{"id":"https://openalex.org/W4416872945","doi":"https://doi.org/10.1371/journal.pcbi.1013758","title":"Nucleotide context models outperform protein language models for predicting antibody affinity maturation","display_name":"Nucleotide context models outperform protein language models for predicting antibody affinity maturation","publication_year":2025,"publication_date":"2025-12-01","ids":{"openalex":"https://openalex.org/W4416872945","doi":"https://doi.org/10.1371/journal.pcbi.1013758","pmid":"https://pubmed.ncbi.nlm.nih.gov/41325480"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1013758","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013758","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1013758","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073373217","display_name":"Mackenzie M. Johnson","orcid":"https://orcid.org/0000-0002-3915-2023"},"institutions":[{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mackenzie M. Johnson","raw_affiliation_strings":["Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I4210089486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103264897","display_name":"Kevin Sung","orcid":"https://orcid.org/0000-0002-7289-845X"},"institutions":[{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kevin Sung","raw_affiliation_strings":["Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I4210089486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056683217","display_name":"Hugh K. Haddox","orcid":"https://orcid.org/0000-0001-8324-8324"},"institutions":[{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hugh K. Haddox","raw_affiliation_strings":["Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I4210089486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016157693","display_name":"A. B. Vora","orcid":"https://orcid.org/0000-0001-7842-5170"},"institutions":[{"id":"https://openalex.org/I83399316","display_name":"Rockefeller University","ror":"https://ror.org/0420db125","country_code":"US","type":"education","lineage":["https://openalex.org/I83399316"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ashni A. Vora","raw_affiliation_strings":["Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, New York, United States of America"],"affiliations":[{"raw_affiliation_string":"Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, New York, United States of America","institution_ids":["https://openalex.org/I83399316"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018664352","display_name":"Tatsuya Araki","orcid":"https://orcid.org/0000-0002-6203-7250"},"institutions":[{"id":"https://openalex.org/I83399316","display_name":"Rockefeller University","ror":"https://ror.org/0420db125","country_code":"US","type":"education","lineage":["https://openalex.org/I83399316"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Tatsuya Araki","raw_affiliation_strings":["Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, New York, United States of America"],"affiliations":[{"raw_affiliation_string":"Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, New York, United States of America","institution_ids":["https://openalex.org/I83399316"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016183751","display_name":"Gabriel D. Victora","orcid":"https://orcid.org/0000-0001-8807-348X"},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I83399316","display_name":"Rockefeller University","ror":"https://ror.org/0420db125","country_code":"US","type":"education","lineage":["https://openalex.org/I83399316"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Gabriel D. Victora","raw_affiliation_strings":["Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America","Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, New York, United States of America"],"affiliations":[{"raw_affiliation_string":"Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America","institution_ids":["https://openalex.org/I1344073410"]},{"raw_affiliation_string":"Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, New York, United States of America","institution_ids":["https://openalex.org/I83399316"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050837693","display_name":"Yun S. Song","orcid":"https://orcid.org/0000-0002-0734-9868"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yun S. Song","raw_affiliation_strings":["Computer Science Division, University of California, Berkeley, Berkeley, California, United States of America","Department of Statistics, University of California, Berkeley, Berkeley, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Computer Science Division, University of California, Berkeley, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Statistics, University of California, Berkeley, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050341558","display_name":"Julia Fukuyama","orcid":"https://orcid.org/0000-0002-7590-5563"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Julia Fukuyama","raw_affiliation_strings":["Department of Statistics, Indiana University Bloomington, Bloomington, Indiana, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Statistics, Indiana University Bloomington, Bloomington, Indiana, United States of America","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084752404","display_name":"F. A. Matsen","orcid":"https://orcid.org/0000-0003-0607-6025"},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Frederick A. Matsen IV","raw_affiliation_strings":["Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America","Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America","Department of Statistics, University of Washington, Seattle, Washington, United States of