{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,3]],"date-time":"2025-10-03T22:07:25Z","timestamp":1759529245284},"reference-count":39,"publisher":"Springer Science and Business Media LLC","issue":"S13","license":[{"start":{"date-parts":[[2015,12,1]],"date-time":"2015-12-01T00:00:00Z","timestamp":1448928000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2015,12]]},"DOI":"10.1186\/1471-2105-16-s13-s9","type":"journal-article","created":{"date-parts":[[2015,9,26]],"date-time":"2015-09-26T04:03:49Z","timestamp":1443240229000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Understanding and predicting binding between human leukocyte antigens (HLAs) and peptides by network analysis"],"prefix":"10.1186","volume":"16","author":[{"given":"Heng","family":"Luo","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hao","family":"Ye","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hui Wen","family":"Ng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leming","family":"Shi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Weida","family":"Tong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"William","family":"Mattes","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Donna","family":"Mendrick","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huixiao","family":"Hong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2015,12,1]]},"reference":[{"key":"7160_CR1","doi-asserted-by":"crossref","unstructured":"Complete sequence and gene map of a human major histocompatibility complex. The MHC sequencing consortium. Nature. 1999, 401 (6756): 921-923. 10.1038\/44853.","DOI":"10.1038\/44853"},{"issue":"11","key":"7160_CR2","doi-asserted-by":"publisher","first-page":"3985","DOI":"10.1073\/pnas.85.11.3985","volume":"85","author":"Y Bushkin","year":"1988","unstructured":"Bushkin Y, Demaria S, Le JM, Schwab R: Physical association between the CD8 and HLA class I molecules on the surface of activated human T lymphocytes. Proc Natl Acad Sci USA. 1988, 85 (11): 3985-3989. 10.1073\/pnas.85.11.3985.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"5","key":"7160_CR3","doi-asserted-by":"publisher","first-page":"1706","DOI":"10.1182\/blood.V99.5.1706","volume":"99","author":"GM Spaggiari","year":"2002","unstructured":"Spaggiari GM, Contini P, Carosio R, Arvigo M, Ghio M, Oddone D, et al: Soluble HLA class I molecules induce natural killer cell apoptosis through the engagement of CD8: evidence for a negative regulation exerted by members of the inhibitory receptor superfamily. Blood. 2002, 99 (5): 1706-1714. 10.1182\/blood.V99.5.1706.","journal-title":"Blood"},{"issue":"12","key":"7160_CR4","doi-asserted-by":"publisher","first-page":"3356","DOI":"10.1002\/eji.200636217","volume":"36","author":"A Mangalam","year":"2006","unstructured":"Mangalam A, Rodriguez M, David C: Role of MHC class II expressing CD4+ T cells in proteolipid protein(91-110)-induced EAE in HLA-DR3 transgenic mice. Eur J Immunol. 2006, 36 (12): 3356-3370. 10.1002\/eji.200636217.","journal-title":"Eur J Immunol"},{"issue":"1","key":"7160_CR5","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1002\/jlb.66.1.105","volume":"66","author":"P Poncet","year":"1999","unstructured":"Poncet P, Arock M, David B: MHC class II-dependent activation of CD4+ T cell hybridomas by human mast cells through superantigen presentation. J Leukoc Biol. 1999, 66 (1): 105-112.","journal-title":"J Leukoc Biol"},{"issue":"Database issue","key":"7160_CR6","doi-asserted-by":"publisher","first-page":"D1222","DOI":"10.1093\/nar\/gks949","volume":"41","author":"J Robinson","year":"2013","unstructured":"Robinson J, Halliwell JA, McWilliam H, Lopez R, Parham P, Marsh SG: The IMGT\/HLA database. Nucleic Acids Res. 2013, 41 (Database issue): D1222-D1227.","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"7160_CR7","doi-asserted-by":"publisher","first-page":"D913","DOI":"10.1093\/nar\/gkq1128","volume":"39","author":"FF Gonzalez-Galarza","year":"2011","unstructured":"Gonzalez-Galarza FF, Christmas S, Middleton D, Jones AR: Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations. Nucleic Acids Res. 2011, 39 (Database issue): D913-D919.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"7160_CR8","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1007\/s002510050162","volume":"45","author":"G Chelvanayagam","year":"1996","unstructured":"Chelvanayagam G: A roadmap for HLA-A, HLA-B, and HLA-C peptide binding specificities. Immunogenetics. 