{"id":"https://openalex.org/W4288421309","doi":"https://doi.org/10.1145/3535508.3545545","title":"Incorporating antigen processing into CD4+ T cell epitope prediction with integer linear programming","display_name":"Incorporating antigen processing into CD4+ T cell epitope prediction with integer linear programming","publication_year":2022,"publication_date":"2022-07-28","ids":{"openalex":"https://openalex.org/W4288421309","doi":"https://doi.org/10.1145/3535508.3545545"},"language":"en","primary_location":{"id":"doi:10.1145/3535508.3545545","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3535508.3545545","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 13th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5074877602","display_name":"Avik Bhattacharya","orcid":"https://orcid.org/0000-0003-4319-9235"},"institutions":[{"id":"https://openalex.org/I114832834","display_name":"Tulane University","ror":"https://ror.org/04vmvtb21","country_code":"US","type":"education","lineage":["https://openalex.org/I114832834"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Avik Bhattacharya","raw_affiliation_strings":["Tulane University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tulane University","institution_ids":["https://openalex.org/I114832834"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008914400","display_name":"Molly C. Lyons","orcid":null},"institutions":[{"id":"https://openalex.org/I114832834","display_name":"Tulane University","ror":"https://ror.org/04vmvtb21","country_code":"US","type":"education","lineage":["https://openalex.org/I114832834"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Molly C. Lyons","raw_affiliation_strings":["Tulane University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tulane University","institution_ids":["https://openalex.org/I114832834"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068670429","display_name":"Samuel J. Landry","orcid":"https://orcid.org/0000-0002-4082-0543"},"institutions":[{"id":"https://openalex.org/I114832834","display_name":"Tulane University","ror":"https://ror.org/04vmvtb21","country_code":"US","type":"education","lineage":["https://openalex.org/I114832834"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Samuel J. Landry","raw_affiliation_strings":["Tulane University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tulane University","institution_ids":["https://openalex.org/I114832834"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063192197","display_name":"Ramgopal R. Mettu","orcid":"https://orcid.org/0000-0001-9479-9156"},"institutions":[{"id":"https://openalex.org/I114832834","display_name":"Tulane University","ror":"https://ror.org/04vmvtb21","country_code":"US","type":"education","lineage":["https://openalex.org/I114832834"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ramgopal R. Mettu","raw_affiliation_strings":["Tulane University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tulane University","institution_ids":["https://openalex.org/I114832834"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.2599,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.51886869,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"10"},"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/T10580","display_name":"Immunotherapy and Immune Responses","score":0.9997000098228455,"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/T10031","display_name":"T-cell and B-cell Immunology","score":0.9976999759674072,"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":0.9565078020095825},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.7069305181503296},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5617097616195679},{"id":"https://openalex.org/keywords/integer-programming","display_name":"Integer programming","score":0.5228539109230042},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.5082718729972839},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4800197184085846},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.41624271869659424},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3324722945690155},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.2785719633102417},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.15337347984313965},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.15122941136360168}],"concepts":[{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.9565078020095825},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.7069305181503296},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5617097616195679},{"id":"https://openalex.org/C56086750","wikidata":"https://www.wikidata.org/wiki/Q6042592","display_name":"Integer programming","level":2,"score":0.5228539109230042},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.5082718729972839},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4800197184085846},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.41624271869659424},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3324722945690155},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.2785719633102417},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.15337347984313965},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.15122941136360168}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3535508.3545545","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3535508.3545545","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 13th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W1537564388","https://openalex.org/W1598405580","https://openalex.org/W1964775314","https://openalex.org/W1966639864","https://openalex.org/W1974449526","https://openalex.org/W2002873117","https://openalex.org/W2018196259","https://openalex.org/W2058466413","https://openalex.org/W2065887759","https://openalex.org/W2067878569","https://openalex.org/W2073508173","https://openalex.org/W2076551443","https://openalex.org/W2076826583","https://openalex.org/W2102004952","https://openalex.org/W2102056663","https://openalex.org/W2106871637","https://openalex.org/W2107019239","https://openalex.org/W2109257525","https://openalex.org/W2112445289","https://openalex.org/W2120399005","https://openalex.org/W2130889202","https://openalex.org/W2146239303","https://openalex.org/W2150750467","https://openalex.org/W2166572749","https://openalex.org/W2169540192","https://openalex.org/W2172210116","https://openalex.org/W2279917062","https://openalex.org/W2310845402","https://openalex.org/W2575902167","https://openalex.org/W2625955672","https://openalex.org/W2724264513","https://openalex.org/W3016853422","https://openalex.org/W3122458452"],"related_works":["https://openalex.org/W2021824670","https://openalex.org/W2009867644","https://openalex.org/W2363997565","https://openalex.org/W1981120125","https://openalex.org/W3036615648","https://openalex.org/W2408448169","https://openalex.org/W2182598264","https://openalex.org/W2075879923","https://openalex.org/W1978626146","https://openalex.org/W2060253881"],"abstract_inverted_index":{"CD4+":[0],"T-cell":[1],"receptors":[2],"recognize":[3],"peptide-MHCII":[4,52],"complexes":[5],"displayed":[6],"on":[7,167],"the":[8,39,49,71,145],"surface":[9],"of":[10,41,51,73,147,171],"antigen-presenting":[11],"cells":[12],"to":[13,24,67,75,88,91,143],"induce":[14,33],"an":[15,31,65,137],"immune":[16],"response.":[17],"A":[18],"fundamental":[19],"problem":[20,40],"in":[21,30,48,70,129,184],"immunology":[22],"is":[23,38],"characterize":[25],"which":[26,76],"peptides":[27,54,74],"(i.e.,":[28],"epitopes)":[29],"antigen":[32,66,118,148],"such":[34],"a":[35,83,155],"response;":[36],"this":[37,133],"computational":[42],"epitope":[43,107,161],"prediction.":[44,108,162],"To":[45],"be":[46,62,68],"presented":[47],"form":[50,92],"complex,":[53],"must":[55],"satisfy":[56],"two":[57],"important":[58],"criteria:":[59],"they":[60],"should":[61,81],"processed":[63],"from":[64],"available":[69],"pool":[72],"MHCII":[77,89],"can":[78],"bind":[79],"and":[80,102,120,150,157,176,178,182],"have":[82,113,121],"sufficiently":[84],"high":[85],"binding":[86,152],"affinity":[87],"molecules":[90],"stable":[93],"complexes.":[94],"This":[95],"latter":[96],"phenomenon":[97],"has":[98,125],"been":[99],"studied":[100],"widely":[101],"used":[103],"almost":[104],"exclusively":[105],"for":[106,116,160],"In":[109,132],"prior":[110],"work":[111],"we":[112,135],"developed":[114],"methods":[115],"modeling":[117],"processing":[119,149],"shown":[122],"that":[123,153],"it":[124],"significant":[126],"predictive":[127],"power":[128],"predicting":[130],"epitopes.":[131],"paper,":[134],"propose":[136],"integer":[138],"linear":[139],"programming":[140],"(ILP)":[141],"approach":[142],"combine":[144],"contributions":[146],"peptide":[151],"provides":[154],"holistic":[156],"flexible":[158],"framework":[159],"We":[163],"validate":[164],"our":[165],"results":[166],"data":[168],"sets":[169],"comprising":[170],"antigens":[172],"associated":[173],"with":[174],"tumors":[175],"pathogens":[177],"show":[179],"consistent":[180],"enrichment":[181],"improvement":[183],"accuracy":[185],"over":[186],"other":[187],"methods.":[188]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
