{"id":"https://openalex.org/W4385564176","doi":"https://doi.org/10.1093/bioinformatics/btad468","title":"BERTrand\u2014peptide:TCR binding prediction using Bidirectional Encoder Representations from Transformers augmented with random TCR pairing","display_name":"BERTrand\u2014peptide:TCR binding prediction using Bidirectional Encoder Representations from Transformers augmented with random TCR pairing","publication_year":2023,"publication_date":"2023-08-01","ids":{"openalex":"https://openalex.org/W4385564176","doi":"https://doi.org/10.1093/bioinformatics/btad468","pmid":"https://pubmed.ncbi.nlm.nih.gov/37535685"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad468","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad468","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad468/51032269/btad468.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/advance-article-pdf/doi/10.1093/bioinformatics/btad468/51032269/btad468.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033228663","display_name":"Alexander Myronov","orcid":"https://orcid.org/0000-0001-6404-270X"},"institutions":[{"id":"https://openalex.org/I108403487","display_name":"Warsaw University of Technology","ror":"https://ror.org/00y0xnp53","country_code":"PL","type":"education","lineage":["https://openalex.org/I108403487"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Alexander Myronov","raw_affiliation_strings":["Ardigen , Krakow, Poland","Faculty of Mathematics and Information Science, Warsaw University of Technology , Warsaw, Poland"],"affiliations":[{"raw_affiliation_string":"Ardigen , Krakow, Poland","institution_ids":[]},{"raw_affiliation_string":"Faculty of Mathematics and Information Science, Warsaw University of Technology , Warsaw, Poland","institution_ids":["https://openalex.org/I108403487"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065133781","display_name":"Giovanni Mazzocco","orcid":"https://orcid.org/0009-0001-8644-5179"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Giovanni Mazzocco","raw_affiliation_strings":["Ardigen , Krakow, Poland"],"affiliations":[{"raw_affiliation_string":"Ardigen , Krakow, Poland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023951474","display_name":"Paulina Kr\u00f3l","orcid":"https://orcid.org/0000-0001-7351-1483"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Paulina Kr\u00f3l","raw_affiliation_strings":["Ardigen , Krakow, Poland"],"affiliations":[{"raw_affiliation_string":"Ardigen , Krakow, Poland","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021916927","display_name":"Dariusz Plewczy\u0144ski","orcid":"https://orcid.org/0000-0002-3840-7610"},"institutions":[{"id":"https://openalex.org/I108403487","display_name":"Warsaw University of Technology","ror":"https://ror.org/00y0xnp53","country_code":"PL","type":"education","lineage":["https://openalex.org/I108403487"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Dariusz Plewczynski","raw_affiliation_strings":["Faculty of Mathematics and Information Science, Warsaw University of Technology , Warsaw, Poland"],"affiliations":[{"raw_affiliation_string":"Faculty of Mathematics and Information Science, Warsaw University of Technology , Warsaw, Poland","institution_ids":["https://openalex.org/I108403487"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5033228663"],"corresponding_institution_ids":["https://openalex.org/I108403487"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.3497,"has_fulltext":true,"cited_by_count":22,"citation_normalized_percentile":{"value":0.9263873,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"39","issue":"8","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9846000075340271,"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/T10580","display_name":"Immunotherapy and Immune Responses","score":0.9843000173568726,"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/t-cell-receptor","display_name":"T-cell receptor","score":0.8246514797210693},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.5896487236022949},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5395523905754089},{"id":"https://openalex.org/keywords/generalization","display_name":"Generalization","score":0.5356321930885315},{"id":"https://openalex.org/keywords/epitope","display_name":"Epitope","score":0.47259506583213806},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.45721957087516785},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4317369759082794},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4099813997745514},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.34464654326438904},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28645065426826477},{"id":"https://openalex.org/keywords/t-cell","display_name":"T cell","score":0.26898062229156494},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.16911056637763977},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.16733571887016296},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.16029325127601624},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.14972928166389465}],"concepts":[{"id":"https://openalex.org/C19317047","wikidata":"https://www.wikidata.org/wiki/Q412037","display_name":"T-cell