{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T05:33:29Z","timestamp":1792042409980,"version":"4.4.0"},"reference-count":113,"publisher":"Elsevier BV","issue":"2","license":[{"start":{"date-parts":[[2022,3,1]],"date-time":"2022-03-01T00:00:00Z","timestamp":1646092800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2022,3,1]],"date-time":"2022-03-01T00:00:00Z","timestamp":1646092800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2022,2,1]],"date-time":"2022-02-01T00:00:00Z","timestamp":1643673600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Genomics"],"published-print":{"date-parts":[[2022,3]]},"DOI":"10.1016\/j.ygeno.2022.110301","type":"journal-article","created":{"date-parts":[[2022,2,8]],"date-time":"2022-02-08T02:03:13Z","timestamp":1644285793000},"page":"110301","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":38,"title":["An integrated in silico based subtractive genomics and reverse vaccinology approach for the identification of novel vaccine candidate and chimeric vaccine against XDR Salmonella typhi H58"],"prefix":"10.1016","volume":"114","author":[{"given":"Kanwal","family":"Khan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Khurshid","family":"Jalal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Reaz","family":"Uddin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"20","key":"10.1016\/j.ygeno.2022.110301_bb0005","doi-asserted-by":"crossref","first-page":"2668","DOI":"10.1001\/jama.283.20.2668","article-title":"Laboratory-based surveillance of Salmonella serotype Typhi infections in the United States: antimicrobial resistance on the rise","volume":"283","author":"Ackers","year":"2000","journal-title":"J. Am. Med. Assoc."},{"issue":"7\u20138","key":"10.1016\/j.ygeno.2022.110301_bb0010","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1016\/S0264-410X(02)00566-2","article-title":"Two years into reverse vaccinology","volume":"21","author":"Adu-Bobie","year":"2003","journal-title":"Vaccine"},{"key":"10.1016\/j.ygeno.2022.110301_bb0015","doi-asserted-by":"crossref","first-page":"260","DOI":"10.3389\/fimmu.2014.00260","article-title":"Leishmania spp. proteome data sets: a comprehensive resource for vaccine development to target visceral leishmaniasis","volume":"5","author":"Aebischer","year":"2014","journal-title":"Front. Immunol."},{"key":"10.1016\/j.ygeno.2022.110301_bb0020","article-title":"A skeleton in the closet: the implications of COVID-19 on XDR strain of typhoid in Pakistan","volume":"2","author":"Ahmad","year":"2021","journal-title":"Public Health Pract."},{"key":"10.1016\/j.ygeno.2022.110301_bb0025","doi-asserted-by":"crossref","DOI":"10.1155\/2020\/6432580","article-title":"Extensively drug-resistant (XDR) typhoid: evolution, prevention, and its management","volume":"2020","author":"Akram","year":"2020","journal-title":"Biomed. Res. Int."},{"issue":"3","key":"10.1016\/j.ygeno.2022.110301_bb0030","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1110\/ps.04882105","article-title":"Normal modes for predicting protein motions: a comprehensive database assessment and associated web tool","volume":"14","author":"Alexandrov","year":"2005","journal-title":"Protein Sci."},{"issue":"4","key":"10.1016\/j.ygeno.2022.110301_bb0035","first-page":"409","article-title":"Phenothiazines, bacterial efflux pumps and targeting the macrophage for enhanced killing of intracellular XDRTB","volume":"24","author":"Amaral","year":"2010","journal-title":"In Vivo"},{"issue":"7","key":"10.1016\/j.ygeno.2022.110301_bb0040","first-page":"576","article-title":"Reverse vaccinology: an approach to search vaccine leads of Shigella sonnei","volume":"7","author":"Anand","year":"2013","journal-title":"J. Pharm. Res."},{"issue":"1","key":"10.1016\/j.ygeno.2022.110301_bb0045","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1002\/prot.21495","article-title":"FireDock: fast interaction refinement in molecular docking","volume":"69","author":"Andrusier","year":"2007","journal-title":"Proteins: Struct. Funct. Bioinform."},{"issue":"6","key":"10.1016\/j.ygeno.2022.110301_bb0050","first-page":"669","article-title":"Study of the immunogenicity of outer membrane protein A (ompA) gene from Acinetobacter baumannii as DNA vaccine candidate in vivo","volume":"22","author":"Ansari","year":"2019","journal-title":"Iran. J. Basic Med. Sci."},{"key":"10.1016\/j.ygeno.2022.110301_bb0055","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/j.gene.2019.03.049","article-title":"Prediction of new vaccine targets in the core genome of Corynebacterium pseudotuberculosis through omics approaches and reverse vaccinology","volume":"702","author":"Ara\u00fajo","year":"2019","journal-title":"Gene"},{"issue":"suppl_1","key":"10.1016\/j.ygeno.2022.110301_bb0060","first-page":"D154","article-title":"The universal protein resource (UniProt)","volume":"33","author":"Bairoch","year":"2005","journal-title":"Nucleic Acids Res."