{"id":"https://openalex.org/W4310949661","doi":"https://doi.org/10.1093/bioinformatics/btac788","title":"TCRconv: predicting recognition between T cell receptors and epitopes using contextualized motifs","display_name":"TCRconv: predicting recognition between T cell receptors and epitopes using contextualized motifs","publication_year":2022,"publication_date":"2022-12-07","ids":{"openalex":"https://openalex.org/W4310949661","doi":"https://doi.org/10.1093/bioinformatics/btac788","pmid":"https://pubmed.ncbi.nlm.nih.gov/36477794"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac788","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac788","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac788/48520736/btac788.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac788/48520736/btac788.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5026003946","display_name":"Emmi Jokinen","orcid":"https://orcid.org/0000-0002-0060-6868"},"institutions":[{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Emmi Jokinen","raw_affiliation_strings":["Department of Computer Science, Aalto University , Espoo 02150, Finland"],"raw_orcid":"https://orcid.org/0000-0002-0060-6868","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Aalto University , Espoo 02150, Finland","institution_ids":["https://openalex.org/I9927081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041028167","display_name":"Alexandru Dumitrescu","orcid":"https://orcid.org/0000-0003-0909-9484"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Alexandru Dumitrescu","raw_affiliation_strings":["Department of Computer Science, Aalto University , Espoo 02150, Finland","Helsinki Institute of Life Science, University of Helsinki , Helsinki 00014, Finland"],"raw_orcid":"https://orcid.org/0000-0003-0909-9484","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Aalto University , Espoo 02150, Finland","institution_ids":["https://openalex.org/I9927081"]},{"raw_affiliation_string":"Helsinki Institute of Life Science, University of Helsinki , Helsinki 00014, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058714222","display_name":"Jani Huuhtanen","orcid":"https://orcid.org/0000-0003-2750-4033"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I2800394112","display_name":"Helsinki University Hospital","ror":"https://ror.org/02e8hzf44","country_code":"FI","type":"healthcare","lineage":["https://openalex.org/I2800394112","https://openalex.org/I4210166427"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Jani Huuhtanen","raw_affiliation_strings":["Department of Clinical Chemistry and Hematology, Translational Immunology Research Program, University of Helsinki , Helsinki 00290, Finland","Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center , Helsinki 00290, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Clinical Chemistry and Hematology, Translational Immunology Research Program, University of Helsinki , Helsinki 00290, Finland","institution_ids":["https://openalex.org/I133731052"]},{"raw_affiliation_string":"Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center , Helsinki 00290, Finland","institution_ids":["https://openalex.org/I2800394112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061943951","display_name":"Vladimir Gligorijevi\u0107","orcid":"https://orcid.org/0000-0002-5165-0973"},"institutions":[{"id":"https://openalex.org/I4210107338","display_name":"Simons Foundation","ror":"https://ror.org/01cmst727","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210107338"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vladimir Gligorijevi\u0107","raw_affiliation_strings":["Center for Computational Biology (CCB), Flatiron Institute, Simons Foundation , New York, NY 10010, USA","Prescient Design, Genentech , New York, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biology (CCB), Flatiron Institute, Simons Foundation , New York, NY 10010, USA","institution_ids":["https://openalex.org/I4210107338"]},{"raw_affiliation_string":"Prescient Design, Genentech , New York, NY, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008868111","display_name":"Satu Mustjoki","orcid":"https://orcid.org/0000-0002-0816-8241"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I2800394112","display_name":"Helsinki University Hospital","ror":"https://ror.org/02e8hzf44","country_code":"FI","type":"healthcare","lineage":["https://openalex.org/I2800394112","https://openalex.org/I4210166427"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Satu Mustjoki","raw_affiliation_strings":["Department of Clinical Chemistry and Hematology, Translational Immunology Research Program, University of Helsinki , Helsinki 00290, Finland","Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center , Helsinki 00290, Finland","iCAN Digital Precision Cancer Medicine Flagship , Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Clinical Chemistry and Hematology, Translational Immunology Research Program, University of Helsinki , Helsinki 00290, Finland","institution_ids":["https://openalex.org/I133731052"]},{"raw_affiliation_string":"Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center , Helsinki 00290, Finland","institution_ids":["https://openalex.org/I2800394112"]},{"raw_affiliation_string":"iCAN