{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T05:33:15Z","timestamp":1773293595266,"version":"3.50.1"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: \u00a0In\u00a0vitro and in\u00a0vivo selection of vaccines is time consuming, expensive and the selected vaccines may not be able to provide protection against broad-spectrum viruses because of emerging antigenically novel disease strains. A powerful computational model that incorporates these protein\/DNA or RNA level fluctuations can effectively predict antigenically variant strains, and can minimize the amount of resources spent on exclusive serological testing of vaccines and make wide spectrum vaccines possible for many diseases. However, in silico vaccine prediction remains a grand challenge. To address the challenge, we investigate the use of linear and non-linear regression models to predict the antigenic similarity in foot-and-mouth disease virus strains and in influenza strains, where the structure and parameters of the non-linear model are optimized using an evolutionary algorithm (EA). In addition, we examine two different scoring methods for weighting the type of amino acid substitutions in the linear and non-linear models. We also test our models with some unseen data.<\/jats:p>\n               <jats:p>Results: We achieved the best prediction results on three datasets of SAT2 (Foot-and-Mouth disease), two datasets of serotype A (Foot-and-Mouth disease) and two datasets of influenza when the scoring method based on biochemical properties of amino acids is employed in combination with a non-linear regression model. Models based on substitutions in the antigenic areas performed better than those that took the entire exposed viral capsid proteins. A majority of the non-linear regression models optimized with the EA performed better than the linear and non-linear models whose parameters are estimated using the least-squares method. In addition, for the best models, optimized non-linear regression models consist of more terms than their linear counterparts, implying a non-linear nature of influences of amino acid substitutions. Our models were also tested on five recently generated FMDV datasets and the best model was able to achieve an 80% agreement rate.<\/jats:p>\n               <jats:p>Contact: \u00a0yaochu.jin@surrey.ac.uk or e.laing@surrey.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu768","type":"journal-article","created":{"date-parts":[[2014,11,21]],"date-time":"2014-11-21T01:18:58Z","timestamp":1416532738000},"page":"834-840","source":"Crossref","is-referenced-by-count":9,"title":["Evolutionary non-linear modelling for selecting vaccines against antigenically variable viruses"],"prefix":"10.1093","volume":"31","author":[{"given":"Tameera","family":"Rahman","sequence":"first","affiliation":[{"name":"1 Department of Computing, University of Surrey, Guildford GU2 7XH, UK, 2The Pirbright Institute, Pirbright GU24 0NF, UK and 3Department of Microbial and Cellular Sciences, University of Surrey, Guildford GU2 7XH, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mana","family":"Mahapatra","sequence":"additional","affiliation":[{"name":"1 Department of Computing, University of Surrey, Guildford GU2 7XH, UK, 2The Pirbright Institute, Pirbright GU24 0NF, UK and 3Department of Microbial and Cellular Sciences, University of Surrey, Guildford GU2 7XH, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emma","family":"Laing","sequence":"additional","affiliation":[{"name":"1 Department of Computing, University of Surrey, Guildford GU2 7XH, UK, 2The Pirbright Institute, Pirbright GU24 0NF, UK and 3Department of Microbial and Cellular Sciences, University of Surrey, Guildford GU2 7XH, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yaochu","family":"Jin","sequence":"additional","affiliation":[{"name":"1 Department of Computing, University of Surrey, Guildford GU2 7XH, UK, 2The Pirbright Institute, Pirbright GU24 0NF, UK and 3Department of Microbial and Cellular Sciences, University of Surrey, Guildford GU2 7XH, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,11,19]]},"reference":[{"key":"2023020116175737000_btu768-B1","doi-asserted-by":"crossref","DOI":"10.1887\/0750308958","volume-title":"Handbook of Evolutionary Computation","author":"Back","year":"1997"},{"key":"2023020116175737000_btu768-B2","doi-asserted-by":"crossref","DOI":"10.1142\/6493","volume-title":"Analysis of Biological Data: A Soft Computing Approach","author":"Bandyopadhyay","year":"2007"},{"key":"2023020116175737000_btu768-B3","doi-asserted-by":"crossref","first-page":"2107","DOI":"10.1016\/S0264-410X(00)00399-6","article-title":"The suitability of the emergency foot-and-mouth disease antigens held by the international vaccine bank within a global context","volume":"19","author":"Barnett","year":"2001","journal-title":"Vaccine"},{"key":"2023020116175737000_btu768-B4","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1002\/0470867302.ch14","article-title":"Amino acid properties and consequences of substitutions","volume":"317","author":"Betts","year":"2003","journal-title":"Bioinform. Genet."