},{"issue":"2","key":"10.1016\/j.ygeno.2022.110301_bb0065","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1002\/ddr.20413","article-title":"In silico subtractive genomics for target identification in human bacterial pathogens","volume":"72","author":"Barh","year":"2011","journal-title":"Drug Dev. Res."},{"key":"10.1016\/j.ygeno.2022.110301_bb0070","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1016\/j.biologicals.2017.08.004","article-title":"Towards a peptide-based vaccine against Shigella sonnei: A subtractive reverse vaccinology based approach","volume":"50","author":"Baseer","year":"2017","journal-title":"Biologicals"},{"issue":"2","key":"10.1016\/j.ygeno.2022.110301_bb0075","doi-asserted-by":"crossref","first-page":"34","DOI":"10.3390\/vaccines7020034","article-title":"In silico designed ebola virus T-cell multi-epitope DNA vaccine constructions are immunogenic in mice","volume":"7","author":"Bazhan","year":"2019","journal-title":"Vaccines"},{"issue":"2","key":"10.1016\/j.ygeno.2022.110301_bb0080","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1080\/07391102.2019.1580222","article-title":"Computational characterization of epitopic region within the outer membrane protein candidate in Flavobacterium columnare for vaccine development","volume":"38","author":"Bhattacharya","year":"2019","journal-title":"J. Biomol. Struct. Dyn."},{"issue":"1","key":"10.1016\/j.ygeno.2022.110301_bb0085","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-020-80899-6","article-title":"In silico analysis of epitope-based vaccine candidate against tuberculosis using reverse vaccinology","volume":"11","author":"Bibi","year":"2021","journal-title":"Sci. Rep."},{"issue":"6","key":"10.1016\/j.ygeno.2022.110301_bb0090","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0178669","article-title":"Evolution of Salmonella Typhi outer membrane protein-specific T and B cell responses in humans following oral Ty21a vaccination: A randomized clinical trial","volume":"12","author":"Carre\u00f1o","year":"2017","journal-title":"PLoS One"},{"issue":"4","key":"10.1016\/j.ygeno.2022.110301_bb0095","doi-asserted-by":"crossref","first-page":"1065","DOI":"10.1080\/21645515.2015.1010910","article-title":"Identification of novel vaccine candidates against Acinetobacter baumannii using reverse vaccinology","volume":"11","author":"Chiang","year":"2015","journal-title":"Hum. Vaccin. Immunother."},{"key":"10.1016\/j.ygeno.2022.110301_bb0100","first-page":"45","article-title":"Analysis of the accuracy and implications of simple method for predicting the secondary structure of globular proteins","volume":"47","author":"Chou","year":"1978","journal-title":"J. Adv. Enzymol."},{"issue":"1","key":"10.1016\/j.ygeno.2022.110301_bb0105","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13073-020-00824-4","article-title":"The identification of novel immunogenic antigens as potential Shigella vaccine components","volume":"13","author":"de Alwis","year":"2021","journal-title":"Genome Med."},{"issue":"1","key":"10.1016\/j.ygeno.2022.110301_bb0110","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1111\/nyas.12046","article-title":"Reverse vaccinology in the 21st century: improvements over the original design","volume":"1285","author":"Donati","year":"2013","journal-title":"Ann. N. Y. Acad. Sci."},{"issue":"1","key":"10.1016\/j.ygeno.2022.110301_bb0115","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-8-4","article-title":"VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines","volume":"8","author":"Doytchinova","year":"2007","journal-title":"BMC Bioinform."},{"issue":"1","key":"10.1016\/j.ygeno.2022.110301_bb0120","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-7-131","article-title":"EpiJen: a server for multistep T cell epitope prediction","volume":"7","author":"Doytchinova","year":"2006","journal-title":"BMC Bioinform."},{"issue":"4","key":"10.1016\/j.ygeno.2022.110301_bb0125","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1002\/jmr.893","article-title":"Predicting linear B-cell epitopes using string kernels","volume":"21","author":"EL-Manzalawy","year":"2008","journal-title":"J. Mol. Rec."},{"issue":"3","key":"10.1016\/j.ygeno.2022.110301_bb0130","doi-asserted-by":"crossref","first-page":"836","DOI":"10.1128\/jvi.55.3.836-839.1985","article-title":"Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide","volume":"55","author":"Emini","year":"1985","journal-title":"J. Virol."