 2","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000085962","descriptor_name":"Angiotensin-Converting Enzyme 2","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000085962","descriptor_name":"Angiotensin-Converting Enzyme 2","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000085962","descriptor_name":"Angiotensin-Converting Enzyme 2","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000085962","descriptor_name":"Angiotensin-Converting Enzyme 2","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000097","qualifier_name":"blood","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000097","qualifier_name":"blood","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000097","qualifier_name":"blood","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000914","descriptor_name":"Antibodies, Viral","qualifier_ui":"Q000097","qualifier_name":"blood","is_major_topic":true},{"descriptor_ui":"D000914","descriptor_name":"Antibodies, Viral","qualifier_ui":"Q000097","qualifier_name":"blood","is_major_topic":true},{"descriptor_ui":"D000914","descriptor_name":"Antibodies, Viral","qualifier_ui":"Q000097","qualifier_name":"blood","is_major_topic":true},{"descriptor_ui":"D000914","descriptor_name":"Antibodies, Viral","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000914","descriptor_name":"Antibodies, Viral","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000914","descriptor_name":"Antibodies, Viral","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"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":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057131","descriptor_name":"Immune Evasion","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D057131","descriptor_name":"Immune Evasion","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D057131","descriptor_name":"Immune Evasion","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000097","qualifier_name":"blood","is_major_topic":false},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000097","qualifier_name":"blood","is_major_topic":false},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000097","qualifier_name":"blood","is_major_topic":false},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1016/j.crmeth.2026.101417","doi":"https://doi.org/10.1016/j.crmeth.2026.101417","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.crmeth.2026.101417","pdf_url":null,"source":{"id":"https://openalex.org/S4210214705","display_name":"Cell Reports Methods","issn_l":"2667-2375","issn":["2667-2375"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","poland-20"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Cell Reports Methods","raw_type":"journal-article"},{"id":"doi:10.1101/2025.05.01.651552","doi":"https://doi.org/10.1101/2025.05.01.651552","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.05.01.651552","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/05/02/2025.05.01.651552.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:42030951","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42030951","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,"listed_in":[],"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":"Cell reports methods","raw_type":"Journal Article"},{"id":"pmh:doi:10.3929/ethz-c-000794377","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/794377","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Working Paper"},{"id":"pmh:doi:10.3929/ethz-c-000799852","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/799852","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13282657","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13282657/","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,"listed_in":[],"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":"Cell Rep Methods","raw_type":"Text"},{"id":"pmh:oai:www.research-collection.ethz.ch:20.500.11850/799852","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/799852","pdf_url":null,"source":{"id":"https://openalex.org/S4306402302","display_name":"Repository for Publications and Research Data (ETH Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I35440088","host_organization_name":"ETH Zurich","host_organization_lineage":["https://openalex.org/I35440088"],"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":"Cell Reports Methods, 6 (6)","raw_type":"info:eu-repo/semantics/article"},{"id":"doi:10.3929/ethz-c-000799852","doi":"https://doi.org/10.3929/ethz-c-000799852","is_oa":true,"landing_page_url":"https://doi.org/10.3929/ethz-c-000799852","pdf_url":null,"source":{"id":"https://openalex.org/S7407051236","display_name":"ETH