},{"key":"2023020116175737000_btu768-B5","first-page":"253","article-title":"Prediction of MHC binding peptides using artificial neural networks","volume-title":"Complex Systems: Mechanism of Adaptation","author":"Brusic","year":"1994"},{"key":"2023020116175737000_btu768-B6","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1006\/jmbi.2001.4510","article-title":"Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: structure-based assessment of amino acid variation","volume":"307","author":"Chasman","year":"2001","journal-title":"J. Mol. Biol."},{"key":"2023020116175737000_btu768-B7","volume-title":"A Concise Dictionary of Chemistry","author":"Daintith","year":"1990"},{"key":"2023020116175737000_btu768-B8","first-page":"345","article-title":"A model of evolutionary change in proteins","volume-title":"Atlas of Protein Sequence and Structure","author":"Dayhoff","year":"1978"},{"key":"2023020116175737000_btu768-B9","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/S0580-9517(02)32089-0","article-title":"Use of bioinformatics to predict MHC ligands and T-cell epitopes: application to epitope-driven vaccine design","volume":"32","author":"De Groot","year":"2002","journal-title":"Methods Microbiol."},{"key":"2023020116175737000_btu768-B10","first-page":"115","article-title":"Simulated binary crossover for continuous search space","volume":"9","author":"Deb","year":"1995","journal-title":"Complex Syst."},{"key":"2023020116175737000_btu768-B11","volume-title":"The Elements of Statistical Learning","author":"Friedman","year":"2001"},{"key":"2023020116175737000_btu768-B12","volume-title":"Genetic Algorithms in Search, Optimization and Machine Learning","author":"Goldberg","year":"1989"},{"key":"2023020116175737000_btu768-B13","doi-asserted-by":"crossref","DOI":"10.7551\/mitpress\/1090.001.0001","volume-title":"Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology, Control and Artificial Intelligence","author":"Holland","year":"1992"},{"key":"2023020116175737000_btu768-B14","doi-asserted-by":"crossref","first-page":"1385","DOI":"10.3201\/eid1008.040107","article-title":"Predicting antigenic variants of influenza a\/h3n2 viruses","volume":"10","author":"Lee","year":"2004","journal-title":"Emerg. Infect. Dis."},{"key":"2023020116175737000_btu768-B15","doi-asserted-by":"crossref","first-page":"8133","DOI":"10.1016\/j.vaccine.2007.09.039","article-title":"Identifying potential immunodominant positions and predicting antigenic variants of influenza a\/h3n2 viruses","volume":"25","author":"Lee","year":"2007","journal-title":"Vaccine"},{"key":"2023020116175737000_btu768-B16","volume-title":"Introduction to Protein Architecture: The Structural Biology of Proteins","author":"Lesk","year":"2001"},{"key":"2023020116175737000_btu768-B17","article-title":"Exploiting noisy and incomplete biological data for prediction and knowledge discovery","author":"Li","year":"2010"},{"key":"2023020116175737000_btu768-B18","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1093\/bioinformatics\/btm638","article-title":"Bioinformatics models for predicting antigenic variants of influenza a\/h3n2 virus","volume":"24","author":"Liao","year":"2008","journal-title":"Bioinformatics"},{"key":"2023020116175737000_btu768-B19","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1016\/0264-410X(94)00014-E","article-title":"Two novel t cell epitope prediction algorithms based on MHC-binding motifs; comparison of predicted and published epitopes from mycobacterium tuberculosis and HIV protein sequences","volume":"13","author":"Meister","year":"1995","journal-title":"Vaccine"},{"key":"2023020116175737000_btu768-B20","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1016\/S0140-6736(11)60407-8","article-title":"The next decade of vaccines: societal and scientific challenges","volume":"378","author":"Moxon","year":"2011","journal-title":"The Lancet"},{"key":"2023020116175737000_btu768-B21","doi-asserted-by":"crossref","first-page":"e1001027","DOI":"10.1371\/journal.pcbi.1001027","article-title":"Sequence-based prediction for vaccine strain selection and identification of antigenic variability in foot-and-mouth disease virus","volume":"6","author":"Reeve","year":"2010","journal-title":"PLoS Comput. Biol."},{"key":"2023020116175737000_btu768-B22","doi-asserted-by":"crossref","first-page":"5467","DOI":"10.1016\/j.vaccine.2011.05.056","article-title":"Reducing animal experimentation in foot-and-mouth disease vaccine potency tests","volume":"29","author":"Reeve","year":"2011","journal-title":"Vaccine"},{"key":"2023020116175737000_btu768-B23","doi-asserted-by":"crossref","first-page":"1880","DOI":"10.1016\/S0264-410X(98)00173-X","article-title":"Prediction of well-conserved HIV-1 ligands using a matrix-based algorithm, epimatrix","volume":"16","author":"Schafer","year":"1998","journal-title":"Vaccine"},{"key":"2023020116175737000_btu768-B24","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1126\/science.1165893","article-title":"Distilling free-form natural laws from experimental data","volume":"324","author":"Schmidt","year":"2009","journal-title":"Science"},{"key":"2023020116175737000_btu768-B25","volume-title":"Evolution and Optimum Seeking","author":"Schwefel","year":"1995"},{"key":"2023020116175737000_btu768-B26","first-page":"2","article-title":"Multiple sequence alignment using clustalw and clustalx","author":"Thompson","year":"2002","journal-title":"Curr. 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