},{"issue":"5","key":"10.1016\/j.ygeno.2022.110301_bb0135","doi-asserted-by":"crossref","first-page":"3374","DOI":"10.1016\/j.ygeno.2020.06.022","article-title":"Identification of novel vaccine candidate against Salmonella enterica serovar Typhi by reverse vaccinology method and evaluation of its immunization","volume":"112","author":"Esmailnia","year":"2020","journal-title":"Genomics"},{"key":"10.1016\/j.ygeno.2022.110301_bb0140","doi-asserted-by":"crossref","DOI":"10.1016\/j.cimid.2020.101413","article-title":"Vaccination with a novel multi-epitope ROP8 DNA vaccine against acute toxoplasma gondii infection induces strong B and T cell responses in mice","volume":"69","author":"Foroutan","year":"2020","journal-title":"Comp. Immunol. Microbiol. Infect. Dis."},{"issue":"2","key":"10.1016\/j.ygeno.2022.110301_bb0145","doi-asserted-by":"crossref","first-page":"74","DOI":"10.6026\/97320630012074","article-title":"MFPPI\u2013multi FASTA ProtParam interface","volume":"12","author":"Garg","year":"2016","journal-title":"Bioinformation"},{"issue":"11","key":"10.1016\/j.ygeno.2022.110301_bb0150","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0142563","article-title":"Improving multi-epitope long peptide vaccine potency by using a strategy that enhances CD4+ T help in BALB\/c mice","volume":"10","author":"Ghaffari-Nazari","year":"2015","journal-title":"PLoS One"},{"issue":"suppl_2","key":"10.1016\/j.ygeno.2022.110301_bb0155","doi-asserted-by":"crossref","first-page":"W526","DOI":"10.1093\/nar\/gki376","article-title":"JCat: a novel tool to adapt codon usage of a target gene to its potential expression host","volume":"33","author":"Grote","year":"2005","journal-title":"Nucleic Acids Res."},{"issue":"3","key":"10.1016\/j.ygeno.2022.110301_bb0160","doi-asserted-by":"crossref","first-page":"495","DOI":"10.3390\/cells10030495","article-title":"Thinking outside the bug: targeting outer membrane proteins for Burkholderia vaccines","volume":"10","author":"Grund","year":"2021","journal-title":"Cells"},{"issue":"9","key":"10.1016\/j.ygeno.2022.110301_bb0165","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0073957","article-title":"In silico approach for predicting toxicity of peptides and proteins","volume":"8","author":"Gupta","year":"2013","journal-title":"PLoS One"},{"issue":"1","key":"10.1016\/j.ygeno.2022.110301_bb0170","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1128\/AAC.01310-13","article-title":"ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes","volume":"58","author":"Gupta","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"issue":"18","key":"10.1016\/j.ygeno.2022.110301_bb0175","doi-asserted-by":"crossref","first-page":"3804","DOI":"10.1016\/j.vaccine.2005.07.111","article-title":"Vaccines against typhoid fever","volume":"24","author":"Guzman","year":"2006","journal-title":"Vaccine"},{"issue":"3","key":"10.1016\/j.ygeno.2022.110301_bb0180","doi-asserted-by":"crossref","first-page":"1159","DOI":"10.1007\/s00253-020-11054-4","article-title":"Identification and evaluation of novel vaccine candidates against Shigella flexneri through reverse vaccinology approach","volume":"105","author":"Hajialibeigi","year":"2021","journal-title":"Appl. Microbiol. Biotechnol."},{"issue":"9","key":"10.1016\/j.ygeno.2022.110301_bb0185","doi-asserted-by":"crossref","first-page":"1461","DOI":"10.1128\/CVI.00093-08","article-title":"Characterization of an outer membrane protein of Salmonella enterica serovar Typhimurium that confers protection against typhoid","volume":"15","author":"Hamid","year":"2008","journal-title":"Clin. Vaccine Immunol."},{"issue":"3","key":"10.1016\/j.ygeno.2022.110301_bb0190","doi-asserted-by":"crossref","first-page":"223","DOI":"10.4103\/0255-0857.83904","article-title":"Antimicrobial resistance in typhoidal salmonellae","volume":"29","author":"Harish","year":"2011","journal-title":"Indian J. Med. Microbiol."},{"issue":"1","key":"10.1016\/j.ygeno.2022.110301_bb0195","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1016\/j.gene.2015.08.044","article-title":"Identification of putative drug targets in Vancomycin-resistant Staphylococcus aureus (VRSA) using computer aided protein data analysis","volume":"575","author":"Hasan","year":"2016","journal-title":"Gene"},{"issue":"11","key":"10.1016\/j.ygeno.2022.110301_bb0200","doi-asserted-by":"crossref","first-page":"2145","DOI":"10.1007\/s10096-019-03658-0","article-title":"Typhoidal Salmonella strains in Pakistan: an impending threat of extensively drug-resistant Salmonella Typhi","volume":"38","author":"Hussain","year":"2019","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"issue":"11","key":"10.1016\/j.ygeno.2022.110301_bb0205","doi-asserted-by":"crossref","first-page":"2953","DOI":"10.1128\/iai.56.11.2953-2959.1988","article-title":"Protection against Salmonella typhi infection in mice after immunization with outer membrane proteins isolated from Salmonella typhi 9, 12, d, Vi","volume":"56","author":"Isibasi","year":"1988","journal-title":"Infect. Immun."