1996, 45 (1): 15-26. 10.1007\/s002510050162.","journal-title":"Immunogenetics"},{"issue":"2","key":"7160_CR9","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1016\/0022-2836(91)90567-P","volume":"219","author":"MA Saper","year":"1991","unstructured":"Saper MA, Bjorkman PJ, Wiley DC: Refined structure of the human histocompatibility antigen HLA-A2 at 2.6 A resolution. J Mol Biol. 1991, 219 (2): 277-319. 10.1016\/0022-2836(91)90567-P.","journal-title":"J Mol Biol"},{"issue":"9308","key":"7160_CR10","doi-asserted-by":"publisher","first-page":"727","DOI":"10.1016\/S0140-6736(02)07873-X","volume":"359","author":"S Mallal","year":"2002","unstructured":"Mallal S, Nolan D, Witt C, Masel G, Martin AM, Moore C, et al: Association between presence of HLA-B*5701, HLA-DR7, and HLA-DQ3 and hypersensitivity to HIV-1 reverse-transcriptase inhibitor abacavir. Lancet. 2002, 359 (9308): 727-732. 10.1016\/S0140-6736(02)07873-X.","journal-title":"Lancet"},{"issue":"6","key":"7160_CR11","doi-asserted-by":"publisher","first-page":"568","DOI":"10.1056\/NEJMoa0706135","volume":"358","author":"S Mallal","year":"2008","unstructured":"Mallal S, Phillips E, Carosi G, Molina JM, Workman C, Tomazic J, et al: HLA-B*5701 screening for hypersensitivity to abacavir. N Engl J Med. 2008, 358 (6): 568-579. 10.1056\/NEJMoa0706135.","journal-title":"N Engl J Med"},{"issue":"12","key":"7160_CR12","doi-asserted-by":"publisher","first-page":"4180","DOI":"10.1073\/pnas.0307067101","volume":"101","author":"AM Martin","year":"2004","unstructured":"Martin AM, Nolan D, Gaudieri S, Almeida CA, Nolan R, James I, et al: Predisposition to abacavir hypersensitivity conferred by HLA-B*5701 and a haplotypic Hsp70-Hom variant. Proc Natl Acad Sci USA. 2004, 101 (12): 4180-4185. 10.1073\/pnas.0307067101.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"7","key":"7160_CR13","doi-asserted-by":"publisher","first-page":"816","DOI":"10.1038\/ng.379","volume":"41","author":"AK Daly","year":"2009","unstructured":"Daly AK, Donaldson PT, Bhatnagar P, Shen Y, Pe'er I, Floratos A, et al: HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin. Nat Genet. 2009, 41 (7): 816-819. 10.1038\/ng.379.","journal-title":"Nat Genet"},{"issue":"6982","key":"7160_CR14","doi-asserted-by":"publisher","first-page":"486","DOI":"10.1038\/428486a","volume":"428","author":"WH Chung","year":"2004","unstructured":"Chung WH, Hung SI, Hong HS, Hsih MS, Yang LC, Ho HC, et al: Medical genetics: a marker for Stevens-Johnson syndrome. Nature. 2004, 428 (6982): 486-10.1038\/428486a.","journal-title":"Nature"},{"key":"7160_CR15","doi-asserted-by":"crossref","unstructured":"Li J, Uetrecht JP: The danger hypothesis applied to idiosyncratic drug reactions. Handb Exp Pharmacol. 2010, 493-509. 196","DOI":"10.1007\/978-3-642-00663-0_18"},{"issue":"7404","key":"7160_CR16","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1038\/nature11147","volume":"486","author":"PT Illing","year":"2012","unstructured":"Illing PT, Vivian JP, Dudek NL, Kostenko L, Chen Z, Bharadwaj M, et al: Immune self-reactivity triggered by drug-modified HLA-peptide repertoire. Nature. 2012, 486 (7404): 554-558.","journal-title":"Nature"},{"key":"7160_CR17","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1146\/annurev-pharmtox-010611-134701","volume":"52","author":"M Bharadwaj","year":"2012","unstructured":"Bharadwaj M, Illing P, Theodossis A, Purcell AW, Rossjohn J, McCluskey J: Drug hypersensitivity and human leukocyte antigens of the major histocompatibility complex. Annu Rev Pharmacol Toxicol. 2012, 52: 401-431. 10.1146\/annurev-pharmtox-010611-134701.","journal-title":"Annu Rev Pharmacol Toxicol"},{"issue":"6","key":"7160_CR18","doi-asserted-by":"publisher","first-page":"1562","DOI":"10.1016\/j.jaci.2011.12.990","volume":"129","author":"CY Wei","year":"2012","unstructured":"Wei CY, Chung WH, Huang HW, Chen YT, Hung SI: Direct interaction between HLA-B and carbamazepine activates T cells in patients with Stevens-Johnson syndrome. J Allergy Clin Immunol. 2012, 129 (6): 1562-1569.e1565. 10.1016\/j.jaci.2011.12.990.","journal-title":"J Allergy Clin Immunol"},{"issue":"3","key":"7160_CR19","doi-asserted-by":"publisher","first-page":"296","DOI":"10.2174\/1386207318666150305144015","volume":"18","author":"H Luo","year":"2015","unstructured":"Luo H, Du T, Zhou P, Yang L, Mei H, Ng H, et al: Molecular docking to identify associations between drugs and class I human leukocyte antigens for predicting idiosyncratic drug reactions. Comb Chem High Throughput Screen. 