receptor","level":4,"score":0.8246514797210693},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.5896487236022949},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5395523905754089},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.5356321930885315},{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.47259506583213806},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.45721957087516785},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4317369759082794},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4099813997745514},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.34464654326438904},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28645065426826477},{"id":"https://openalex.org/C2776090121","wikidata":"https://www.wikidata.org/wiki/Q193529","display_name":"T cell","level":3,"score":0.26898062229156494},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.16911056637763977},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.16733571887016296},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.16029325127601624},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.14972928166389465},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"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":"D000939","descriptor_name":"Epitopes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad468","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad468","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad468/51032269/btad468.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:37535685","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37535685","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:10444968","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10444968","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10444968/pdf/btad468.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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad468","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad468","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad468/51032269/btad468.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":[{"score":0.6499999761581421,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G4124455718","display_name":null,"funder_award_id":"POIR.01.01","funder_id":"https://openalex.org/F4320335039","funder_display_name":"Narodowe Centrum Bada\u0144 i Rozwoju"}],"funders":[{"id":"https://openalex.org/F4320322637","display_name":"Politechnika Warszawska","ror":"https://ror.org/00y0xnp53"},{"id":"https://openalex.org/F4320335039","display_name":"Narodowe Centrum Bada\u0144 i Rozwoju","ror":"https://ror.org/05pwfyy15"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4385564176.pdf"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1973639800","https://openalex.org/W1986216579","https://openalex.org/W1998713127","https://openalex.org/W2141312574","https://openalex.org/W2146074801","https://openalex.org/W2164015638","https://openalex.org/W2172893229","https://openalex.org/W2368915317","https://openalex.org/W2584586929","https://openalex.org/W2589139221","https://openalex.org/W2605177850","https://openalex.org/W2613978126","https://openalex.org/W2670890989","https://openalex.org/W2671261300","https://openalex.org/W2752126733","https://openalex.org/W2754733375","https://openalex.org/W2763756177","https://openalex.org/W2778215749","https://openalex.org/W2789481083","https://openalex.org/W2797380951","https://openalex.org/W2797967938","https://openalex.org/W2897427714","https://openalex.org/W2899327929","https://openalex.org/W2906243310","https://openalex.org/W2913665794","https://openalex.org/W2948516395","https://openalex.org/W2949600892","https://openalex.org/W2951433247","https://openalex.org/W2965921152","https://openalex.org/W2971227267","https://openalex.org/W2981521939","https://openalex.org/W2990308980","https://openalex.org/W2995389725","https://openalex.org/W3080758869","https://openalex.org/W3127238141","https://openalex.org/W3135351475","https://openalex.org/W3138156743","https://openalex.org/W3160101264","https://openalex.org/W3160420762","https://openalex.org/W3196225703","https://openalex.org/W3196626346","https://openalex.org/W3198942356","https://openalex.org/W4285621013","https://openalex.org/W4313366361","https://openalex.org/W4319159750","https://openalex.org/W4323320132","https://openalex.org/W6763868836"],"related_works":["https://openalex.org/W1979044599","https://openalex.org/W2021824670","https://openalex.org/W2009867644","https://openalex.org/W2363997565","https://openalex.org/W1981120125","https://openalex.org/W3036615648","https://openalex.org/W2408448169","https://openalex.org/W2182598264","https://openalex.org/W2075879923","https://openalex.org/W2060253881"],"abstract_inverted_index":{"The":[0],"datasets":[1],"and":[2],"the":[3],"code":[4],"for":[5],"model":[6],"training":[7],"are":[8],"available":[9],"at":[10],"https://github.com/SFGLab/bertrand.":[11]},"counts_by_year":[{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}