America","Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America"],"affiliations":[{"raw_affiliation_string":"Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I4210089486"]},{"raw_affiliation_string":"Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Statistics, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America","institution_ids":["https://openalex.org/I1344073410"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5016157693","https://openalex.org/A5016183751","https://openalex.org/A5018664352","https://openalex.org/A5050341558","https://openalex.org/A5050837693","https://openalex.org/A5056683217","https://openalex.org/A5073373217","https://openalex.org/A5084752404","https://openalex.org/A5103264897"],"corresponding_institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I201448701","https://openalex.org/I4210089486","https://openalex.org/I4210119109","https://openalex.org/I83399316","https://openalex.org/I95457486"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.767,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.78141792,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"21","issue":"12","first_page":"e1013758","last_page":"e1013758"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.7760000228881836,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.7760000228881836,"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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.13899999856948853,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"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/T10031","display_name":"T-cell and B-cell Immunology","score":0.0617000013589859,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/affinity-maturation","display_name":"Affinity maturation","score":0.6880999803543091},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6396999955177307},{"id":"https://openalex.org/keywords/somatic-hypermutation","display_name":"Somatic hypermutation","score":0.6132000088691711},{"id":"https://openalex.org/keywords/repertoire","display_name":"Repertoire","score":0.48100000619888306},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.3682999908924103},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.3547999858856201},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.3319999873638153},{"id":"https://openalex.org/keywords/feature-selection","display_name":"Feature selection","score":0.3264000117778778}],"concepts":[{"id":"https://openalex.org/C2781377902","wikidata":"https://www.wikidata.org/wiki/Q21418769","display_name":"Affinity maturation","level":3,"score":0.6880999803543091},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6396999955177307},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.621999979019165},{"id":"https://openalex.org/C128526571","wikidata":"https://www.wikidata.org/wiki/Q619302","display_name":"Somatic hypermutation","level":4,"score":0.6132000088691711},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5350000262260437},{"id":"https://openalex.org/C2778473898","wikidata":"https://www.wikidata.org/wiki/Q2145110","display_name":"Repertoire","level":2,"score":0.48100000619888306},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4447999894618988},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.427700012922287},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.3682999908924103},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.3547999858856201},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.33329999446868896},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.3319999873638153},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.3264000117778778},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.31869998574256897},{"id":"https://openalex.org/C2778136018","wikidata":"https://www.wikidata.org/wiki/Q10350689","display_name":"Predictive power","level":2,"score":0.31130000948905945},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.30970001220703125},{"id":"https://openalex.org/C43907098","wikidata":"https://www.wikidata.org/wiki/Q903924","display_name":"breakpoint cluster region","level":3,"score":0.3077999949455261},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.30720001459121704},{"id":"https://openalex.org/C12713177","wikidata":"https://www.wikidata.org/wiki/Q1900281","display_name":"Perspective (graphical)","level":2,"score":0.2849999964237213},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.2770000100135803},{"id":"https://openalex.org/C195324797","wikidata":"https://www.wikidata.org/wiki/Q33742","display_name":"Natural language","level":2,"score":0.2632000148296356},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.2565999925136566},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2556000053882599}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000915","descriptor_name":"Antibody Affinity","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000915","descriptor_name":"Antibody Affinity","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000915","descriptor_name":"Antibody Affinity","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000915","descriptor_name":"Antibody Affinity","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000915","descriptor_name":"Antibody Affinity","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000915","descriptor_name":"Antibody Affinity","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000915","descriptor_name":"Antibody Affinity","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000915","descriptor_name":"Antibody Affinity","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000915","descriptor_name":"Antibody Affinity","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000915","descriptor_name":"Antibody Affinity","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D001402","descriptor_name":"B-Lymphocytes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D001402","descriptor_name":"B-Lymphocytes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D001402","descriptor_name":"B-Lymphocytes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D001402","descriptor_name":"B-Lymphocytes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D001402","descriptor_name":"B-Lymphocytes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009711","descriptor_name":"Nucleotides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009711","descriptor_name":"Nucleotides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009711","descriptor_name":"Nucleotides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009711","descriptor_name":"Nucleotides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009711","descriptor_name":"Nucleotides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D027041","descriptor_name":"Somatic Hypermutation, Immunoglobulin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D027041","descriptor_name":"Somatic Hypermutation, Immunoglobulin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D027041","descriptor_name":"Somatic Hypermutation, Immunoglobulin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D027041","descriptor_name":"Somatic Hypermutation, Immunoglobulin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D027041","descriptor_name":"Somatic