2015, 18 (3): 296-304. 10.2174\/1386207318666150305144015.","journal-title":"Comb Chem High Throughput Screen"},{"key":"7160_CR20","doi-asserted-by":"publisher","first-page":"467852","DOI":"10.1155\/2013\/467852","volume":"2013","author":"S Paul","year":"2013","unstructured":"Paul S, Kolla RV, Sidney J, Weiskopf D, Fleri W, Kim Y, et al: Evaluating the immunogenicity of protein drugs by applying in vitro MHC binding data and the immune epitope database and analysis resource. Clin Dev Immunol. 2013, 2013: 467852-","journal-title":"Clin Dev Immunol"},{"issue":"8","key":"7160_CR21","doi-asserted-by":"publisher","first-page":"469","DOI":"10.1016\/j.autrev.2011.02.003","volume":"10","author":"WW Liao","year":"2011","unstructured":"Liao WW, Arthur JW: Predicting peptide binding to Major Histocompatibility Complex molecules. Autoimmunity reviews. 2011, 10 (8): 469-473. 10.1016\/j.autrev.2011.02.003.","journal-title":"Autoimmunity reviews"},{"issue":"4","key":"7160_CR22","doi-asserted-by":"publisher","first-page":"e1000048","DOI":"10.1371\/journal.pcbi.1000048","volume":"4","author":"P Wang","year":"2008","unstructured":"Wang P, Sidney J, Dow C, Mothe B, Sette A, Peters B: A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach. PLoS Comput Biol. 2008, 4 (4): e1000048-10.1371\/journal.pcbi.1000048.","journal-title":"PLoS Comput Biol"},{"issue":"10","key":"7160_CR23","doi-asserted-by":"publisher","first-page":"e13348","DOI":"10.1371\/journal.pone.0013348","volume":"5","author":"R Colak","year":"2010","unstructured":"Colak R, Moser F, Chu JS, Schonhuth A, Chen N, Ester M: Module discovery by exhaustive search for densely connected, co-expressed regions in biomolecular interaction networks. PloS One. 2010, 5 (10): e13348-10.1371\/journal.pone.0013348.","journal-title":"PloS One"},{"key":"7160_CR24","doi-asserted-by":"publisher","first-page":"066111","DOI":"10.1103\/PhysRevE.70.066111","volume":"70","author":"A Clauset","year":"2004","unstructured":"Clauset A, Newman ME, Moore C: Finding community structure in very large networks. Phys Rev E. 2004, 70: 066111-","journal-title":"Phys Rev E"},{"issue":"Database issue","key":"7160_CR25","doi-asserted-by":"publisher","first-page":"D854","DOI":"10.1093\/nar\/gkp1004","volume":"38","author":"R Vita","year":"2010","unstructured":"Vita R, Zarebski L, Greenbaum JA, Emami H, Hoof I, Salimi N, et al: The immune epitope database 2.0. Nucleic Acids Res. 2010, 38 (Database issue): D854-D862.","journal-title":"Nucleic Acids Res"},{"issue":"3-4","key":"7160_CR26","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1007\/s002510050595","volume":"50","author":"H Rammensee","year":"1999","unstructured":"Rammensee H, Bachmann J, Emmerich NP, Bachor OA, Stevanovic S: SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics. 1999, 50 (3-4): 213-219. 10.1007\/s002510050595.","journal-title":"Immunogenetics"},{"key":"7160_CR27","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1186\/1756-0500-2-61","volume":"2","author":"S Lata","year":"2009","unstructured":"Lata S, Bhasin M, Raghava GP: MHCBN 4.0: A database of MHC\/TAP binding peptides and T-cell epitopes. BMC Res Notes. 2009, 2: 61-10.1186\/1756-0500-2-61.","journal-title":"BMC Res Notes"},{"issue":"1","key":"7160_CR28","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1186\/1745-7580-1-4","volume":"1","author":"CP Toseland","year":"2005","unstructured":"Toseland CP, Clayton DJ, McSparron H, Hemsley SL, Blythe MJ, Paine K, et al: AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data. Immunome Res. 2005, 1 (1): 4-10.1186\/1745-7580-1-4.","journal-title":"Immunome Res"},{"key":"7160_CR29","volume-title":"Proceedings of the 1st International Forum on the Application and Management of Personal Electronic Information","author":"M van Meeteren","year":"2009","unstructured":"van Meeteren M, Poorthuis A, Dugundji E: Mapping communities in large virtual social networks. Proceedings of the 1st International Forum on the Application and Management of Personal Electronic Information. 2009, Cambridge"},{"issue":"10","key":"7160_CR30","doi-asserted-by":"publisher","first-page":"2731","DOI":"10.1093\/molbev\/msr121","volume":"28","author":"K Tamura","year":"2011","unstructured":"Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S: MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011, 28 (10): 2731-2739. 