},{"issue":"5","key":"10.1016\/j.ygeno.2022.110301_bb0210","doi-asserted-by":"crossref","first-page":"1340","DOI":"10.1007\/s12010-012-9649-0","article-title":"A reverse vaccinology approach for the identification of potential vaccine candidates from Leishmania spp","volume":"167","author":"John","year":"2012","journal-title":"Appl. Biochem. Biotechnol."},{"issue":"6","key":"10.1016\/j.ygeno.2022.110301_bb0215","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1111\/j.1708-8305.2011.00563.x","article-title":"From the CDC: new country-specific recommendations for pre-travel typhoid vaccination","volume":"18","author":"Johnson","year":"2011","journal-title":"J. Travel Med."},{"issue":"6","key":"10.1016\/j.ygeno.2022.110301_bb0220","doi-asserted-by":"crossref","first-page":"906","DOI":"10.1016\/j.vaccine.2017.12.001","article-title":"Self-assembling protein nanoparticles with built-in flagellin domains increases protective efficacy of a plasmodium falciparum based vaccine","volume":"36","author":"Kaba","year":"2018","journal-title":"Vaccine"},{"issue":"1","key":"10.1016\/j.ygeno.2022.110301_bb0225","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: Kyoto encyclopedia of genes and genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res."},{"issue":"4","key":"10.1016\/j.ygeno.2022.110301_bb0230","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1007\/BF01195768","article-title":"Prediction of chain flexibility in proteins","volume":"72","author":"Karplus","year":"1985","journal-title":"Naturwissenschaften"},{"issue":"6","key":"10.1016\/j.ygeno.2022.110301_bb0235","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1038\/nprot.2015.053","article-title":"The Phyre2 web portal for protein modeling, prediction and analysis","volume":"10","author":"Kelley","year":"2015","journal-title":"Nat. Protoc."},{"issue":"W1","key":"10.1016\/j.ygeno.2022.110301_bb0240","doi-asserted-by":"crossref","first-page":"W525","DOI":"10.1093\/nar\/gks438","article-title":"Immune epitope database analysis resource","volume":"40","author":"Kim","year":"2012","journal-title":"Nucleic Acids Res."},{"issue":"3","key":"10.1016\/j.ygeno.2022.110301_bb0245","first-page":"208","article-title":"Insights into the dynamics of cyclic diguanosine monophosphate I riboswitch using molecular dynamics simulation","volume":"58","author":"Kumari","year":"2021","journal-title":"Indian J. Biochem. Biophys."},{"issue":"1","key":"10.1016\/j.ygeno.2022.110301_bb0250","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1093\/nar\/29.1.221","article-title":"PDBsum: summaries and analyses of PDB structures","volume":"29","author":"Laskowski","year":"2001","journal-title":"Nucleic Acids Res."},{"issue":"2","key":"10.1016\/j.ygeno.2022.110301_bb0255","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1107\/S0021889892009944","article-title":"PROCHECK: a program to check the stereochemical quality of protein structures","volume":"26","author":"Laskowski","year":"1993","journal-title":"J. Appl. Crystallogr."},{"issue":"1","key":"10.1016\/j.ygeno.2022.110301_bb0260","doi-asserted-by":"crossref","first-page":"15","DOI":"10.7774\/cevr.2020.9.1.15","article-title":"Reverse vaccinology approach for the identification and characterization of outer membrane proteins of Shigella flexneri as potential cellular-and antibody-dependent vaccine candidates","volume":"9","author":"Leow","year":"2020","journal-title":"Clin. Exp. Vaccine Res."},{"issue":"13","key":"10.1016\/j.ygeno.2022.110301_bb0265","doi-asserted-by":"crossref","first-page":"1658","DOI":"10.1093\/bioinformatics\/btl158","article-title":"Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences","volume":"22","author":"Li","year":"2006","journal-title":"Bioinformatics"},{"issue":"W1","key":"10.1016\/j.ygeno.2022.110301_bb0270","doi-asserted-by":"crossref","first-page":"W271","DOI":"10.1093\/nar\/gku339","article-title":"iMODS: internal coordinates normal mode analysis server","volume":"42","author":"L\u00f3pez-Blanco","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ygeno.2022.110301_bb0275","series-title":"Conference Proceedings\u20134 Th International Conference on Molecular Diagnostics and Biomarker Discovery: Antibody Technology","author":"Malaysia","year":"2019"},{"key":"10.1016\/j.ygeno.2022.110301_bb0280","doi-asserted-by":"crossref","first-page":"751","DOI":"10.3389\/fimmu.2019.00751","article-title":"The development of a vaccine against meningococcus B using reverse vaccinology","volume":"10","author":"Masignani","year":"2019","journal-title":"Front. Immunol."},{"issue":"8","key":"10.1016\/j.ygeno.2022.110301_bb0285","doi-asserted-by":"crossref","first-page":"895","DOI":"10.1517\/14712598.2.8.895","article-title":"Reverse vaccinology: a genome-based approach for vaccine development","volume":"2","author":"Masignani","year":"2002","journal-title":"Expert. Opin. Biol. Ther."