{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T04:20:51Z","timestamp":1775276451889,"version":"3.50.1"},"reference-count":94,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2018,8,20]],"date-time":"2018-08-20T00:00:00Z","timestamp":1534723200000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001775","name":"University of Technology Sydney","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001775","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Genet."],"DOI":"10.3389\/fgene.2018.00332","type":"journal-article","created":{"date-parts":[[2018,8,20]],"date-time":"2018-08-20T04:12:00Z","timestamp":1534738320000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":23,"title":["A Gene-Based Positive Selection Detection Approach to Identify Vaccine Candidates Using Toxoplasma gondii as a Test Case Protozoan Pathogen"],"prefix":"10.3389","volume":"9","author":[{"given":"Stephen J.","family":"Goodswen","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paul J.","family":"Kennedy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John T.","family":"Ellis","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2018,8,20]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"D415","DOI":"10.1093\/nar\/gkp941","article-title":"EuPathDB: a portal to eukaryotic pathogen databases.","volume":"38","author":"Aurrecoechea","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"B2","doi-asserted-by":"publisher","first-page":"795","DOI":"10.1128\/cmr.00001-10","article-title":"Importance of nonenteric protozoan infections in immunocompromised people.","volume":"23","author":"Barratt","year":"2010","journal-title":"Clin. Microbiol. Rev."},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2014.00359","article-title":"Strategies for designing and monitoring malaria vaccines targeting diverse antigens.","volume":"5","author":"Barry","year":"2014","journal-title":"Front. Immunol."},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1005434","article-title":"Rhoptry proteins ROP5 and ROP18 are major murine virulence factors in genetically divergent South American strains of Toxoplasma gondii.","volume":"11","author":"Behnke","year":"2015","journal-title":"PLoS Genet."},{"key":"B5","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1007\/s00439-018-1866-3","article-title":"Complex signatures of natural selection at GYPA.","volume":"137","author":"Bigham","year":"2018","journal-title":"Hum. Genet."},{"key":"B6","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1186\/BF03546972","article-title":"Evidence that Neospora caninum is identical to the Toxoplasma-like parasite of Norwegian dogs.","volume":"32","author":"Bjerkas","year":"1991","journal-title":"Acta Vet. Scand."},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2009-10-5-r53","article-title":"Whole genome sequencing of a natural recombinant Toxoplasma gondii strain reveals chromosome sorting and local allelic variants.","volume":"10","author":"Bontell","year":"2009","journal-title":"Genome Biol."},{"key":"B8","doi-asserted-by":"publisher","first-page":"8156","DOI":"10.1016\/j.vaccine.2011.07.142","article-title":"Improving reverse vaccinology with a machine learning approach.","volume":"29","author":"Bowman","year":"2011","journal-title":"Vaccine"},{"key":"B9","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1007\/bf00958921","article-title":"Estimation of Wright\u2019s fixation index from genotypic frequencies.","volume":"41","author":"Brown","year":"1970","journal-title":"Genetica"},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST plus: architecture and applications.","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"B11","article-title":"Comprehensive proteomic analysis of membrane proteins in Toxoplasma gondii.","volume":"10","author":"Che","year":"2010","journal-title":"Mol. Cell. Proteomics"},{"key":"B12","doi-asserted-by":"publisher","first-page":"617","DOI":"10.1586\/14760584.2015.1011133","article-title":"DNA vaccination with genes encoding Toxoplasma gondii antigens ROP5 and GRA15 induces protective immunity against toxoplasmosis in Kunming mice.","volume":"14","author":"Chen","year":"2015","journal-title":"Expert Rev. Vaccines"},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0003611","article-title":"In silico identification of specialized