{"id":"https://openalex.org/W4406924635","doi":"https://doi.org/10.1093/bioinformatics/btaf022","title":"TPepRet: a deep learning model for characterizing T-cell receptors\u2013antigen binding patterns","display_name":"TPepRet: a deep learning model for characterizing T-cell receptors\u2013antigen binding patterns","publication_year":2024,"publication_date":"2024-12-26","ids":{"openalex":"https://openalex.org/W4406924635","doi":"https://doi.org/10.1093/bioinformatics/btaf022","pmid":"https://pubmed.ncbi.nlm.nih.gov/39880376"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf022","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf022","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf022/61686009/btaf022.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/btaf022/61686009/btaf022.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100377181","display_name":"Meng Wang","orcid":"https://orcid.org/0000-0002-6626-8857"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Meng Wang","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University , Changsha 410083,","School of Computer Science and engineering, Central South University, Changsha, 410083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University , Changsha 410083,","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"School of Computer Science and engineering, Central South University, Changsha, 410083, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058044263","display_name":"Wei Fan","orcid":"https://orcid.org/0000-0001-7054-2698"},"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":"Wei Fan","raw_affiliation_strings":["Nuffield Department of Women\u2019s and Reproductive Health, University of Oxford , Oxford OX39DU,","Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, OX39DU, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Nuffield Department of Women\u2019s and Reproductive Health, University of Oxford , Oxford OX39DU,","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, OX39DU, United Kingdom","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101319821","display_name":"Tianrui Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tianrui Wu","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University , Changsha 410083,","School of Computer Science and engineering, Central South University, Changsha, 410083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University , Changsha 410083,","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"School of Computer Science and engineering, Central South University, Changsha, 410083, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100719013","display_name":"Min Li","orcid":"https://orcid.org/0000-0002-0188-1394"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Min Li","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University , Changsha 410083,","School of Computer Science and engineering, Central South University, Changsha, 410083, China"],"raw_orcid":"https://orcid.org/0000-0002-0188-1394","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University , Changsha 410083,","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"School of Computer Science and engineering, Central South University, Changsha, 410083, China","institution_ids":["https://openalex.org/I139660479"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5100719013"],"corresponding_institution_ids":["https://openalex.org/I139660479"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.15,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.7801524,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"41","issue":"1","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":0.9581999778747559,"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":0.9581999778747559,"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/T10031","display_name":"T-cell and B-cell Immunology","score":0.015200000256299973,"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"}},{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.00570000009611249,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.5540404915809631},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5469505786895752},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5335012078285217},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.47829991579055786},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.34258055686950684},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.31993091106414795},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.24132764339447021},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.19567349553108215}],"concepts":[{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.5540404915809631},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5469505786895752},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5335012078285217},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.47829991579055786},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.34258055686950684},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31993091106414795},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.24132764339447021},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.19567349553108215}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","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},{"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":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"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":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaf022","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf022","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf022/61686009/btaf022.