},{"issue":"4","key":"10.1016\/j.ygeno.2022.110301_bb0290","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1093\/bioinformatics\/16.4.404","article-title":"The PSIPRED protein structure prediction server","volume":"16","author":"McGuffin","year":"2000","journal-title":"Bioinformatics"},{"issue":"10","key":"10.1016\/j.ygeno.2022.110301_bb0295","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1016\/S1359-6446(03)02689-8","article-title":"Reverse vaccinology","volume":"8","author":"Mora","year":"2003","journal-title":"Drug Discov. Today"},{"key":"10.1016\/j.ygeno.2022.110301_bb0300","doi-asserted-by":"crossref","first-page":"2776","DOI":"10.3389\/fimmu.2019.02776","article-title":"reverse vaccinology","volume":"10","author":"Moxon","year":"2019","journal-title":"Front. Immunol."},{"key":"10.1016\/j.ygeno.2022.110301_bb0305","first-page":"521518","article-title":"Identification of potential new vaccine candidates in Salmonella typhi using reverse vaccinology and subtractive genomics-based approach","author":"Mukherjee","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.ygeno.2022.110301_bb0310","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1016\/j.meegid.2015.03.027","article-title":"Identification of putative vaccine candidates against helicobacter pylori exploiting exoproteome and secretome: a reverse vaccinology based approach","volume":"32","author":"Naz","year":"2015","journal-title":"Infect. Genet. Evol."},{"key":"10.1016\/j.ygeno.2022.110301_bb0315","doi-asserted-by":"crossref","DOI":"10.1074\/mcp.R120.002309","article-title":"The peptide vaccine of the future","volume":"20","author":"Nelde","year":"2021","journal-title":"Mol. Cell. Proteomics"},{"issue":"2","key":"10.1016\/j.ygeno.2022.110301_bb0320","doi-asserted-by":"crossref","first-page":"458","DOI":"10.3390\/ijms18020458","article-title":"Antibiotic resistance determinant-focused Acinetobacter baumannii vaccine designed using reverse vaccinology","volume":"18","author":"Ni","year":"2017","journal-title":"Int. J. Mol. Sci."},{"issue":"1","key":"10.1016\/j.ygeno.2022.110301_bb0325","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13104-020-4917-5","article-title":"Outer membrane protein A (OmpA) of extraintestinal pathogenic Escherichia coli","volume":"13","author":"Nielsen","year":"2020","journal-title":"BMC Res. Notes"},{"issue":"aop","key":"10.1016\/j.ygeno.2022.110301_bb0330","article-title":"Continued outbreak of ceftriaxone-resistant salmonella enterica serotype typhi across Pakistan and assessment of knowledge and practices among healthcare workers","volume":"1","author":"Nizamuddin","year":"2021","journal-title":"Am. J. Trop. Med. Hygiene"},{"key":"10.1016\/j.ygeno.2022.110301_bb0335","first-page":"2017","article-title":"Vaccinomics approach for designing potential peptide vaccine by targeting Shigella spp. serine protease autotransporter subfamily protein SigA","author":"Oany","year":"2017","journal-title":"J Immunol Res"},{"issue":"2","key":"10.1016\/j.ygeno.2022.110301_bb0340","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1016\/j.vaccine.2018.04.022","article-title":"Typhoid vaccines: WHO position paper, march 2018\u2013recommendations","volume":"37","author":"Organization","year":"2019","journal-title":"Vaccine"},{"issue":"1","key":"10.1016\/j.ygeno.2022.110301_bb0345","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1016\/j.ijmyco.2015.10.005","article-title":"Analysis of the DosR regulon genes to select cytotoxic T lymphocyte epitope specific vaccine candidates using a reverse vaccinology approach","volume":"5","author":"Pandey","year":"2016","journal-title":"Int. J, Mycobacteriol."},{"issue":"19","key":"10.1016\/j.ygeno.2022.110301_bb0350","doi-asserted-by":"crossref","first-page":"5425","DOI":"10.1021\/bi00367a013","article-title":"New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites","volume":"25","author":"Parker","year":"1986","journal-title":"Biochemistry"},{"key":"10.1016\/j.ygeno.2022.110301_bb0355","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1016\/j.micpath.2018.05.037","article-title":"An in silico study: novel targets for potential drug and vaccine design against drug resistant H. pylori","volume":"122","author":"Pasala","year":"2018","journal-title":"Microb. Pathog."},{"issue":"13","key":"10.1016\/j.ygeno.2022.110301_bb0360","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF chimera\u2014a visualization system for exploratory research and analysis","volume":"25","author":"Pettersen","year":"2004","journal-title":"J. Comput. Chem."},{"issue":"1","key":"10.1016\/j.ygeno.2022.110301_bb0365","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-9-514","article-title":"ElliPro: a new structure-based tool for the prediction of antibody epitopes","volume":"9","author":"Ponomarenko","year":"2008","journal-title":"BMC Bioinform."