Hypermutation, Immunoglobulin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1013758","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013758","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:41325480","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41325480","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:f1e618f7f68d490ab1e9054946dca182","is_oa":true,"landing_page_url":"https://doaj.org/article/f1e618f7f68d490ab1e9054946dca182","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 21, Iss 12, p e1013758 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12685221","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12685221/","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1013758","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013758","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1497406915","display_name":null,"funder_award_id":"R01-AI146028","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4654028682","display_name":null,"funder_award_id":"S10OD028685","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5299964279","display_name":null,"funder_award_id":"R56-HG013117","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6699846162","display_name":null,"funder_award_id":"R01-HG013117","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306082","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":53,"referenced_works":["https://openalex.org/W1423495995","https://openalex.org/W1802312377","https://openalex.org/W1855237549","https://openalex.org/W1901318710","https://openalex.org/W1993476635","https://openalex.org/W2102461176","https://openalex.org/W2114850508","https://openalex.org/W2143210482","https://openalex.org/W2151558930","https://openalex.org/W2163641974","https://openalex.org/W2171634310","https://openalex.org/W2289890884","https://openalex.org/W2317651087","https://openalex.org/W2344940607","https://openalex.org/W2615321354","https://openalex.org/W2616207459","https://openalex.org/W2750920587","https://openalex.org/W2755280714","https://openalex.org/W2768215828","https://openalex.org/W2769778634","https://openalex.org/W2805330890","https://openalex.org/W2811364409","https://openalex.org/W2920915242","https://openalex.org/W2949537553","https://openalex.org/W2950118240","https://openalex.org/W2979682945","https://openalex.org/W2979751218","https://openalex.org/W3005235420","https://openalex.org/W3021143157","https://openalex.org/W3045355398","https://openalex.org/W3111174583","https://openalex.org/W3206187363","https://openalex.org/W4200209280","https://openalex.org/W4283068487","https://openalex.org/W4283746734","https://openalex.org/W4307839767","https://openalex.org/W4310089615","https://openalex.org/W4327550249","https://openalex.org/W4362692173","https://openalex.org/W4366823175","https://openalex.org/W4385064650","https://openalex.org/W4386156557","https://openalex.org/W4393386306","https://openalex.org/W4399052323","https://openalex.org/W4399053249","https://openalex.org/W4403800888","https://openalex.org/W4404200234","https://openalex.org/W4405104445","https://openalex.org/W4405909579","https://openalex.org/W4407772398","https://openalex.org/W4408570378","https://openalex.org/W4409800693","https://openalex.org/W4413341299"],"related_works":[],"abstract_inverted_index":{"Antibodies":[0],"play":[1],"a":[2,34,156,174,188,215,240,253],"crucial":[3],"role":[4],"in":[5,225,249],"adaptive":[6],"immunity.":[7],"They":[8],"develop":[9],"as":[10,148,150],"B":[11,26],"cell":[12],"receptors":[13],"(BCRs):":[14],"membrane-bound":[15],"forms":[16],"of":[17,25,36,51,90,109,116,122,125,131,166,177,184,211,237],"antibodies":[18],"that":[19,163],"are":[20,29],"expressed":[21],"on":[22,70,102,205,214],"the":[23,79,107,170,182],"surfaces":[24],"cells.":[27],"BCRs":[28],"refined":[30],"through":[31],"affinity":[32,52,111,185],"maturation,":[33],"process":[35],"somatic":[37],"hypermutation":[38],"(SHM)":[39],"and":[40,62,77,133,260],"natural":[41],"selection,":[42,132],"to":[43,46,74,105,243],"improve":[44],"binding":[45],"an":[47,129,151],"antigen.":[48],"Computational":[49],"models":[50,98,121,124,140],"maturation":[53,112],"have":[54],"developed":[55],"from":[56,86,99],"two":[57],"main":[58],"perspectives:":[59],"molecular":[60,66],"evolution":[61,67,259],"language":[63,80,135,199,250],"modeling.":[64],"The":[65],"perspective":[68,82],"focuses":[69],"nucleotide":[71,171],"sequence":[72],"context":[73],"describe":[75],"mutation":[76],"selection;":[78],"modeling":[81,165,194],"involves":[83],"learning":[84],"patterns":[85],"large":[87,142],"data":[88,146],"sets":[89],"protein":[91,134,198],"sequences.":[92,118,207],"In":[93],"this":[94],"paper,":[95],"we":[96,232],"compared":[97],"both":[100],"perspectives":[101],"their":[103],"ability":[104],"predict":[106],"course":[108,183],"antibody":[110,206,258],"along":[113],"phylogenetic":[114],"trees":[115],"BCR":[117,144],"This":[119],"included":[120],"SHM,":[123,167],"SHM":[126,195],"combined":[127],"with":[128,155,247],"estimate":[130],"models.":[136,263],"We":[137,161],"evaluated":[138],"these":[139],"for":[141,180,256],"human":[143],"repertoire":[145],"sets,":[147],"well":[149],"antigen-specific":[152],"mouse":[153],"experiment":[154,220],"pre-rearranged":[157],"cognate":[158],"naive":[159],"antibody.":[160],"demonstrated":[162],"precise":[164],"which":[168],"requires":[169],"context,":[172],"provides":[173],"substantial":[175],"amount":[176],"predictive":[178,226,262],"power":[179],"predicting":[181],"maturation.":[186],"Notably,":[187],"simple":[189],"nucleotide-based":[190],"convolutional":[191],"neural":[192],"network":[193],"outperformed":[196],"state-of-the-art":[197],"models,":[200],"including":[201],"one":[202],"trained":[203],"exclusively":[204],"Furthermore,":[208],"incorporating":[209],"estimates":[210],"selection":[212],"based":[213],"custom":[216],"deep":[217],"mutational":[218],"scanning":[219],"brought":[221],"only":[222],"modest":[223],"improvement":[224],"power.":[227],"To":[228],"support":[229],"further":[230],"research,":[231],"introduce":[233],"EPAM":[234],"(Evaluating":[235],"Predictions":[236],"Affinity":[238],"Maturation),":[239],"benchmarking":[241],"framework":[242],"integrate":[244],"evolutionary":[245],"principles":[246],"advances":[248],"modeling,":[251],"offering":[252],"road":[254],"map":[255],"understanding":[257],"improving":[261]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-12-01T00:00:00"}