{"id":"https://openalex.org/W4294908236","doi":"https://doi.org/10.1093/bib/bbac382","title":"Not all T cell epitopes are equally desired: a review of<i>in silico</i>tools for the prediction of cytokine-inducing potential of T-cell epitopes","display_name":"Not all T cell epitopes are equally desired: a review of<i>in silico</i>tools for the prediction of cytokine-inducing potential of T-cell epitopes","publication_year":2022,"publication_date":"2022-09-01","ids":{"openalex":"https://openalex.org/W4294908236","doi":"https://doi.org/10.1093/bib/bbac382","pmid":"https://pubmed.ncbi.nlm.nih.gov/36070623"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac382","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac382","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":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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067192427","display_name":"Sandeep Kumar Dhanda","orcid":"https://orcid.org/0000-0003-1381-7434"},"institutions":[{"id":"https://openalex.org/I1313298211","display_name":"St. Jude Children's Research Hospital","ror":"https://ror.org/02r3e0967","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1313298211","https://openalex.org/I2802152183"]},{"id":"https://openalex.org/I85461943","display_name":"Saveetha University","ror":"https://ror.org/0034me914","country_code":"IN","type":"education","lineage":["https://openalex.org/I85461943"]}],"countries":["IN","US"],"is_corresponding":true,"raw_author_name":"Sandeep Kumar Dhanda","raw_affiliation_strings":["Center for Transdisciplinary Research, Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical Science , Chennai, India","Department of Oncology, St Jude Children\u2019s Research Hospital , Memphis, Tennessee, USA -38015","Center for Transdisciplinary Research, Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical Science, Chennai, India"],"raw_orcid":"https://orcid.org/0000-0003-1381-7434","affiliations":[{"raw_affiliation_string":"Center for Transdisciplinary Research, Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical Science , Chennai, India","institution_ids":["https://openalex.org/I85461943"]},{"raw_affiliation_string":"Department of Oncology, St Jude Children\u2019s Research Hospital , Memphis, Tennessee, USA -38015","institution_ids":["https://openalex.org/I1313298211"]},{"raw_affiliation_string":"Center for Transdisciplinary Research, Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical Science, Chennai, India","institution_ids":["https://openalex.org/I85461943"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075299540","display_name":"Jitendra Malviya","orcid":"https://orcid.org/0000-0001-7501-0121"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jitendra Malviya","raw_affiliation_strings":["Department of Life Sciences and Biological Science, IES University Bhopal , India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Life Sciences and Biological Science, IES University Bhopal , India","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103132728","display_name":"Sudheer Gupta","orcid":"https://orcid.org/0000-0002-6836-6696"},"institutions":[{"id":"https://openalex.org/I4210100303","display_name":"Biotech Park","ror":"https://ror.org/00mv0vt78","country_code":"IN","type":"government","lineage":["https://openalex.org/I4210100303"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Sudheer Gupta","raw_affiliation_strings":["NGS & Bioinformatics Division, 3B BlackBio Biotech India Ltd., 7-C, Industrial Area , Govindpura, Bhopal, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NGS & Bioinformatics Division, 3B BlackBio Biotech India Ltd., 7-C, Industrial Area , Govindpura, Bhopal, India","institution_ids":["https://openalex.org/I4210100303"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5067192427","https://openalex.org/A5103132728"],"corresponding_institution_ids":["https://openalex.org/I1313298211","https://openalex.org/I4210100303","https://openalex.org/I85461943"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.5197,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.61830048,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"23","issue":"5","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":1.0,"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":1.0,"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":0.996399998664856,"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":0.9948999881744385,"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/epitope","display_name":"Epitope","score":0.9147857427597046},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.7737476825714111},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6328644156455994},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.5492808222770691},{"id":"https://openalex.org/keywords/t-cell","display_name":"T