},{"issue":"1","key":"10.1016\/j.ygeno.2022.110301_bb0370","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1472-6807-7-64","article-title":"Antibody-protein interactions: benchmark datasets and prediction tools evaluation","volume":"7","author":"Ponomarenko","year":"2007","journal-title":"BMC Struct. Biol."},{"issue":"7","key":"10.1016\/j.ygeno.2022.110301_bb0375","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1093\/bioinformatics\/btt055","article-title":"GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit","volume":"29","author":"Pronk","year":"2013","journal-title":"Bioinformatics"},{"issue":"suppl_1","key":"10.1016\/j.ygeno.2022.110301_bb0380","first-page":"D501","article-title":"NCBI reference sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins","volume":"33","author":"Pruitt","year":"2005","journal-title":"Nucleic Acids Res."},{"issue":"7","key":"10.1016\/j.ygeno.2022.110301_bb0385","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1016\/S0167-739X(02)00075-4","article-title":"IMMSIM, a flexible model for in machina experiments on immune system responses","volume":"18","author":"Puzone","year":"2002","journal-title":"Futur. Gener. Comput. Syst."},{"issue":"3","key":"10.1016\/j.ygeno.2022.110301_bb0390","doi-asserted-by":"crossref","first-page":"423","DOI":"10.3390\/vaccines8030423","article-title":"Vaccine design from the ensemble of surface glycoprotein epitopes of SARS-CoV-2: an immunoinformatics approach","volume":"8","author":"Rahman","year":"2020","journal-title":"Vaccines"},{"key":"10.1016\/j.ygeno.2022.110301_bb0395","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1016\/j.cbpa.2018.06.004","article-title":"Inhibitors of protein\u2013protein interactions (PPIs): an analysis of scaffold choices and buried surface area","volume":"44","author":"Ran","year":"2018","journal-title":"Curr. Opin. Chem. Biol."},{"issue":"5","key":"10.1016\/j.ygeno.2022.110301_bb0400","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1016\/S1369-5274(00)00119-3","article-title":"Reverse vaccinology","volume":"3","author":"Rappuoli","year":"2000","journal-title":"Curr. Opin. Microbiol."},{"issue":"17\u201319","key":"10.1016\/j.ygeno.2022.110301_bb0405","doi-asserted-by":"crossref","first-page":"2688","DOI":"10.1016\/S0264-410X(00)00554-5","article-title":"Reverse vaccinology, a genome-based approach to vaccine development","volume":"19","author":"Rappuoli","year":"2001","journal-title":"Vaccine"},{"issue":"9","key":"10.1016\/j.ygeno.2022.110301_bb0410","doi-asserted-by":"crossref","first-page":"1336","DOI":"10.3390\/microorganisms8091336","article-title":"Emergence of resistance to fluoroquinolones and third-generation cephalosporins in Salmonella Typhi in Lahore, Pakistan","volume":"8","author":"Rasheed","year":"2020","journal-title":"Microorganisms"},{"issue":"2","key":"10.1016\/j.ygeno.2022.110301_bb0415","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0057047","article-title":"Disease isolates of Streptococcus pseudopneumoniae and non-typeable S. pneumoniae presumptively identified as atypical S. pneumoniae in Spain","volume":"8","author":"Rolo","year":"2013","journal-title":"PLoS One"},{"issue":"3","key":"10.1016\/j.ygeno.2022.110301_bb0420","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1038\/nm0398-321","article-title":"Immunologic and therapeutic evaluation of a synthetic peptide vaccine for the treatment of patients with metastatic melanoma","volume":"4","author":"Rosenberg","year":"1998","journal-title":"Nat. Med."},{"issue":"9","key":"10.1016\/j.ygeno.2022.110301_bb0425","article-title":"An overview of extensively drug-resistant Salmonella Typhi from a tertiary care hospital in Pakistan","volume":"11","author":"Saeed","year":"2019","journal-title":"Cureus"},{"issue":"5","key":"10.1016\/j.ygeno.2022.110301_bb0430","doi-asserted-by":"crossref","first-page":"1327","DOI":"10.1093\/cid\/ciz1204","article-title":"A novel lineage of ceftriaxone-resistant Salmonella Typhi from India that is closely related to XDR S. Typhi found in Pakistan","volume":"71","author":"Sah","year":"2020","journal-title":"Clin. Infect. Dis."},{"issue":"1","key":"10.1016\/j.ygeno.2022.110301_bb0435","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1002\/prot.21078","article-title":"Prediction of continuous B-cell epitopes in an antigen using recurrent neural network","volume":"65","author":"Saha","year":"2006","journal-title":"Proteins: Struct. Funct. Bioinform."},{"issue":"suppl_2","key":"10.1016\/j.ygeno.2022.110301_bb0440","doi-asserted-by":"crossref","first-page":"W363","DOI":"10.1093\/nar\/gki481","article-title":"PatchDock and SymmDock: servers for rigid and symmetric docking","volume":"33","author":"Schneidman-Duhovny","year":"2005","journal-title":"Nucleic Acids Res."