{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,10]],"date-time":"2026-02-10T01:07:43Z","timestamp":1770685663294,"version":"3.49.0"},"reference-count":42,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2017,12]]},"DOI":"10.1186\/s12859-017-1540-0","type":"journal-article","created":{"date-parts":[[2017,2,13]],"date-time":"2017-02-13T13:04:51Z","timestamp":1486991091000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":92,"title":["VacSol: a high throughput in silico pipeline to predict potential therapeutic targets in prokaryotic pathogens using subtractive reverse vaccinology"],"prefix":"10.1186","volume":"18","author":[{"given":"Muhammad","family":"Rizwan","sequence":"first","affiliation":[]},{"given":"Anam","family":"Naz","sequence":"additional","affiliation":[]},{"given":"Jamil","family":"Ahmad","sequence":"additional","affiliation":[]},{"given":"Kanwal","family":"Naz","sequence":"additional","affiliation":[]},{"given":"Ayesha","family":"Obaid","sequence":"additional","affiliation":[]},{"given":"Tamsila","family":"Parveen","sequence":"additional","affiliation":[]},{"given":"Muhammad","family":"Ahsan","sequence":"additional","affiliation":[]},{"given":"Amjad","family":"Ali","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2017,2,13]]},"reference":[{"issue":"6","key":"1540_CR1","doi-asserted-by":"crossref","first-page":"e116","DOI":"10.1371\/journal.pcbi.0030116","volume":"3","author":"AL Tarca","year":"2007","unstructured":"Tarca AL, et al. Machine learning and its applications to biology. PLoS Comput Biol. 2007;3(6):e116.","journal-title":"PLoS Comput Biol"},{"key":"1540_CR2","first-page":"17","volume":"6","author":"B Capecchi","year":"2004","unstructured":"Capecchi B, et al. The genome revolution in vaccine research. Curr Issues Mol Biol. 2004;6:17\u201328.","journal-title":"Curr Issues Mol Biol"},{"issue":"3","key":"1540_CR3","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1080\/01652176.1992.9694344","volume":"14","author":"T Kimman","year":"1992","unstructured":"Kimman T. Risks connected with the use of conventional and genetically engineerd vaccines. Vet Q. 1992;14(3):110\u20138.","journal-title":"Vet Q"},{"issue":"9","key":"1540_CR4","doi-asserted-by":"crossref","first-page":"2515","DOI":"10.1172\/JCI38330","volume":"119","author":"CD Rinaudo","year":"2009","unstructured":"Rinaudo CD, et al. Vaccinology in the genome era. J Clin Invest. 2009;119(9):2515\u201325.","journal-title":"J Clin Invest"},{"issue":"5459","key":"1540_CR5","doi-asserted-by":"crossref","first-page":"1816","DOI":"10.1126\/science.287.5459.1816","volume":"287","author":"M Pizza","year":"2000","unstructured":"Pizza M, et al. Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing. Science. 2000;287(5459):1816\u201320.","journal-title":"Science"},{"issue":"17","key":"1540_CR6","doi-asserted-by":"crossref","first-page":"2688","DOI":"10.1016\/S0264-410X(00)00554-5","volume":"19","author":"R Rappuoli","year":"2001","unstructured":"Rappuoli R. Reverse vaccinology, a genome-based approach to vaccine development. Vaccine. 2001;19(17):2688\u201391.","journal-title":"Vaccine"},{"issue":"12","key":"1540_CR7","doi-asserted-by":"crossref","first-page":"6817","DOI":"10.1128\/IAI.70.12.6817-6827.2002","volume":"70","author":"N Ariel","year":"2002","unstructured":"Ariel N, et al. Search for potential vaccine candidate open reading frames in the Bacillus anthracis virulence plasmid pXO1: in silico and in vitro screening. Infect Immun. 2002;70(12):6817\u201327.","journal-title":"Infect Immun"},{"issue":"1","key":"1540_CR8","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1128\/IAI.70.1.368-379.2002","volume":"70","author":"S Montigiani","year":"2002","unstructured":"Montigiani S, et al. Genomic approach for analysis of surface proteins in Chlamydia pneumoniae. Infect Immun. 