Digital Precision Cancer Medicine Flagship , Helsinki, Finland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055203249","display_name":"Richard Bonneau","orcid":"https://orcid.org/0000-0003-4354-7906"},"institutions":[{"id":"https://openalex.org/I36672615","display_name":"Courant Institute of Mathematical Sciences","ror":"https://ror.org/037tm7f56","country_code":"US","type":"education","lineage":["https://openalex.org/I36672615","https://openalex.org/I57206974"]},{"id":"https://openalex.org/I4210107338","display_name":"Simons Foundation","ror":"https://ror.org/01cmst727","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210107338"]},{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Richard Bonneau","raw_affiliation_strings":["Center for Computational Biology (CCB), Flatiron Institute, Simons Foundation , New York, NY 10010, USA","Center for Data Science, New York University , New York, NY 10011, USA","Department of Computer Science, New York University, Courant Institute of Mathematical Sciences , New York, NY 10012, USA","Prescient Design, Genentech , New York, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biology (CCB), Flatiron Institute, Simons Foundation , New York, NY 10010, USA","institution_ids":["https://openalex.org/I4210107338"]},{"raw_affiliation_string":"Center for Data Science, New York University , New York, NY 10011, USA","institution_ids":["https://openalex.org/I57206974"]},{"raw_affiliation_string":"Department of Computer Science, New York University, Courant Institute of Mathematical Sciences , New York, NY 10012, USA","institution_ids":["https://openalex.org/I36672615","https://openalex.org/I57206974"]},{"raw_affiliation_string":"Prescient Design, Genentech , New York, NY, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101444999","display_name":"Markus Heinonen","orcid":"https://orcid.org/0000-0002-7741-2279"},"institutions":[{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Markus Heinonen","raw_affiliation_strings":["Department of Computer Science, Aalto University , Espoo 02150, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Aalto University , Espoo 02150, Finland","institution_ids":["https://openalex.org/I9927081"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049442192","display_name":"Harri L\u00e4hdesm\u00e4ki","orcid":"https://orcid.org/0000-0002-0373-139X"},"institutions":[{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Harri L\u00e4hdesm\u00e4ki","raw_affiliation_strings":["Department of Computer Science, Aalto University , Espoo 02150, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Aalto University , Espoo 02150, Finland","institution_ids":["https://openalex.org/I9927081"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5026003946","https://openalex.org/A5049442192"],"corresponding_institution_ids":["https://openalex.org/I9927081"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3171,"currency":"EUR","value_usd":3419},"fwci":1.8812,"has_fulltext":false,"cited_by_count":31,"citation_normalized_percentile":{"value":0.86581449,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"39","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":0.9635999798774719,"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":0.9635999798774719,"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":0.01720000058412552,"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/T10158","display_name":"Cancer Immunotherapy and Biomarkers","score":0.002899999963119626,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"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/epitope","display_name":"Epitope","score":0.8270465731620789},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5436685085296631},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.5237947702407837},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5141115784645081},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.46439889073371887},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.44212692975997925},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2793857157230377},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18642881512641907},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.1242520809173584}],"concepts":[{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.8270465731620789},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5436685085296631},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.5237947702407837},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5141115784645081},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.46439889073371887},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.44212692975997925},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2793857157230377},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18642881512641907},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.1242520809173584}],"mesh":[{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D000941","descriptor_name":"Antigens","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000941","descriptor_name":"Antigens","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000941","descriptor_name":"Antigens","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":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013601","descriptor_name":"T-Lymphocytes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013601","descriptor_name":"T-Lymphocytes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013601","descriptor_name":"T-Lymphocytes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btac788","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac788","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac788/48520736/btac788.