secretory-organelle proteins in apicomplexan parasites and In vivo validation in Toxoplasma gondii.","volume":"3","author":"Chen","year":"2008","journal-title":"PLoS One"},{"key":"B14","doi-asserted-by":"publisher","first-page":"754","DOI":"10.1016\/j.vaccine.2010.11.015","article-title":"Towards an immunosense vaccine to prevent toxoplasmosis: protective Toxoplasma gondii epitopes restricted by HLA-A\u22170201.","volume":"29","author":"Cong","year":"2011","journal-title":"Vaccine"},{"key":"B15","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1016\/j.molbiopara.2007.02.013","article-title":"Increased efficiency of homologous recombination in Toxoplasma gondii dense granule protein 3 demonstrates that GRA3 is not necessary in cell culture but does contribute to virulence.","volume":"153","author":"Craver","year":"2007","journal-title":"Mol. Biochem. Parasitol."},{"key":"B16","doi-asserted-by":"publisher","first-page":"389","DOI":"10.1016\/j.drudis.2007.03.010","article-title":"Harnessing bioinformatics to discover new vaccines.","volume":"12","author":"Davies","year":"2007","journal-title":"Drug Discov. Today"},{"key":"B17","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1128\/CMR.11.4.569","article-title":"Regulation and function of T-cell-mediated immunity during Toxoplasma gondii infection.","volume":"11","author":"Denkers","year":"1998","journal-title":"Clin. Microbiol. Rev."},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.1155\/2008\/632424","article-title":"Toxoplasma rhoptries: unique secretory organelles and source of promising vaccine proteins for immunoprevention of toxoplasmosis.","volume":"2008","author":"Dlugonska","year":"2008","journal-title":"J. Biomed. Biotechnol."},{"key":"B19","doi-asserted-by":"publisher","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":"Year Immunol."},{"key":"B20","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/j.ijpara.2010.08.002","article-title":"Plasmodium immunomics.","volume":"41","author":"Doolan","year":"2011","journal-title":"Int. J. Parasitol."},{"key":"B21","doi-asserted-by":"publisher","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 Bioinformatics"},{"key":"B22","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1016\/s1471-4922(01)02172-9","article-title":"Neospora, caninum and Hammondia heydorni are separate species.","volume":"18","author":"Dubey","year":"2002","journal-title":"Trends Parasitol."},{"key":"B23","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1016\/j.exppara.2012.02.026","article-title":"Toxoplasma gondii: the vaccine potential of three trivalent antigen-cocktails composed of recombinant ROP 2, ROP 4, GRA4 and SAG1 proteins against chronic toxoplasmosis in BALB\/c mice.","volume":"131","author":"Dziadek","year":"2012","journal-title":"Exp. Parasitol."},{"key":"B24","doi-asserted-by":"publisher","first-page":"452","DOI":"10.1007\/s00436-004-1237-y","article-title":"Sarcocystis neurona major surface antigen gene 1 (SAG1) shows evidence of having evolved under positive selection pressure.","volume":"94","author":"Elsheikha","year":"2004","journal-title":"Parasitol. Res."},{"key":"B25","doi-asserted-by":"publisher","first-page":"953","DOI":"10.1038\/nprot.2007.131","article-title":"Locating proteins in the cell using TargetP, SignalP and related tools.","volume":"2","author":"Emanuelsson","year":"2007","journal-title":"Nat. Protoc."},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.1186\/1745-7580-6-S2-S1","article-title":"Computer aided selection of candidate vaccine antigens.","author":"Flower","year":"2010","journal-title":"Immunome Res."},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1002355","article-title":"Signatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution.","volume":"7","author":"Fumagalli","year":"2011","journal-title":"PLoS Genet."},{"key":"B28","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2018.00010","article-title":"Identifying potential Plasmodium vivax sporozoite stage vaccine candidates: an analysis of genetic diversity and natural selection.","volume":"9","author":"Garzon-Ospina","year":"2018","journal-title":"Front. Genet."