},{"issue":"13","key":"10.1016\/j.ygeno.2022.110301_bb0445","doi-asserted-by":"crossref","first-page":"3381","DOI":"10.1093\/nar\/gkg520","article-title":"SWISS-MODEL: an automated protein homology-modeling server","volume":"31","author":"Schwede","year":"2003","journal-title":"Nucleic Acids Res."},{"issue":"4","key":"10.1016\/j.ygeno.2022.110301_bb0450","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1016\/j.tim.2019.12.005","article-title":"Vaccines to overcome antibiotic resistance: the challenge of Burkholderia cenocepacia","volume":"28","author":"Scoffone","year":"2020","journal-title":"Trends Microbiol."},{"key":"10.1016\/j.ygeno.2022.110301_bb0455","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1111\/j.1469-0691.2012.03939.x","article-title":"Developing vaccines in the era of genomics: a decade of reverse vaccinology","volume":"18","author":"Seib","year":"2012","journal-title":"Clin. Microbiol. Infect."},{"key":"10.1016\/j.ygeno.2022.110301_bb0460","first-page":"1","article-title":"Design, synthesis, and molecular dynamics simulation studies of quinoline derivatives as protease inhibitors against SARS-CoV-2","author":"Singh","year":"2021","journal-title":"J. Biomol. Struct. Dyn."},{"issue":"2","key":"10.1016\/j.ygeno.2022.110301_bb0465","doi-asserted-by":"crossref","first-page":"1177","DOI":"10.1007\/s10989-021-10159-2","article-title":"Subtractive proteomics and reverse vaccinology strategies for designing a multiepitope vaccine targeting membrane proteins of Klebsiella pneumoniae","volume":"27","author":"Solanki","year":"2021","journal-title":"Int. J. Pept. Res. Ther."},{"issue":"1","key":"10.1016\/j.ygeno.2022.110301_bb0470","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-018-26689-7","article-title":"Subtractive proteomics to identify novel drug targets and reverse vaccinology for the development of chimeric vaccine against Acinetobacter baumannii","volume":"8","author":"Solanki","year":"2018","journal-title":"Sci. Rep."},{"key":"10.1016\/j.ygeno.2022.110301_bb0475","doi-asserted-by":"crossref","first-page":"D362","DOI":"10.1093\/nar\/gkw937","article-title":"The STRING database in 2017: quality-controlled protein\u2013protein association networks, made broadly accessible","volume":"45","author":"Szklarczyk","year":"2017","journal-title":"Nucleic Acids Res."},{"issue":"6","key":"10.1016\/j.ygeno.2022.110301_bb0480","doi-asserted-by":"crossref","first-page":"3026","DOI":"10.1007\/s12010-014-0749-x","article-title":"Identification of potential vaccine candidates against Streptococcus pneumoniae by reverse vaccinology approach","volume":"172","author":"Talukdar","year":"2014","journal-title":"Appl. Biochem. Biotechnol."},{"issue":"9","key":"10.1016\/j.ygeno.2022.110301_bb0485","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1007\/s00251-013-0714-9","article-title":"MHCcluster, a method for functional clustering of MHC molecules","volume":"65","author":"Thomsen","year":"2013","journal-title":"Immunogenetics"},{"issue":"3","key":"10.1016\/j.ygeno.2022.110301_bb0490","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00638-15","article-title":"Toll-like receptor 3 signaling via TRIF contributes to a protective innate immune response to severe acute respiratory syndrome coronavirus infection","volume":"6","author":"Totura","year":"2015","journal-title":"MBio"},{"issue":"suppl_2","key":"10.1016\/j.ygeno.2022.110301_bb0495","doi-asserted-by":"crossref","first-page":"W310","DOI":"10.1093\/nar\/gkl206","article-title":"GRAMM-X public web server for protein\u2013protein docking","volume":"34","author":"Tovchigrechko","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ygeno.2022.110301_bb0500","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1016\/j.compbiolchem.2018.02.017","article-title":"Prioritization of potential drug targets against P. aeruginosa by core proteomic analysis using computational subtractive genomics and protein-protein interaction network","volume":"74","author":"Uddin","year":"2018","journal-title":"Comput. Biol. Chem."},{"key":"10.1016\/j.ygeno.2022.110301_bb0505","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1016\/j.compbiolchem.2013.11.005","article-title":"Identification and characterization of potential drug targets by subtractive genome analyses of methicillin resistant Staphylococcus aureus","volume":"48","author":"Uddin","year":"2014","journal-title":"Comput. Biol. Chem."},{"issue":"5","key":"10.1016\/j.ygeno.2022.110301_bb0510","doi-asserted-by":"crossref","first-page":"368","DOI":"10.3390\/pathogens9050368","article-title":"Genome subtraction and comparison for the identification of novel drug targets against mycobacterium avium subsp. hominissuis","volume":"9","author":"Uddin","year":"2020","journal-title":"Pathogens"},{"key":"10.1016\/j.ygeno.2022.110301_bb0515","article-title":"Designing multi-epitope vaccine against Staphylococcus aureus by employing subtractive proteomics, reverse vaccinology and immuno-informatics approaches","volume":"132","author":"Ul Qamar","year":"2021","journal-title":"Comput. Biol. Med."