2002;70(1):368\u201379.","journal-title":"Infect Immun"},{"issue":"30","key":"1540_CR9","doi-asserted-by":"crossref","first-page":"4135","DOI":"10.1016\/S0264-410X(01)00173-6","volume":"19","author":"BC Ross","year":"2001","unstructured":"Ross BC, et al. Identification of vaccine candidate antigens from a genomic analysis of Porphyromonas gingivalis. Vaccine. 2001;19(30):4135\u201342.","journal-title":"Vaccine"},{"issue":"5","key":"1540_CR10","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1016\/S1369-5274(00)00119-3","volume":"3","author":"R Rappuoli","year":"2000","unstructured":"Rappuoli R. Reverse vaccinology. Curr Opin Microbiol. 2000;3(5):445\u201350.","journal-title":"Curr Opin Microbiol"},{"issue":"1","key":"1540_CR11","doi-asserted-by":"crossref","first-page":"732","DOI":"10.1186\/s12864-016-2951-4","volume":"17","author":"A Hassan","year":"2016","unstructured":"Hassan A, et al. Pangenome and immuno-proteomics analysis of Acinetobacter baumannii strains revealed the core peptide vaccine targets. BMC Genomics. 2016;17(1):732.","journal-title":"BMC Genomics"},{"key":"1540_CR12","first-page":"29750","volume":"2010","author":"Y He","year":"2010","unstructured":"He Y, Xiang Z, Mobley HL. Vaxign: the first web-based vaccine design program for reverse vaccinology and applications for vaccine development. Biomed Res Int. 2010;2010:29750.","journal-title":"Biomed Res Int"},{"issue":"1","key":"1540_CR13","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/1471-2105-8-4","volume":"8","author":"IA Doytchinova","year":"2007","unstructured":"Doytchinova IA, Flower DR. VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics. 2007;8(1):4.","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"1540_CR14","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1186\/1471-2105-14-211","volume":"14","author":"V Jaiswal","year":"2013","unstructured":"Jaiswal V, et al. Jenner-predict server: prediction of protein vaccine candidates (PVCs) in bacteria based on host-pathogen interactions. BMC Bioinformatics. 2013;14(1):211.","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"1540_CR15","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1186\/1472-6750-6-35","volume":"6","author":"S Vivona","year":"2006","unstructured":"Vivona S, Bernante F, Filippini F. NERVE: new enhanced reverse vaccinology environment. BMC Biotechnol. 2006;6(1):35.","journal-title":"BMC Biotechnol"},{"key":"1540_CR16","doi-asserted-by":"crossref","first-page":"2381","DOI":"10.1093\/bioinformatics\/btu300","volume":"30","author":"SJ Goodswen","year":"2014","unstructured":"Goodswen SJ, Kennedy PJ, Ellis JT. Vacceed: a high-throughput in silico vaccine candidate discovery pipeline for eukaryotic pathogens based on reverse vaccinology. Bioinformatics. 2014;30:2381\u20133.","journal-title":"Bioinformatics"},{"issue":"5","key":"1540_CR17","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1093\/bioinformatics\/bti057","volume":"21","author":"JL Gardy","year":"2005","unstructured":"Gardy JL, et al. PSORTb v. 2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics. 2005;21(5):617\u201323.","journal-title":"Bioinformatics"},{"key":"1540_CR18","volume-title":"Specification language for defining user interface panels that are platform-independent","author":"DR Petty","year":"2002","unstructured":"Petty DR, Sylvester SA. Specification language for defining user interface panels that are platform-independent. 2002. Google Patents."},{"issue":"1","key":"1540_CR19","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1128\/JB.01416-08","volume":"191","author":"DA Baltrus","year":"2009","unstructured":"Baltrus DA, et al. The complete genome sequence of Helicobacter pylori strain G27. J Bacteriol. 2009;191(1):447\u20138.","journal-title":"J Bacteriol"},{"issue":"1","key":"1540_CR20","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1006\/clin.1995.1003","volume":"74","author":"M Kotb","year":"1995","unstructured":"Kotb M. Infection and autoimmunity: a story of the host, the pathogen, and the copathogen. Clin Immunol Immunopathol. 