Z\u00fcrich Research Collection","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Other"}],"best_oa_location":{"id":"doi:10.1016/j.crmeth.2026.101417","doi":"https://doi.org/10.1016/j.crmeth.2026.101417","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.crmeth.2026.101417","pdf_url":null,"source":{"id":"https://openalex.org/S4210214705","display_name":"Cell Reports Methods","issn_l":"2667-2375","issn":["2667-2375"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","poland-20"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Cell Reports Methods","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.8048999905586243}],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321652","display_name":"Eidgen\u00f6ssische Technische Hochschule Z\u00fcrich","ror":"https://ror.org/05a28rw58"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W1990789777","https://openalex.org/W2060588922","https://openalex.org/W2095815964","https://openalex.org/W3036607916","https://openalex.org/W3086125063","https://openalex.org/W3104722250","https://openalex.org/W3125266951","https://openalex.org/W3127852352","https://openalex.org/W3129414840","https://openalex.org/W3144378969","https://openalex.org/W3149428818","https://openalex.org/W3160471157","https://openalex.org/W3171375949","https://openalex.org/W3179071715","https://openalex.org/W3179259355","https://openalex.org/W3189387362","https://openalex.org/W3199849883","https://openalex.org/W4220807057","https://openalex.org/W4226047149","https://openalex.org/W4226443473","https://openalex.org/W4283646162","https://openalex.org/W4293746450","https://openalex.org/W4311330242","https://openalex.org/W4312019047","https://openalex.org/W4312067520","https://openalex.org/W4317401716","https://openalex.org/W4364355476","https://openalex.org/W4384206834","https://openalex.org/W4387475691","https://openalex.org/W4390674232","https://openalex.org/W4402087798","https://openalex.org/W4408160955","https://openalex.org/W4408811221","https://openalex.org/W4412785630","https://openalex.org/W4414305622","https://openalex.org/W6600763685"],"related_works":["https://openalex.org/W2391139619","https://openalex.org/W2148639698","https://openalex.org/W2363804818","https://openalex.org/W3127156785","https://openalex.org/W3009669391","https://openalex.org/W4200329650","https://openalex.org/W4205215807","https://openalex.org/W3005417802","https://openalex.org/W4205754011","https://openalex.org/W4226296940"],"abstract_inverted_index":{"Deep":[0],"mutational":[1,43,49],"scanning":[2],"(DMS)":[3],"has":[4],"been":[5],"extensively":[6],"used":[7,133],"to":[8,66,134],"investigate":[9],"how":[10],"single-position":[11],"mutations":[12,27,34],"in":[13,148],"the":[14,41,149],"receptor-binding":[15],"domain":[16],"(RBD)":[17],"affect":[18],"binding":[19,102,120],"of":[20,40,151],"ACE2":[21],"and":[22,62,103,144],"neutralizing":[23],"antibodies,":[24],"thus":[25],"revealing":[26],"that":[28,100],"drive":[29],"immune":[30,142],"escape.":[31,71],"However,":[32],"these":[33],"represent":[35],"only":[36],"a":[37,52],"small":[38],"fraction":[39],"combinatorial":[42,55],"space.":[44],"Here,":[45],"we":[46],"present":[47],"deep":[48,60],"learning":[50,64],"(DML),":[51],"method":[53],"integrating":[54],"mutagenesis,":[56],"yeast":[57],"surface":[58],"display,":[59],"sequencing,":[61],"machine":[63],"(ML),":[65],"analyze":[67],"serum":[68,101],"polyclonal":[69],"antibody":[70],"Sera":[72],"from":[73],"coronavirus":[74],"disease":[75],"2019":[76],"(COVID-19)-vaccinated":[77],"individuals":[78],"were":[79,116,122],"screened":[80],"against":[81],"diverse":[82],"RBD":[83,110,138],"variant":[84],"libraries,":[85],"validating":[86],"300":[87],"serum-variant":[88],"interactions":[89],"across":[90,96],"10":[91],"individuals.":[92],"Performance":[93],"remained":[94],"consistent":[95],"ML":[97],"architectures,":[98],"suggesting":[99],"escape":[104,114],"are":[105],"governed":[106],"by":[107],"distinct,":[108],"localized":[109],"sequence":[111],"features.":[112],"Notably,":[113],"profiles":[115],"highly":[117],"individualized,":[118],"whereas":[119],"signatures":[121],"more":[123],"conserved,":[124],"reflecting":[125],"convergent":[126],"epitope":[127],"targeting.":[128],"Thus,":[129],"DML":[130],"can":[131],"be":[132],"generalize":[135],"beyond":[136],"observed":[137],"variants,":[139],"assess":[140],"cohort-specific":[141],"breadth,":[143],"inform":[145],"vaccine":[146],"design":[147],"face":[150],"viral":[152],"evolution.":[153]},"counts_by_year":[],"updated_date":"2026-10-16T09:59:22.235173","created_date":"2025-10-10T00:00:00"}