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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:36477794","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36477794","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:aaltodoc.aalto.fi:123456789/119173","is_oa":true,"landing_page_url":"https://research.aalto.fi/en/publications/c90c7d0a-61c0-4f4f-9e3e-bacc95115c46","pdf_url":null,"source":{"id":"https://openalex.org/S4306401662","display_name":"Aaltodoc (Aalto University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I9927081","host_organization_name":"Aalto University","host_organization_lineage":["https://openalex.org/I9927081"],"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":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:helda.helsinki.fi:10138/356034","is_oa":true,"landing_page_url":"http://hdl.handle.net/10138/356034","pdf_url":null,"source":{"id":"https://openalex.org/S4210213322","display_name":"Ty\u00f6v\u00e4entutkimus Vuosikirja","issn_l":"0784-1272","issn":["0784-1272","1459-7780"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"publishedVersion"},{"id":"pmh:oai:pubmedcentral.nih.gov:9825763","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9825763","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"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/btac788","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac788","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac788/48520736/btac788.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":[{"id":"https://metadata.un.org/sdg/3","score":0.550000011920929,"display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G17168737","display_name":null,"funder_award_id":"313271","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G4551937887","display_name":null,"funder_award_id":"314445","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"}],"funders":[{"id":"https://openalex.org/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W1973639800","https://openalex.org/W2605177850","https://openalex.org/W2670890989","https://openalex.org/W2671261300","https://openalex.org/W2979330275","https://openalex.org/W3024643080","https://openalex.org/W3036326371","https://openalex.org/W3119872582","https://openalex.org/W3135351475","https://openalex.org/W3138156743","https://openalex.org/W3163602801","https://openalex.org/W3164046276","https://openalex.org/W4210792795","https://openalex.org/W6791129610"],"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/W2205639271","https://openalex.org/W2033914206","https://openalex.org/W2042327336"],"abstract_inverted_index":{"MOTIVATION:":[0],"T":[1,4,32,44,127],"cells":[2,45],"use":[3],"cell":[5,33,128],"receptors":[6],"(TCRs)":[7],"to":[8,103],"recognize":[9],"small":[10],"parts":[11],"of":[12,43],"antigens,":[13],"called":[14],"epitopes,":[15],"presented":[16],"by":[17,37],"major":[18],"histocompatibility":[19],"complexes.":[20],"Once":[21],"an":[22,26],"epitope":[23],"is":[24,29,139],"recognized,":[25],"immune":[27],"response":[28],"initiated":[30],"and":[31,35,60,76,92,101,107,130],"activation":[34],"proliferation":[36],"clonal":[38],"expansion":[39],"begin.":[40],"Clonal":[41],"populations":[42],"with":[46],"identical":[47],"TCRs":[48,91],"can":[49,123],"remain":[50],"in":[51,69],"the":[52,133],"body":[53],"for":[54,87],"years,":[55],"thus":[56],"forming":[57],"immunological":[58,63],"memory":[59],"potentially":[61],"mappable":[62],"signatures,":[64],"which":[65],"could":[66],"have":[67],"implications":[68],"clinical":[70],"applications":[71],"including":[72],"infectious":[73],"diseases,":[74],"autoimmunity":[75],"tumor":[77],"immunology.":[78],"RESULTS:":[79],"We":[80],"introduce":[81],"TCRconv,":[82],"a":[83,96],"deep":[84,97],"learning":[85],"model":[86,100],"predicting":[88],"recognition":[89],"between":[90],"epitopes.":[93],"TCRconv":[94,122,138],"uses":[95],"protein":[98],"language":[99],"convolutions":[102],"extract":[104],"contextualized":[105],"motifs":[106],"provides":[108],"state-of-the-art":[109],"TCR-epitope":[110],"prediction":[111],"accuracy.":[112],"Using":[113],"TCR":[114],"repertoires":[115],"from":[116],"COVID-19":[117],"patients,":[118],"we":[119],"demonstrate":[120],"that":[121],"provide":[124],"insight":[125],"into":[126],"dynamics":[129],"phenotypes":[131],"during":[132],"disease.":[134],"AVAILABILITY":[135],"AND":[136],"IMPLEMENTATION:":[137],"available":[140,148],"at":[141,149],"https://github.com/emmijokinen/tcrconv.":[142],"SUPPLEMENTARY":[143],"INFORMATION:":[144],"Supplementary":[145],"data":[146],"are":[147],"Bioinformatics":[150],"online.":[151]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":10}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