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:39880376","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39880376","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:11784750","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11784750","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11784750/pdf/btaf022.pdf","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,"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"},{"id":"pmh:oai:ora.ox.ac.uk:uuid:e6dac24f-e676-447c-811b-97e3a4c29a45","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402636","display_name":"Oxford University Research Archive (ORA) (University of Oxford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40120149","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/I40120149"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Jisc Publications Router","raw_type":"http://purl.org/coar/resource_type/c_dcae04bc"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf022","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf022","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf022/61686009/btaf022.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/G3865462418","display_name":null,"funder_award_id":"62225209","funder_id":"https://openalex.org/F4320336125","funder_display_name":"National Science Fund for Distinguished Young Scholars"}],"funders":[{"id":"https://openalex.org/F4320321514","display_name":"Central South University","ror":"https://ror.org/00f1zfq44"},{"id":"https://openalex.org/F4320336125","display_name":"National Science Fund for Distinguished Young Scholars","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4406924635.pdf","grobid_xml":"https://content.openalex.org/works/W4406924635.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W1502735160","https://openalex.org/W1778195690","https://openalex.org/W1989527063","https://openalex.org/W2031011895","https://openalex.org/W2067069532","https://openalex.org/W2163660115","https://openalex.org/W2293719487","https://openalex.org/W2319450666","https://openalex.org/W2613978126","https://openalex.org/W2670890989","https://openalex.org/W2671261300","https://openalex.org/W2737196618","https://openalex.org/W2752126733","https://openalex.org/W2898389621","https://openalex.org/W2899327929","https://openalex.org/W2937667996","https://openalex.org/W2968849363","https://openalex.org/W2990308980","https://openalex.org/W3005844923","https://openalex.org/W3020331344","https://openalex.org/W3039313607","https://openalex.org/W3113525558","https://openalex.org/W3127841695","https://openalex.org/W3135351475","https://openalex.org/W3138156743","https://openalex.org/W3160101264","https://openalex.org/W3160420762","https://openalex.org/W3196626346","https://openalex.org/W3198942356","https://openalex.org/W4213345021","https://openalex.org/W4286631898","https://openalex.org/W4311619464","https://openalex.org/W4323320132","https://openalex.org/W4323974789","https://openalex.org/W4360999048","https://openalex.org/W4366085055","https://openalex.org/W4385693120","https://openalex.org/W4388847467","https://openalex.org/W6633658626"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W1971568933"],"abstract_inverted_index":{"MOTIVATION:":[0],"T-cell":[1],"receptors":[2],"(TCRs)":[3],"elicit":[4],"and":[5,23,34,112,128,182],"mediate":[6],"the":[7,28,52,88,91,104,122],"adaptive":[8],"immune":[9],"response":[10],"by":[11],"recognizing":[12],"antigenic":[13],"peptides,":[14],"a":[15,135],"process":[16],"pivotal":[17],"for":[18,38,62,98,205],"cancer":[19],"immunotherapy,":[20],"vaccine":[21],"design,":[22],"autoimmune":[24],"disease":[25],"management.":[26],"Understanding":[27],"intricate":[29],"binding":[30,124,152,170,208],"patterns":[31],"between":[32,126],"TCRs":[33,127],"peptides":[35],"is":[36],"critical":[37],"advancing":[39],"these":[40],"clinical":[41,210],"applications.":[42],"While":[43],"several":[44],"computational":[45],"tools":[46,145],"have":[47,131],"been":[48],"developed,":[49],"they":[50],"neglect":[51],"directional":[53],"semantics":[54],"inherent":[55],"in":[56,164,209],"sequence":[57,101],"data,":[58],"which":[59,116],"are":[60],"essential":[61],"accurately":[63,120],"characterizing":[64],"TCR-peptide":[65,207],"interactions.":[66],"RESULTS:":[67],"To":[68],"address":[69],"this":[70],"gap,":[71],"we":[72],"develop":[73],"TPepRet,":[74],"an":[75,202],"innovative":[76],"model":[77],"that":[78,192],"integrates":[79],"subsequence":[80],"mining":[81],"with":[82,103],"semantic":[83,123],"integration":[84],"capabilities.":[85],"TPepRet":[86,118,133,193,199],"combines":[87],"strengths":[89],"of":[90,137,150,155,161,168],"Bidirectional":[92],"Gated":[93],"Recurrent":[94],"Unit":[95],"(BiGRU)":[96],"network":[97],"capturing":[99],"bidirectional":[100],"dependencies":[102],"Large":[105],"Language":[106],"Model":[107],"framework":[108],"to":[109,119,134,184],"analyze":[110],"subsequences":[111],"global":[113],"sequences":[114],"comprehensively,":[115],"enables":[117],"decipher":[121],"relationship":[125],"peptides.":[129],"We":[130,197],"evaluated":[132],"range":[136],"challenging":[138],"scenarios,":[139],"including":[140],"performance":[141],"benchmarking":[142],"against":[143,176],"other":[144],"using":[146],"diverse":[147],"datasets,":[148,181],"analysis":[149],"peptide":[151],"preferences,":[153],"characterization":[154],"T":[156],"cells":[157],"clonal":[158],"expansion,":[159],"identification":[160],"true":[162],"binder":[163],"complex":[165],"environments,":[166],"assessment":[167],"key":[169],"sites":[171],"through":[172],"alanine":[173],"scanning,":[174],"validation":[175],"expression":[177],"rates":[178],"from":[179,221],"large-scale":[180],"ability":[183],"screen":[185],"SARS-CoV-2":[186],"TCRs.":[187],"The":[188,215],"comprehensive":[189],"results":[190],"suggest":[191],"outperforms":[194],"existing":[195],"tools.":[196],"believe":[198],"will":[200],"become":[201],"effective":[203],"tool":[204],"understanding":[206],"treatment.":[211],"AVAILABILITY":[212],"AND":[213],"IMPLEMENTATION:":[214],"source":[216],"code":[217],"can":[218],"be":[219],"obtained":[220],"https://github.com/CSUBioGroup/TPepRet.git.":[222]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
