{"id":"https://openalex.org/W4403800888","doi":"https://doi.org/10.1093/bioinformatics/btae618","title":"Addressing the antibody germline bias and its effect on language models for improved antibody design","display_name":"Addressing the antibody germline bias and its effect on language models for improved antibody design","publication_year":2024,"publication_date":"2024-10-23","ids":{"openalex":"https://openalex.org/W4403800888","doi":"https://doi.org/10.1093/bioinformatics/btae618","pmid":"https://pubmed.ncbi.nlm.nih.gov/39460949"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae618","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae618","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/11/btae618/60530393/btae618.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/40/11/btae618/60530393/btae618.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064133250","display_name":"Tobias Hegelund Olsen","orcid":"https://orcid.org/0000-0002-6348-4650"},"institutions":[{"id":"https://openalex.org/I2800110054","display_name":"Age UK","ror":"https://ror.org/050x9d346","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2800110054"]},{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Tobias H Olsen","raw_affiliation_strings":["Department of Statistics, University of Oxford , Oxford OX1 3LB,","GSK Medicines Research Centre, GSK , Stevenage SG1 2NY,","University of Oxford Department of Statistics, , Oxford, OX1 3LB,","GSK Medicines Research Centre, GSK , Stevenage, SG1 2NY,"],"affiliations":[{"raw_affiliation_string":"Department of Statistics, University of Oxford , Oxford OX1 3LB,","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"GSK Medicines Research Centre, GSK , Stevenage SG1 2NY,","institution_ids":["https://openalex.org/I2800110054"]},{"raw_affiliation_string":"University of Oxford Department of Statistics, , Oxford, OX1 3LB,","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"GSK Medicines Research Centre, GSK , Stevenage, SG1 2NY,","institution_ids":["https://openalex.org/I2800110054"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060836019","display_name":"Iain H. Moal","orcid":"https://orcid.org/0000-0002-4960-5487"},"institutions":[{"id":"https://openalex.org/I2800110054","display_name":"Age UK","ror":"https://ror.org/050x9d346","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2800110054"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Iain H Moal","raw_affiliation_strings":["GSK Medicines Research Centre, GSK , Stevenage SG1 2NY,","GSK Medicines Research Centre, GSK , Stevenage, SG1 2NY,"],"affiliations":[{"raw_affiliation_string":"GSK Medicines Research Centre, GSK , Stevenage SG1 2NY,","institution_ids":["https://openalex.org/I2800110054"]},{"raw_affiliation_string":"GSK Medicines Research Centre, GSK , Stevenage, SG1 2NY,","institution_ids":["https://openalex.org/I2800110054"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015572211","display_name":"Charlotte M. Deane","orcid":"https://orcid.org/0000-0003-1388-2252"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Charlotte M Deane","raw_affiliation_strings":["Department of Statistics, University of Oxford , Oxford OX1 3LB,","University of Oxford Department of Statistics, , Oxford, OX1 3LB,"],"affiliations":[{"raw_affiliation_string":"Department of Statistics, University of Oxford , Oxford OX1 3LB,","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"University of Oxford Department of Statistics, , Oxford, OX1 3LB,","institution_ids":["https://openalex.org/I40120149"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5064133250"],"corresponding_institution_ids":["https://openalex.org/I2800110054","https://openalex.org/I40120149"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":20.3814,"has_fulltext":true,"cited_by_count":52,"citation_normalized_percentile":{"value":0.99691549,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"40","issue":"11","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9991999864578247,"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"}},"topics":[{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9991999864578247,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9912999868392944,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9764000177383423,"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/germline","display_name":"Germline","score":0.8073912858963013},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.548126220703125},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5445111989974976},{"id":"https://openalex.org/keywords/germline-mutation","display_name":"Germline mutation","score":0.5116870403289795},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.47212204337120056},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45819056034088135},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.41832977533340454},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.36874109506607056},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.35610371828079224},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.3360007703304291},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2637934684753418},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1606852412223816},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11403191089630127}],"concepts":[{"id":"https://openalex.org/C109825262","wikidata":"https://www.wikidata.org/wiki/Q1139164","display_name":"Germline","level":3,"score":0.8073912858963013},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.548126220703125},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5445111989974976},{"id":"https://openalex.org/C13514818","wikidata":"https://www.wikidata.org/wiki/Q5552256","display_name":"Germline