},{"key":"B29","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-14-315","article-title":"A novel strategy for classifying the output from an in silico vaccine discovery pipeline for eukaryotic pathogens using machine learning algorithms.","volume":"14","author":"Goodswen","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"B30","doi-asserted-by":"publisher","first-page":"2381","DOI":"10.1093\/bioinformatics\/btu300","article-title":"Vacceed: a high-throughput in silico vaccine candidate discovery pipeline for eukaryotic pathogens based on reverse vaccinology.","volume":"30","author":"Goodswen","year":"2014","journal-title":"Bioinformatics"},{"key":"B31","doi-asserted-by":"publisher","first-page":"4553","DOI":"10.1007\/s00436-015-4701-y","article-title":"Towards vaccine against toxoplasmosis: evaluation of the immunogenic and protective activity of recombinant ROP5 and ROP18 Toxoplasma gondii proteins.","volume":"114","author":"Grzybowski","year":"2015","journal-title":"Parasitol. Res."},{"key":"B32","doi-asserted-by":"publisher","first-page":"252","DOI":"10.1038\/nature02240","article-title":"Immune recognition of a human renal cancer antigen through post-translational protein splicing.","volume":"427","author":"Hanada","year":"2004","journal-title":"Nature"},{"key":"B33","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1002\/ajpa.20518","article-title":"The molecular signature of selection underlying human adaptations.","volume":"49","author":"Harris","year":"2006","journal-title":"Yearb. Phys. Anthropol."},{"key":"B34","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-015-1225-x","article-title":"Asexual expansion of Toxoplasma gondii merozoites is distinct from tachyzoites and entails expression of non-overlapping gene families to attach, invade, and replicate within feline enterocytes.","volume":"16","author":"Hehl","year":"2015","journal-title":"BMC Genomics"},{"key":"B35","doi-asserted-by":"publisher","first-page":"W585","DOI":"10.1093\/nar\/gkm259","article-title":"WoLF PSORT: protein localization predictor.","author":"Horton","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"B36","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1093\/genetics\/127.2.345","article-title":"Circumsporozoite protein genes of malaria parasites (Plasmodium spp): evidence for positive selection on immunogenic regions.","volume":"127","author":"Hughes","year":"1991","journal-title":"Genetics"},{"key":"B37","doi-asserted-by":"publisher","first-page":"497","DOI":"10.1016\/s1471-4922(02)02372-3","article-title":"Immune responses to Neospora caninum and prospects for vaccination.","volume":"18","author":"Innes","year":"2002","journal-title":"Trends Parasitol."},{"key":"B38","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4939-1438-8_4","article-title":"\u201cA beginners guide to estimating the non-synonymous to synonymous rate ratio of all protein-coding genes in a genome,\u201d in","author":"Jeffares","year":"2015","journal-title":"Parasite Genomics Protocols. Methods in Molecular Biology"},{"key":"B39","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1017\/s0031182099004618","article-title":"The relationship of Hammondia hammondi and Sarcocystis mucosa to other heteroxenous cyst-farming coccidia as inferred by phylogenetic analysis of the 18S SSU ribosomal DNA sequence.","volume":"119","author":"Jenkins","year":"1999","journal-title":"Parasitology"},{"key":"B40","doi-asserted-by":"publisher","first-page":"519","DOI":"10.1101\/gr.124784.111","article-title":"Genome-wide detection of natural selection in African Americans pre- and post-admixture.","volume":"22","author":"Jin","year":"2012","journal-title":"Genome Res."},{"key":"B41","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1038\/nrd3679","article-title":"Reverse vaccinology on the cusp.","volume":"11","author":"Jones","year":"2012","journal-title":"Nat. Rev. Drug Discov."},{"key":"B42","doi-asserted-by":"publisher","first-page":"1027","DOI":"10.1016\/j.jmb.2004.03.016","article-title":"A combined transmembrane topology and signal peptide prediction method.","volume":"338","author":"Kall","year":"2004","journal-title":"J. Mol. Biol."},{"key":"B43","doi-asserted-by":"publisher","first-page":"1027","DOI":"10.1016\/j.jmb.2004.03.016","article-title":"A combined transmembrane topology and signal peptide prediction method.","volume":"338","author":"K\u00e4ll","year":"2004","journal-title":"J. Mol. Biol."