1995;74(1):10\u201322.","journal-title":"Clin Immunol Immunopathol"},{"key":"1540_CR21","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1016\/j.meegid.2015.03.027","volume":"32","author":"A Naz","year":"2015","unstructured":"Naz A, et al. Identification of putative vaccine candidates against Helicobacter pylori exploiting exoproteome and secretome: a reverse vaccinology based approach. Infect Genet Evol. 2015;32:280\u201391.","journal-title":"Infect Genet Evol"},{"issue":"suppl 1","key":"1540_CR22","doi-asserted-by":"crossref","first-page":"D61","DOI":"10.1093\/nar\/gkl842","volume":"35","author":"KD Pruitt","year":"2007","unstructured":"Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2007;35 suppl 1:D61\u20135.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"1540_CR23","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1093\/nar\/gkg095","volume":"31","author":"B Boeckmann","year":"2003","unstructured":"Boeckmann B, et al. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 2003;31(1):365\u201370.","journal-title":"Nucleic Acids Res"},{"issue":"10","key":"1540_CR24","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/gb-2001-2-10-reviews2002","volume":"2","author":"A Pertsemlidis","year":"2001","unstructured":"Pertsemlidis A, Fondon JW, John W. Having a BLAST with bioinformatics (and avoiding BLASTphemy). Genome Biol. 2001;2(10):1\u201310.","journal-title":"Genome Biol"},{"key":"1540_CR25","doi-asserted-by":"crossref","unstructured":"Kaufmann SH, Lambert PH. The grand challenge for the future: vaccines for poverty-related diseases from bench to field. Springer Science & Business Media; 2005. http:\/\/www.springer.com\/br\/book\/9783764371753 .","DOI":"10.1007\/3-7643-7381-4"},{"issue":"3","key":"1540_CR26","first-page":"R","volume":"56","author":"G Grandi","year":"2007","unstructured":"Grandi G. Bacterial surface proteins and vaccines. Ital J Biochem. 2007;56(3):R.","journal-title":"Ital J Biochem"},{"issue":"6","key":"1540_CR27","doi-asserted-by":"crossref","first-page":"e99368","DOI":"10.1371\/journal.pone.0099368","volume":"9","author":"C-S Yu","year":"2014","unstructured":"Yu C-S, et al. CELLO2GO: a Web server for protein subCELlular LOcalization prediction with functional gene ontology annotation. PLoS One. 2014;9(6):e99368.","journal-title":"PLoS One"},{"issue":"D1","key":"1540_CR28","doi-asserted-by":"crossref","first-page":"D574","DOI":"10.1093\/nar\/gkt1131","volume":"42","author":"H Luo","year":"2013","unstructured":"Luo H, et al. DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements. Nucleic Acids Res. 2013;42(D1):D574\u2013D80.","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"1540_CR29","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1128\/CMR.14.2.229-243.2001","volume":"14","author":"E Handman","year":"2001","unstructured":"Handman E. Leishmaniasis: current status of vaccine development. Clin Microbiol Rev. 2001;14(2):229\u201343.","journal-title":"Clin Microbiol Rev"},{"issue":"1","key":"1540_CR30","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/j.ygeno.2014.05.002","volume":"104","author":"SA Muhammad","year":"2014","unstructured":"Muhammad SA, et al. Prioritizing drug targets in Clostridium botulinum with a computational systems biology approach. Genomics. 2014;104(1):24\u201335.","journal-title":"Genomics"},{"issue":"suppl 1","key":"1540_CR31","first-page":"D325","volume":"33","author":"L Chen","year":"2005","unstructured":"Chen L, et al. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res. 2005;33 suppl 1:D325\u20138.","journal-title":"Nucleic Acids Res"},{"issue":"9","key":"1540_CR32","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1093\/bioinformatics\/17.9.849","volume":"17","author":"GE Tusnady","year":"2001","unstructured":"Tusnady GE, Simon I. The HMMTOP transmembrane topology prediction server. Bioinformatics. 