cell","score":0.5257409811019897},{"id":"https://openalex.org/keywords/cytokine","display_name":"Cytokine","score":0.5075896978378296},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.499798059463501},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.45641663670539856},{"id":"https://openalex.org/keywords/immunotherapy","display_name":"Immunotherapy","score":0.41723647713661194},{"id":"https://openalex.org/keywords/epitope-mapping","display_name":"Epitope mapping","score":0.4102104902267456},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.4089464545249939},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.37647849321365356}],"concepts":[{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.9147857427597046},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.7737476825714111},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6328644156455994},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.5492808222770691},{"id":"https://openalex.org/C2776090121","wikidata":"https://www.wikidata.org/wiki/Q193529","display_name":"T cell","level":3,"score":0.5257409811019897},{"id":"https://openalex.org/C2778690821","wikidata":"https://www.wikidata.org/wiki/Q212354","display_name":"Cytokine","level":2,"score":0.5075896978378296},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.499798059463501},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45641663670539856},{"id":"https://openalex.org/C2777701055","wikidata":"https://www.wikidata.org/wiki/Q1427096","display_name":"Immunotherapy","level":3,"score":0.41723647713661194},{"id":"https://openalex.org/C2781241564","wikidata":"https://www.wikidata.org/wiki/Q1347450","display_name":"Epitope mapping","level":4,"score":0.4102104902267456},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.4089464545249939},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.37647849321365356},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D001402","descriptor_name":"B-Lymphocytes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001402","descriptor_name":"B-Lymphocytes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001402","descriptor_name":"B-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":"D013601","descriptor_name":"T-Lymphocytes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014612","descriptor_name":"Vaccines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014612","descriptor_name":"Vaccines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014612","descriptor_name":"Vaccines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016207","descriptor_name":"Cytokines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016207","descriptor_name":"Cytokines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016207","descriptor_name":"Cytokines","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":true},{"descriptor_ui":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbac382","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac382","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":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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36070623","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36070623","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":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.6600000262260437,"id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":123,"referenced_works":["https://openalex.org/W1482271921","https://openalex.org/W1557599311","https://openalex.org/W1973980688","https://openalex.org/W1976214076","https://openalex.org/W1981106544","https://openalex.org/W1987628377","https://openalex.org/W1991461541","https://openalex.org/W2006249161","https://openalex.org/W2012166770","https://openalex.org/W2015759485","https://openalex.org/W2019711015","https://openalex.org/W2026527144","https://openalex.org/W2029202594","https://openalex.org/W2041820432","https://openalex.org/W2050658429","https://openalex.org/W2050906796","https://openalex.org/W2081716830","https://openalex.org/W2092304883","https://openalex.org/W2096015012","https://openalex.org/W2099500226","https://openalex.org/W2100350770","https://openalex.org/W2101005439","https://openalex.org/W2110574412","https://openalex.org/W2120467372","https://openalex.org/W2122842217","https://openalex.org/W2125014261","https://openalex.org/W2125732073","https://openalex.org/W2127635589","https://openalex.org/W2132609988","https://openalex.org/W2152186450","https://openalex.org/W2154509769","https://openalex.org/W2157009395","https://openalex.org/W2158355296","https://openalex.org/W2163706782","https://openalex.org/W2164205671","https://openalex.org/W2180512905","https://openalex.org/W2336694015","https://