},{"key":"B44","doi-asserted-by":"crossref","first-page":"887","DOI":"10.1093\/genetics\/123.4.887","article-title":"The \u201chitchhiking effect\u201d revisited.","volume":"123","author":"Kaplan","year":"1989","journal-title":"Genetics"},{"key":"B45","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1016\/j.ijpara.2003.12.009","article-title":"Toxoplasma gondii: the model apicomplexan.","volume":"34","author":"Kim","year":"2004","journal-title":"Int. J. Parasitol."},{"key":"B46","doi-asserted-by":"publisher","first-page":"1626","DOI":"10.1128\/iai.01862-06","article-title":"Bradyzoite-specific surface antigen SRS9 plays a role in maintaining Toxoplasma gondii persistence in the brain and in host control of parasite replication in the intestine.","volume":"75","author":"Kim","year":"2007","journal-title":"Infect. Immun."},{"key":"B47","doi-asserted-by":"publisher","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."},{"key":"B48","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.0020071","article-title":"Immunoinformatics comes of age.","volume":"2","author":"Korber","year":"2006","journal-title":"PLoS Comput. Biol."},{"key":"B49","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1006\/jmbi.2000.4315","article-title":"Predicting transmembrane protein topology with a hidden markov model: application to complete genomes.","volume":"305","author":"Krogh","year":"2001","journal-title":"J. Mol. Biol."},{"key":"B50","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1000304","article-title":"The population genetics of dN\/dS.","volume":"4","author":"Kryazhimskiy","year":"2008","journal-title":"PLoS Genet."},{"key":"B51","doi-asserted-by":"publisher","first-page":"2689","DOI":"10.1093\/molbev\/msn213","article-title":"The apicomplexan whole-genome phylogeny: an analysis of incongruence among gene trees.","volume":"25","author":"Kuo","year":"2008","journal-title":"Mol. Biol. Evol."},{"key":"B52","doi-asserted-by":"publisher","first-page":"791","DOI":"10.1586\/erv.09.27","article-title":"Current status of toxoplasmosis vaccine development.","volume":"8","author":"Kur","year":"2009","journal-title":"Expert Rev. Vaccines"},{"key":"B53","doi-asserted-by":"publisher","first-page":"2178","DOI":"10.1101\/gr.1224503","article-title":"OrthoMCL: identification of ortholog groups for eukaryotic genomes.","volume":"13","author":"Li","year":"2003","journal-title":"Genome Res."},{"key":"B54","doi-asserted-by":"publisher","first-page":"2059","DOI":"10.1128\/iai.01285-10","article-title":"Extensive polymorphism and evidence of immune selection in a highly dominant antigen recognized by bovine CD8 T cells specific for Theileria annulata.","volume":"79","author":"MacHugh","year":"2011","journal-title":"Infect. Immun."},{"key":"B55","doi-asserted-by":"publisher","first-page":"652","DOI":"10.1038\/351652a0","article-title":"Adaptive protein evolution at the Adh locus in Drosophila.","volume":"351","author":"McDonald","year":"1991","journal-title":"Nature"},{"key":"B56","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2334-13-494","article-title":"DNA prime and peptide boost immunization protocol encoding the Toxoplasma gondii GRA4 induces strong protective immunity in BALB\/c mice.","volume":"13","author":"Meng","year":"2013","journal-title":"BMC Infect. Dis."},{"key":"B57","doi-asserted-by":"publisher","first-page":"368","DOI":"10.1128\/iai.70.1.368-379.2002","article-title":"Genomic approach for analysis of surface proteins in Chlamydia pneumoniae.","volume":"70","author":"Montigiani","year":"2002","journal-title":"Infect. Immun."},{"key":"B58","doi-asserted-by":"publisher","first-page":"1965","DOI":"10.1016\/S0140-6736(04)16412-X","article-title":"Toxoplasmosis.","volume":"363","author":"Montoya","year":"2004","journal-title":"Lancet"},{"key":"B59","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1093\/bioinformatics\/btm585","article-title":"Choosing BLAST options for better detection of orthologs as reciprocal best hits.","volume":"24","author":"Moreno-Hagelsieb","year":"2008","journal-title":"Bioinformatics"},{"key":"B60","doi-asserted-by":"publisher","first-page":"375","DOI":"10.1016\/j.pt.2009.05.010","article-title":"Evolution of the Apicomplexa: where are we now?","volume":"25","author":"Morrison","year":"2009","journal-title":"Trends Parasitol."