2001;17(9):849\u201350.","journal-title":"Bioinformatics"},{"issue":"suppl 1","key":"1540_CR33","first-page":"D190","volume":"36","author":"U Consortium","year":"2008","unstructured":"Consortium U. The universal protein resource (UniProt). Nucleic Acids Res. 2008;36 suppl 1:D190\u20135.","journal-title":"Nucleic Acids Res"},{"issue":"12","key":"1540_CR34","doi-asserted-by":"crossref","first-page":"1717","DOI":"10.1086\/588383","volume":"197","author":"P-F Hsieh","year":"2008","unstructured":"Hsieh P-F, et al. Serum-induced iron-acquisition systems and TonB contribute to virulence in Klebsiella pneumoniae causing primary pyogenic liver abscess. J Infect Dis. 2008;197(12):1717\u201327.","journal-title":"J Infect Dis"},{"key":"1540_CR35","first-page":"1","volume":"7","author":"C Constantinescu","year":"2014","unstructured":"Constantinescu C, Constantinescu E. Could knowledge of H. pylori pathogenicity factors lead to the emergence of new methods for identifying bacteria? Bull Transilvania University of Brasov, Seriels VI: Medical Sciences. 2014;7:1.","journal-title":"Bull Transilvania University of Brasov, Seriels VI: Medical Sciences"},{"issue":"4","key":"1540_CR36","doi-asserted-by":"crossref","first-page":"542","DOI":"10.1128\/CDLI.10.4.542-545.2003","volume":"10","author":"PR Mittl","year":"2003","unstructured":"Mittl PR, et al. Detection of high titers of antibody against Helicobacter cysteine-rich proteins A, B, C, and E in Helicobacter pylori-infected individuals. Clin Diagn Lab Immunol. 2003;10(4):542\u20135.","journal-title":"Clin Diagn Lab Immunol"},{"issue":"1","key":"1540_CR37","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.cellsig.2006.05.034","volume":"19","author":"PR Mittl","year":"2007","unstructured":"Mittl PR, Schneider-Brachert W. Sel1-like repeat proteins in signal transduction. Cell Signal. 2007;19(1):20\u201331.","journal-title":"Cell Signal"},{"issue":"1","key":"1540_CR38","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","volume":"10","author":"C Camacho","year":"2009","unstructured":"Camacho C, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10(1):421.","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"1540_CR39","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1093\/bib\/3.3.265","volume":"3","author":"CJ Sigrist","year":"2002","unstructured":"Sigrist CJ, et al. PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform. 2002;3(3):265\u201374.","journal-title":"Brief Bioinform"},{"issue":"1","key":"1540_CR40","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1002\/prot.21078","volume":"65","author":"S Saha","year":"2006","unstructured":"Saha S, Raghava G. Prediction of continuous B\u2010cell epitopes in an antigen using recurrent neural network. Proteins. 2006;65(1):40\u20138.","journal-title":"Proteins"},{"issue":"8","key":"1540_CR41","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1093\/bioinformatics\/btg108","volume":"19","author":"H Singh","year":"2003","unstructured":"Singh H, Raghava G. ProPred1: prediction of promiscuous MHC Class-I binding sites. Bioinformatics. 2003;19(8):1009\u201314.","journal-title":"Bioinformatics"},{"issue":"12","key":"1540_CR42","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1093\/bioinformatics\/17.12.1236","volume":"17","author":"H Singh","year":"2001","unstructured":"Singh H, Raghava G. ProPred: prediction of HLA-DR binding sites. Bioinformatics. 2001;17(12):1236\u20137.","journal-title":"Bioinformatics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-017-1540-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,10,2]],"date-time":"2020-10-02T09:16:31Z","timestamp":1601630191000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-017-1540-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,2,13]]},"references-count":42,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2017,12]]}},"alternative-id":["1540"],"URL":"https:\/\/doi.org\/10.1186\/s12859-017-1540-0","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,2,13]]},"article-number":"106"}}