10.1093\/molbev\/msr121.","journal-title":"Mol Biol Evol"},{"key":"7160_CR31","first-page":"539","volume":"7","author":"F Sievers","year":"2011","unstructured":"Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, et al: Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Biol Evol. 2011, 7: 539-","journal-title":"Mol Biol Evol"},{"key":"7160_CR32","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1145\/371920.372071","volume-title":"Proceedings of the 10th international conference on World Wide Web","author":"B Sarwar","year":"2001","unstructured":"Sarwar B, Karypis G, Konstan J, Riedl J: Item-based collaborative filtering recommendation algorithms. Proceedings of the 10th international conference on World Wide Web. 2001, 285-295."},{"issue":"7","key":"7160_CR33","doi-asserted-by":"publisher","first-page":"e41064","DOI":"10.1371\/journal.pone.0041064","volume":"7","author":"F Cheng","year":"2012","unstructured":"Cheng F, Zhou Y, Li W, Liu G, Tang Y: Prediction of chemical-protein interactions network with weighted network-based inference method. PLoS One. 2012, 7 (7): e41064-10.1371\/journal.pone.0041064.","journal-title":"PLoS One"},{"issue":"5","key":"7160_CR34","doi-asserted-by":"publisher","first-page":"e1002503","DOI":"10.1371\/journal.pcbi.1002503","volume":"8","author":"F Cheng","year":"2012","unstructured":"Cheng F, Liu C, Jiang J, Lu W, Li W, Liu G, et al: Prediction of drug-target interactions and drug repositioning via network-based inference. PLoS Comput Biol. 2012, 8 (5): e1002503-10.1371\/journal.pcbi.1002503.","journal-title":"PLoS Comput Biol"},{"issue":"12","key":"7160_CR35","doi-asserted-by":"publisher","first-page":"1671","DOI":"10.1089\/cmb.2008.0115","volume":"16","author":"H Hong","year":"2009","unstructured":"Hong H, Hong Q, Perkins R, Shi L, Fang H, Su Z, et al: The accurate prediction of protein family from amino acid sequence by measuring features of sequence fragments. J Comput Biol. 2009, 16 (12): 1671-1688. 10.1089\/cmb.2008.0115.","journal-title":"J Comput Biol"},{"issue":"25","key":"7160_CR36","doi-asserted-by":"publisher","first-page":"9959","DOI":"10.1073\/pnas.1207934109","volume":"109","author":"DA Ostrov","year":"2012","unstructured":"Ostrov DA, Grant BJ, Pompeu YA, Sidney J, Harndahl M, Southwood S, et al: Drug hypersensitivity caused by alteration of the MHC-presented self-peptide repertoire. Proc Natl Acad Sci U S A. 2012, 109 (25): 9959-9964. 10.1073\/pnas.1207934109.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"8","key":"7160_CR37","doi-asserted-by":"publisher","first-page":"e796","DOI":"10.1371\/journal.pone.0000796","volume":"2","author":"M Nielsen","year":"2007","unstructured":"Nielsen M, Lundegaard C, Blicher T, Lamberth K, Harndahl M, Justesen S, et al: NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence. PLoS One. 2007, 2 (8): e796-10.1371\/journal.pone.0000796.","journal-title":"PLoS One"},{"key":"7160_CR38","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1186\/1471-2105-3-25","volume":"3","author":"P Donnes","year":"2002","unstructured":"Donnes P, Elofsson A: Prediction of MHC class I binding peptides, using SVMHC. BMC Bioinformatics. 2002, 3: 25-10.1186\/1471-2105-3-25.","journal-title":"BMC Bioinformatics"},{"key":"7160_CR39","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1186\/1471-2105-10-296","volume":"10","author":"M Nielsen","year":"2009","unstructured":"Nielsen M, Lund O: NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction. BMC Bioinformatics. 2009, 10: 296-10.1186\/1471-2105-10-296.","journal-title":"BMC Bioinformatics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-16-S13-S9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-16-S13-S9\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-16-S13-S9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T19:45:29Z","timestamp":1630611929000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-16-S13-S9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,12]]},"references-count":39,"journal-issue":{"issue":"S13","published-print":{"date-parts":[[2015,12]]}},"alternative-id":["7160"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-16-s13-s9","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,12]]},"assertion":[{"value":"1 December 2015","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S9"}}