{"id":"https://openalex.org/W1768175145","doi":"https://doi.org/10.1093/bioinformatics/btv371","title":"High-order neural networks and kernel methods for peptide-MHC binding prediction","display_name":"High-order neural networks and kernel methods for peptide-MHC binding prediction","publication_year":2015,"publication_date":"2015-07-23","ids":{"openalex":"https://openalex.org/W1768175145","doi":"https://doi.org/10.1093/bioinformatics/btv371","mag":"1768175145","pmid":"https://pubmed.ncbi.nlm.nih.gov/26206306"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv371","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv371","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/22/3600/49036320/bioinformatics_31_22_3600.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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/22/3600/49036320/bioinformatics_31_22_3600.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028780139","display_name":"Pavel P. Kuksa","orcid":"https://orcid.org/0000-0003-2248-6403"},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pavel P. Kuksa","raw_affiliation_strings":["1 Institute for Biomedical Informatics,","2 Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA,","3 Department of Machine Learning, NEC Laboratories America, Princeton, NJ 08540, USA,"],"affiliations":[{"raw_affiliation_string":"1 Institute for Biomedical Informatics,","institution_ids":[]},{"raw_affiliation_string":"2 Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA,","institution_ids":["https://openalex.org/I79576946"]},{"raw_affiliation_string":"3 Department of Machine Learning, NEC Laboratories America, Princeton, NJ 08540, USA,","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065576006","display_name":"Martin Renqiang Min","orcid":"https://orcid.org/0000-0002-8563-6133"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Martin Renqiang Min","raw_affiliation_strings":["3 Department of Machine Learning, NEC Laboratories America, Princeton, NJ 08540, USA,"],"affiliations":[{"raw_affiliation_string":"3 Department of Machine Learning, NEC Laboratories America, Princeton, NJ 08540, USA,","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013978810","display_name":"Rishabh Dugar","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Rishabh Dugar","raw_affiliation_strings":["3 Department of Machine Learning, NEC Laboratories America, Princeton, NJ 08540, USA,"],"affiliations":[{"raw_affiliation_string":"3 Department of Machine Learning, NEC Laboratories America, Princeton, NJ 08540, USA,","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042321575","display_name":"Mark Gerstein","orcid":"https://orcid.org/0000-0002-9746-3719"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]},{"id":"https://openalex.org/I4210150971","display_name":"Institute of Molecular Biology and Biophysics","ror":"https://ror.org/051f11n17","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210110862","https://openalex.org/I4210150971"]}],"countries":["RU","US"],"is_corresponding":true,"raw_author_name":"Mark Gerstein","raw_affiliation_strings":["4 Program of Computational Biology and Bioinformatics and","5 Department of Molecular Biophysics and Biochemistry and","6 Department of Computer Science, Yale University, New Haven, CT 06511, USA"],"affiliations":[{"raw_affiliation_string":"4 Program of Computational Biology and Bioinformatics and","institution_ids":[]},{"raw_affiliation_string":"5 Department of Molecular Biophysics and Biochemistry and","institution_ids":["https://openalex.org/I4210150971"]},{"raw_affiliation_string":"6 Department of Computer Science, Yale University, New Haven, CT 06511, USA","institution_ids":["https://openalex.org/I32971472"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5042321575","https://openalex.org/A5065576006"],"corresponding_institution_ids":["https://openalex.org/I32971472","https://openalex.org/I4210150971"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.3197,"has_fulltext":false,"cited_by_count":40,"citation_normalized_percentile":{"value":0.92570233,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"31","issue":"22","first_page":"3600","last_page":"3607"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9943000078201294,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9891999959945679,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6574127674102783},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.6390432119369507},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4879738688468933},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.4774535298347473},{"id":"https://openalex.org/keywords/major-histocompatibility-complex","display_name":"Major histocompatibility complex","score":0.4223778247833252},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4138606786727905},{"id":"https://openalex.org/keywords/order","display_name":"Order (exchange)","score":0.4127453565597534},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3784927725791931},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.20154926180839539},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18515366315841675},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.16565504670143127},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.11351805925369263},{"id":"https://openalex.org/keywords/discrete-mathematics","display_name":"Discrete mathematics","score":0.10874682664871216}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6574127674102783},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.6390432119369507},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4879738688468933},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.4774535298347473},{"id":"https://openalex.org/C207936829","wikidata":"https://www.wikidata.org/wiki/Q423163","display_name":"Major histocompatibility complex","level":3,"score":0.4223778247833252},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4138606786727905},{"id":"https://openalex.org/C182306322","wikidata":"https://www.wikidata.org/wiki/Q1779371","display_name":"Order (exchange)","level":2,"score":0.4127453565597534},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3784927725791931},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.20154926180839539},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18515366315841675},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.16565504670143127},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.11351805925369263},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.10874682664871216},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C10138342","wikidata":"https://www.wikidata.org/wiki/Q43015","display_name":"Finance","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D008285","descriptor_name":"Major Histocompatibility Complex","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008285","descriptor_name":"Major Histocompatibility Complex","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008285","descriptor_name":"Major Histocompatibility Complex","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"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":"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":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019540","descriptor_name":"Area Under Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019540","descriptor_name":"Area Under Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019540","descriptor_name":"Area Under Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btv371","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv371","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/22/3600/49036320/bioinformatics_31_22_3600.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26206306","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26206306","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:CiteSeerX.psu:10.1.1.1004.1454","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1004.1454","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2015/07/22/bioinformatics.btv371.full.pdf","raw_type":"text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:31/22/3600","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/22/3600","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv371","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv371","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/22/3600/49036320/bioinformatics_31_22_3600.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1768175145.pdf","grobid_xml":"https://content.openalex.org/works/W1768175145.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W17594683","https://openalex.org/W186232887","https://openalex.org/W1824426708","https://openalex.org/W2012385803","https://openalex.org/W2012523084","https://openalex.org/W2020564539","https://openalex.org/W2028339001","https://openalex.org/W2040713134","https://openalex.org/W2063409538","https://openalex.org/W2072128103","https://openalex.org/W2072784497","https://openalex.org/W2074551195","https://openalex.org/W2076639605","https://openalex.org/W2103498243","https://openalex.org/W2110574412","https://openalex.org/W2111066113","https://openalex.org/W2116064496","https://openalex.org/W2119574220","https://openalex.org/W2125732073","https://openalex.org/W2126952406","https://openalex.org/W2136922672","https://openalex.org/W2143797877","https://openalex.org/W2150286046","https://openalex.org/W2153531183","https://openalex.org/W2168688111","https://openalex.org/W3105403777","https://openalex.org/W4231109964","https://openalex.org/W6600695662","https://openalex.org/W6607473935","https://openalex.org/W6681474766"],"related_works":["https://openalex.org/W1996781584","https://openalex.org/W2961085424","https://openalex.org/W2391251536","https://openalex.org/W2362198218","https://openalex.org/W2019521278","https://openalex.org/W1984922432","https://openalex.org/W2375008505","https://openalex.org/W2086348228","https://openalex.org/W2350679292","https://openalex.org/W1982750869"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":12},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}