mutation","level":4,"score":0.5116870403289795},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.47212204337120056},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45819056034088135},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.41832977533340454},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.36874109506607056},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.35610371828079224},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.3360007703304291},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2637934684753418},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1606852412223816},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11403191089630127}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":"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":"D018095","descriptor_name":"Germ-Line Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018095","descriptor_name":"Germ-Line Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018095","descriptor_name":"Germ-Line Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018095","descriptor_name":"Germ-Line Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018095","descriptor_name":"Germ-Line Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018095","descriptor_name":"Germ-Line Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae618","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae618","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/11/btae618/60530393/btae618.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39460949","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39460949","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:pubmedcentral.nih.gov:11543624","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11543624","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11543624/pdf/btae618.pdf","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae618","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae618","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/11/btae618/60530393/btae618.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4886476515","display_name":null,"funder_award_id":"EP/S024093","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G6908532722","display_name":"EPSRC CDT in Sustainable Approaches to Biomedical Science: Responsible and Reproducible Research - SABS:R^3","funder_award_id":"EP/S024093/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320307773","display_name":"GlaxoSmithKline","ror":"https://ror.org/01xsqw823"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4403800888.pdf","grobid_xml":"https://content.openalex.org/works/W4403800888.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W1855237549","https://openalex.org/W2029525307","https://openalex.org/W2102461176","https://openalex.org/W2490420619","https://openalex.org/W2596798204","https://openalex.org/W2610547910","https://openalex.org/W2766842037","https://openalex.org/W2884561390","https://openalex.org/W2896457183","https://openalex.org/W2910384850","https://openalex.org/W2913847447","https://openalex.org/W2950888501","https://openalex.org/W2953008890","https://openalex.org/W2965373594","https://openalex.org/W2974982237","https://openalex.org/W2978709467","https://openalex.org/W2980681402","https://openalex.org/W2999958881","https://openalex.org/W3017045680","https://openalex.org/W3025261372","https://openalex.org/W3037076666","https://openalex.org/W3146944767","https://openalex.org/W3177500196","https://openalex.org/W3179485843","https://openalex.org/W3199404008","https://openalex.org/W3206187363","https://openalex.org/W4200635416","https://openalex.org/W4206415401","https://openalex.org/W4220757565","https://openalex.org/W4280625391","https://openalex.org/W4283068487","https://openalex.org/W4285273243","https://openalex.org/W4288066876","https://openalex.org/W4292779060","https://openalex.org/W4301581299","https://openalex.org/W4304697829","https://openalex.org/W4307839767","https://openalex.org/W4310875677","https://openalex.org/W4327550249","https://openalex.org/W4366823175","https://openalex.org/W4387233802","https://openalex.org/W4388024559","https://openalex.org/W4393950286","https://openalex.org/W6929296873"],"related_works":["https://openalex.org/W2067324420","https://openalex.org/W2613868166","https://openalex.org/W4247239363","https://openalex.org/W4296060409","https://openalex.org/W4221137512","https://openalex.org/W2009580730","https://openalex.org/W3216631139","https://openalex.org/W2041452721","https://openalex.org/W3117759755","https://openalex.org/W3208984277"],"abstract_inverted_index":{"AbLang-2":[0],"is":[1,10],"trained":[2],"on":[3],"both":[4],"unpaired":[5],"and":[6,9],"paired":[7],"data,":[8],"freely":[11],"available":[12],"at":[13],"https://github.com/oxpig/AbLang2.git.":[14]},"counts_by_year":[{"year":2026,"cited_by_count":13},{"year":2025,"cited_by_count":33},{"year":2024,"cited_by_count":6}],"updated_date":"2026-04-15T08:11:43.952461","created_date":"2025-10-10T00:00:00"}