openalex.org/W2440607563","https://openalex.org/W2568893370","https://openalex.org/W2588895177","https://openalex.org/W2607286972","https://openalex.org/W2617038565","https://openalex.org/W2757372365","https://openalex.org/W2763611883","https://openalex.org/W2766220551","https://openalex.org/W2771547340","https://openalex.org/W2773845003","https://openalex.org/W2783102765","https://openalex.org/W2786914011","https://openalex.org/W2794956775","https://openalex.org/W2803285381","https://openalex.org/W2806925824","https://openalex.org/W2809165679","https://openalex.org/W2887293266","https://openalex.org/W2898389621","https://openalex.org/W2900127803","https://openalex.org/W2913828980","https://openalex.org/W2918929658","https://openalex.org/W2945153532","https://openalex.org/W2953065444","https://openalex.org/W2982769959","https://openalex.org/W2997888749","https://openalex.org/W3001644051","https://openalex.org/W3007974386","https://openalex.org/W3015044299","https://openalex.org/W3016853422","https://openalex.org/W3016922254","https://openalex.org/W3031211151","https://openalex.org/W3037309373","https://openalex.org/W3043122291","https://openalex.org/W3046477863","https://openalex.org/W3047935184","https://openalex.org/W3048101367","https://openalex.org/W3055872152","https://openalex.org/W3069141436","https://openalex.org/W3087999559","https://openalex.org/W3088621177","https://openalex.org/W3092381885","https://openalex.org/W3093114725","https://openalex.org/W3104792601","https://openalex.org/W3109460359","https://openalex.org/W3110768477","https://openalex.org/W3114520155","https://openalex.org/W3116245443","https://openalex.org/W3117693236","https://openalex.org/W3118097269","https://openalex.org/W3119878768","https://openalex.org/W3119894254","https://openalex.org/W3119974921","https://openalex.org/W3121970976","https://openalex.org/W3135293699","https://openalex.org/W3135333533","https://openalex.org/W3136283554","https://openalex.org/W3138433505","https://openalex.org/W3157601550","https://openalex.org/W3158261633","https://openalex.org/W3159193120","https://openalex.org/W3159532955","https://openalex.org/W3160609996","https://openalex.org/W3161175300","https://openalex.org/W3163720137","https://openalex.org/W3165745610","https://openalex.org/W3167140978","https://openalex.org/W3167976439","https://openalex.org/W3176607125","https://openalex.org/W3180713168","https://openalex.org/W3184818553","https://openalex.org/W3185715596","https://openalex.org/W3185748810","https://openalex.org/W3186768695","https://openalex.org/W3186999162","https://openalex.org/W3202367516","https://openalex.org/W4256407664","https://openalex.org/W4296588353","https://openalex.org/W6628771186","https://openalex.org/W6674565261","https://openalex.org/W6738672142","https://openalex.org/W6739276506","https://openalex.org/W6773285901","https://openalex.org/W6781118307","https://openalex.org/W6788192829","https://openalex.org/W6791168143","https://openalex.org/W6791443567"],"related_works":["https://openalex.org/W3189724180","https://openalex.org/W2471846512","https://openalex.org/W4214932605","https://openalex.org/W3096915742","https://openalex.org/W2393351343","https://openalex.org/W2019166448","https://openalex.org/W4214758967","https://openalex.org/W3006433770","https://openalex.org/W2444058223","https://openalex.org/W2800235700"],"abstract_inverted_index":{"Assessment":[0],"of":[1,22,47,85],"protective":[2],"or":[3],"harmful":[4],"T":[5,51,63],"cell":[6,49,52,64],"response":[7],"induced":[8],"by":[9],"any":[10,17],"antigenic":[11],"epitope":[12,65],"is":[13],"important":[14],"in":[15,55,75,94,100],"designing":[16],"immunotherapeutic":[18],"molecule.":[19],"The":[20,39],"understanding":[21],"cytokine":[23],"induction":[24],"potential":[25],"also":[26,70],"helps":[27],"us":[28],"to":[29],"monitor":[30],"antigen-specific":[31],"cellular":[32],"immune":[33],"responses":[34],"and":[35,50,73,97],"rational":[36],"vaccine":[37],"design.":[38],"classical":[40],"immunoinformatics":[41],"tools":[42],"served":[43],"well":[44],"for":[45,62],"prediction":[46,60],"B":[48],"epitopes.":[53],"However,":[54],"the":[56,59,76,82,101],"last":[57],"decade,":[58],"algorithms":[61],"inducing":[66],"specific":[67],"cytokines":[68],"have":[69],"been":[71],"developed":[72],"appreciated":[74],"scientific":[77],"community.":[78],"This":[79],"review":[80],"summarizes":[81],"current":[83],"status":[84],"such":[86],"tools,":[87],"their":[88,92],"applications,":[89],"background":[90],"algorithms,":[91],"use":[93],"experimental":[95],"setup":[96],"functionalities":[98],"available":[99],"tools/web":[102],"servers.":[103]},"counts_by_year":[{"year":2025,"cited_by_count":5},{"year":2022,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2022-09-07T00:00:00"}
