{"id":"https://openalex.org/W7164911704","doi":"https://doi.org/10.1093/bib/bbag310","title":"Cytokine-driven immunogenicity prediction: integrating HLA binding and cytokine induction","display_name":"Cytokine-driven immunogenicity prediction: integrating HLA binding and cytokine induction","publication_year":2026,"publication_date":"2026-05-01","ids":{"openalex":"https://openalex.org/W7164911704","doi":"https://doi.org/10.1093/bib/bbag310","pmid":"https://pubmed.ncbi.nlm.nih.gov/42302278"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbag310","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag310","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bib/bbag310","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5138712294","display_name":"Alexander Gavrilenko","orcid":"https://orcid.org/0009-0007-0893-8895"},"institutions":[{"id":"https://openalex.org/I1315649409","display_name":"Institute on Taxation and Economic Policy","ror":"https://ror.org/00w9dm031","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1315649409"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexander Gavrilenko","raw_affiliation_strings":["AIDD , AXXX, 6c2 Presnenskaya emb, Moscow ,"],"raw_orcid":"https://orcid.org/0009-0007-0893-8895","affiliations":[{"raw_affiliation_string":"AIDD , AXXX, 6c2 Presnenskaya emb, Moscow ,","institution_ids":["https://openalex.org/I1315649409"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073407846","display_name":"Maria Sindeeva","orcid":"https://orcid.org/0000-0002-1629-7756"},"institutions":[{"id":"https://openalex.org/I1315649409","display_name":"Institute on Taxation and Economic Policy","ror":"https://ror.org/00w9dm031","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1315649409"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maria Sindeeva","raw_affiliation_strings":["AIDD , AXXX, 6c2 Presnenskaya emb, Moscow ,"],"raw_orcid":"https://orcid.org/0000-0002-1629-7756","affiliations":[{"raw_affiliation_string":"AIDD , AXXX, 6c2 Presnenskaya emb, Moscow ,","institution_ids":["https://openalex.org/I1315649409"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020182590","display_name":"Tatiana Shashkova","orcid":"https://orcid.org/0000-0002-8754-8727"},"institutions":[{"id":"https://openalex.org/I1315649409","display_name":"Institute on Taxation and Economic Policy","ror":"https://ror.org/00w9dm031","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1315649409"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Tatiana Shashkova","raw_affiliation_strings":["AIDD , AXXX, 6c2 Presnenskaya emb, Moscow ,"],"raw_orcid":"https://orcid.org/0000-0002-8754-8727","affiliations":[{"raw_affiliation_string":"AIDD , AXXX, 6c2 Presnenskaya emb, Moscow ,","institution_ids":["https://openalex.org/I1315649409"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5020182590"],"corresponding_institution_ids":["https://openalex.org/I1315649409"],"apc_list":{"value":3885,"currency":"USD","value_usd":3885},"apc_paid":{"value":3885,"currency":"USD","value_usd":3885},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.55244109,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"3","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":0.9732999801635742,"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":0.9732999801635742,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.014800000004470348,"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/T11103","display_name":"Antimicrobial Peptides and Activities","score":0.004000000189989805,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"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/immunogenicity","display_name":"Immunogenicity","score":0.8808000087738037},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.6804999709129333},{"id":"https://openalex.org/keywords/cytokine","display_name":"Cytokine","score":0.6628999710083008},{"id":"https://openalex.org/keywords/human-leukocyte-antigen","display_name":"Human leukocyte antigen","score":0.6003000140190125},{"id":"https://openalex.org/keywords/major-histocompatibility-complex","display_name":"Major histocompatibility complex","score":0.4636000096797943},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.3984000086784363}],"concepts":[{"id":"https://openalex.org/C2780868878","wikidata":"https://www.wikidata.org/wiki/Q1660197","display_name":"Immunogenicity","level":3,"score":0.8808000087738037},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.6804999709129333},{"id":"https://openalex.org/C2778690821","wikidata":"https://www.wikidata.org/wiki/Q212354","display_name":"Cytokine","level":2,"score":0.6628999710083008},{"id":"https://openalex.org/C188280979","wikidata":"https://www.wikidata.org/wiki/Q911125","display_name":"Human leukocyte antigen","level":3,"score":0.6003000140190125},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5874999761581421},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.5317999720573425},{"id":"https://openalex.org/C207936829","wikidata":"https://www.wikidata.org/wiki/Q423163","display_name":"Major histocompatibility complex","level":3,"score":0.4636000096797943},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.43709999322891235},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.3984000086784363},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.38769999146461487},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.38449999690055847},{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.3280999958515167},{"id":"https://openalex.org/C83464605","wikidata":"https://www.wikidata.org/wiki/Q575296","display_name":"Antigen presentation","level":4,"score":0.326200008392334},{"id":"https://openalex.org/C2779341262","wikidata":"https://www.wikidata.org/wiki/Q182581","display_name":"Immunity","level":3,"score":0.30480000376701355},{"id":"https://openalex.org/C193419808","wikidata":"https://www.wikidata.org/wiki/Q1645075","display_name":"Acquired immune system","level":3,"score":0.28130000829696655},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.2700999975204468},{"id":"https://openalex.org/C2777702733","wikidata":"https://www.wikidata.org/wiki/Q1356761","display_name":"Immune