},{"key":"10.1016\/j.ygeno.2022.110301_bb0520","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1016\/j.micpath.2017.12.063","article-title":"Subtractive genome analysis for in silico identification and characterization of novel drug targets in Streptococcus pneumonia strain JJA","volume":"115","author":"Wadood","year":"2018","journal-title":"Microb. Pathog."},{"key":"10.1016\/j.ygeno.2022.110301_bb0525","first-page":"3529","article-title":"Identification of Vibrio parahaemolyticus and Vibrio Spp. specific outer membrane proteins by reverse vaccinology and surface proteome","volume":"11","author":"Wang","year":"2020","journal-title":"Front. Microbiol."},{"issue":"D1","key":"10.1016\/j.ygeno.2022.110301_bb0530","doi-asserted-by":"crossref","first-page":"D1074","DOI":"10.1093\/nar\/gkx1037","article-title":"DrugBank 5.0: a major update to the DrugBank database for 2018","volume":"46","author":"Wishart","year":"2018","journal-title":"Nucleic Acids Res."},{"issue":"7","key":"10.1016\/j.ygeno.2022.110301_bb0535","doi-asserted-by":"crossref","first-page":"3752","DOI":"10.1128\/AAC.02770-13","article-title":"Emergence of clinical Salmonella enterica serovar Typhimurium isolates with concurrent resistance to ciprofloxacin, ceftriaxone, and azithromycin","volume":"58","author":"Wong","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.ygeno.2022.110301_bb0540","doi-asserted-by":"crossref","DOI":"10.1016\/j.idcr.2019.e00492","article-title":"The first Canadian pediatric case of extensively drug-resistant Salmonella Typhi originating from an outbreak in Pakistan and its implication for empiric antimicrobial choices","volume":"15","author":"Wong","year":"2019","journal-title":"IDCases"},{"issue":"1","key":"10.1016\/j.ygeno.2022.110301_bb0545","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12879-018-3258-7","article-title":"Identification of immunogenic outer membrane proteins and evaluation of their protective efficacy against Stenotrophomonas maltophilia","volume":"18","author":"Xu","year":"2018","journal-title":"BMC Infect. Dis."},{"issue":"3","key":"10.1016\/j.ygeno.2022.110301_bb0550","doi-asserted-by":"crossref","first-page":"795","DOI":"10.1080\/21645515.2015.1012017","article-title":"In silico design of a DNA-based HIV-1 multi-epitope vaccine for Chinese populations","volume":"11","author":"Yang","year":"2015","journal-title":"Hum. Vaccin. Immunother."},{"issue":"6","key":"10.1016\/j.ygeno.2022.110301_bb0555","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0099368","article-title":"CELLO2GO: a web server for protein subCELlular LOcalization prediction with functional gene ontology annotation","volume":"9","author":"Yu","year":"2014","journal-title":"PLoS One"},{"issue":"13","key":"10.1016\/j.ygeno.2022.110301_bb0560","doi-asserted-by":"crossref","first-page":"1608","DOI":"10.1093\/bioinformatics\/btq249","article-title":"PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes","volume":"26","author":"Yu","year":"2010","journal-title":"Bioinformatics"},{"issue":"suppl_1","key":"10.1016\/j.ygeno.2022.110301_bb0565","doi-asserted-by":"crossref","first-page":"D455","DOI":"10.1093\/nar\/gkn858","article-title":"DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes","volume":"37","author":"Zhang","year":"2009","journal-title":"Nucleic Acids Res."}],"container-title":["Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0888754322000465?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0888754322000465?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T06:36:31Z","timestamp":1760164591000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0888754322000465"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,3]]},"references-count":113,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2022,3]]}},"alternative-id":["S0888754322000465"],"URL":"https:\/\/doi.org\/10.1016\/j.ygeno.2022.110301","relation":{},"ISSN":["0888-7543"],"issn-type":[{"value":"0888-7543","type":"print"}],"subject":[],"published":{"date-parts":[[2022,3]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"An integrated in silico based subtractive genomics and reverse vaccinology approach for the identification of novel vaccine candidate and chimeric vaccine against XDR Salmonella typhi H58","name":"articletitle","label":"Article Title"},{"value":"Genomics","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.ygeno.2022.110301","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2022 The Authors. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"110301"}}