tolerance","level":3,"score":0.25690001249313354}],"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":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095763","descriptor_name":"Immunoinformatics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095763","descriptor_name":"Immunoinformatics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095763","descriptor_name":"Immunoinformatics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095763","descriptor_name":"Immunoinformatics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098437","descriptor_name":"Prediction Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098437","descriptor_name":"Prediction Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098437","descriptor_name":"Prediction Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098437","descriptor_name":"Prediction Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006680","descriptor_name":"HLA Antigens","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D006680","descriptor_name":"HLA Antigens","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D006680","descriptor_name":"HLA Antigens","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D006680","descriptor_name":"HLA Antigens","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D006680","descriptor_name":"HLA Antigens","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D006680","descriptor_name":"HLA Antigens","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D006680","descriptor_name":"HLA Antigens","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D006680","descriptor_name":"HLA Antigens","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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":"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":"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":"D016207","descriptor_name":"Cytokines","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D016207","descriptor_name":"Cytokines","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D016207","descriptor_name":"Cytokines","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D016207","descriptor_name":"Cytokines","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D016207","descriptor_name":"Cytokines","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D016207","descriptor_name":"Cytokines","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D016207","descriptor_name":"Cytokines","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D016207","descriptor_name":"Cytokines","qualifier_ui":"Q000378","qualifier_name":"metabolism","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},{"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/bib/bbag310","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag310","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:42302278","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42302278","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":"Briefings in bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13271414","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13271414/","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbag310","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag310","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W2024831496","https://openalex.org/W2029836713","https://openalex.org/W2031501484","https://openalex.org/W2100350770","https://openalex.org/W2102237050","https://openalex.org/W2102367710","https://openalex.org/W2106684817","https://openalex.org/W2114850508","https://openalex.org/W2123169315","https://openalex.org/W2148143831","https://openalex.org/W2152014155","https://openalex.org/W2153060237","https://openalex.org/W2167751983","https://openalex.org/W2588895177","https://openalex.org/W2595452534","https://openalex.org/W2806925824","https://openalex.org/W2995494055","https://openalex.org/W3016853422","https://openalex.org/W3025320502","https://openalex.org/W4200448109","https://openalex.org/W4280537238","https://openalex.org/W4290738903","https://openalex.org/W4307188346","https://openalex.org/W4317374308","https://openalex.org/W4388126046","https://openalex.org/W4389086850","https://openalex.org/W4404054932","https://openalex.org/W4404225840","https://openalex.org/W4404458588","https://openalex.org/W4404511368","https://openalex.org/W4408333972","https://openalex.org/W4412152241","https://openalex.org/W4412461859"],"related_works":[],"abstract_inverted_index":{"Cytokines":[0],"are":[1,140],"central":[2],"to":[3,12,62,89,105,131,152],"the":[4,30,64,135,164,186],"immune":[5,31,68,172,179],"response,":[6,32],"determining":[7],"whether":[8],"T-cell":[9],"activation":[10],"leads":[11],"protective":[13],"immunity":[14],"or":[15,54],"tolerance.":[16],"The":[17],"secretion":[18,108],"of":[19,67,95],"key":[20],"cytokines":[21],"such":[22],"as":[23],"IFN-$\\gamma$,":[24],"IL-2,":[25],"IL-4,":[26],"and":[27,37,84,112,148,170,181],"IL-10":[28],"shapes":[29],"influencing":[33],"its":[34],"presence,":[35],"pathways,":[36],"magnitude.":[38],"While":[39],"most":[40],"existing":[41],"computational":[42,77],"methods":[43],"for":[44],"predicting":[45,178],"peptide":[46,96,111,149],"immunogenicity":[47,156],"typically":[48],"focus":[49],"on":[50,110,134,185],"either":[51],"cytokine":[52,82,107,121,138],"induction":[53,83],"histocompatibility":[55],"complex":[56],"binding":[57,86,145],"affinity":[58,87,146],"separately,":[59],"they":[60],"fail":[61],"capture":[63],"full":[65],"complexity":[66],"activation.":[69],"In":[70],"this":[71],"study,":[72],"we":[73,99],"introduce":[74],"a":[75,91,154],"two-stage":[76],"framework":[78],"that":[79],"integrates":[80],"both":[81],"HLA":[85,144],"predictions":[88,147],"provide":[90],"more":[92],"comprehensive":[93],"prediction":[94,123,158],"immunogenicity.":[97],"First,":[98],"develop":[100,153],"machine":[101],"learning":[102],"models":[103,117],"EpiLAMA-IL":[104],"predict":[106],"based":[109],"parent":[113],"protein":[114],"sequences.":[115],"These":[116,137],"outperform":[118],"current":[119],"state-of-the-art":[120],"release":[122],"methods,":[124],"achieving":[125],"ROC":[126],"AUC":[127],"from":[128],"0.79":[129],"up":[130],"0.92":[132],"depending":[133],"task.":[136],"scores":[139],"then":[141],"combined":[142],"with":[143],"physico-chemical":[150],"descriptors":[151],"composite":[155],"score":[157],"model":[159],"EpiLAMA-IM.":[160],"This":[161],"approach":[162],"bridges":[163],"gap":[165],"between":[166],"sequence-based":[167],"antigen":[168],"presentation":[169],"functional":[171],"outcomes,":[173],"offering":[174],"improved":[175],"accuracy":[176],"in":[177],"responses":[180],"achieves":[182],"MCC":[183],"0.47":[184],"CD4Episcore":[187],"dataset.":[188]},"counts_by_year":[],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2026-06-17T00:00:00"}