},{"key":"B61","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1001099","article-title":"Long- and short-term selective forces on malaria parasite genomes.","volume":"6","author":"Nygaard","year":"2010","journal-title":"PLoS Genet."},{"key":"B62","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1007\/s00251-016-0902-5","article-title":"Sequence diversity between class I MHC loci of African native and introduced Bos taurus cattle in Theileria parva endemic regions: in silico peptide binding prediction identifies distinct functional clusters.","volume":"68","author":"Obara","year":"2016","journal-title":"Immunogenetics"},{"key":"B63","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1098\/rstb.2009.0219","article-title":"Genome-wide scans for footprints of natural selection.","volume":"365","author":"Oleksyk","year":"2010","journal-title":"Philos. Trans. R. Soc. B Biol. Sci."},{"key":"B64","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1016\/j.biologicals.2013.03.001","article-title":"Reverse-vaccinology strategy for designing T-cell epitope candidates for Staphylococcus aureus endocarditis vaccine.","volume":"41","author":"Oprea","year":"2013","journal-title":"Biologicals"},{"key":"B65","doi-asserted-by":"publisher","first-page":"978","DOI":"10.1016\/j.meegid.2012.02.009","article-title":"Evidence of purifying selection on merozoite surface protein 8 (MSP8) and 10 (MSP10) in Plasmodium spp.","volume":"12","author":"Pacheco","year":"2012","journal-title":"Infect. Genet. Evol."},{"key":"B66","doi-asserted-by":"publisher","first-page":"883","DOI":"10.4269\/ajtmh.12-0727","article-title":"Protective immune response in BALB\/c mice induced by DNA vaccine of the ROP8 gene of Toxoplasma gondii.","volume":"88","author":"Parthasarathy","year":"2013","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"B67","doi-asserted-by":"publisher","first-page":"785","DOI":"10.1038\/nmeth.1701","article-title":"SignalP 4.0: discriminating signal peptides from transmembrane regions.","volume":"8","author":"Petersen","year":"2011","journal-title":"Nat. Methods"},{"key":"B68","doi-asserted-by":"publisher","first-page":"1816","DOI":"10.1126\/science.287.5459.1816","article-title":"Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing.","volume":"287","author":"Pizza","year":"2000","journal-title":"Science"},{"key":"B69","doi-asserted-by":"publisher","first-page":"2593","DOI":"10.1007\/s00436-013-3425-0","article-title":"Evaluation of protective effect of multiantigenic DNA vaccine encoding MIC3 and ROP18 antigen segments of Toxoplasma gondii in mice.","volume":"112","author":"Qu","year":"2013","journal-title":"Parasitol. Res."},{"key":"B70","doi-asserted-by":"publisher","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."},{"key":"B71","doi-asserted-by":"publisher","first-page":"469","DOI":"10.1084\/jem.20151960","article-title":"Reverse vaccinology 2.0: human immunology instructs vaccine antigen design.","volume":"213","author":"Rappuoli","year":"2016","journal-title":"J. Exp. Med."},{"key":"B72","first-page":"195","article-title":"Transport and trafficking: Toxoplasma as a model for Plasmodium.","volume":"226","author":"Roos","year":"1999","journal-title":"Novartis Found. Symp."},{"key":"B73","doi-asserted-by":"publisher","first-page":"2489","DOI":"10.1016\/j.vaccine.2009.02.058","article-title":"Induction of partial protection against infection with Toxoplasma gondii genotype II by DNA vaccination with recombinant chimeric tachyzoite antigens.","volume":"27","author":"Rosenberg","year":"2009","journal-title":"Vaccine"},{"key":"B74","doi-asserted-by":"publisher","first-page":"4135","DOI":"10.1016\/s0264-410x(01)00173-6","article-title":"Identification of vaccine candidate antigens from a genomic analysis of Porphyromonas gingivalis.","volume":"19","author":"Ross","year":"2001","journal-title":"Vaccine"},{"key":"B75","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0018755","article-title":"Evaluating ortholog prediction algorithms in a yeast model clade.","volume":"6","author":"Salichos","year":"2011","journal-title":"PLoS One"},{"key":"B76","doi-asserted-by":"publisher","DOI":"10.1038\/msb.2011.75","article-title":"Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.","volume":"7","author":"Sievers","year":"2011","journal-title":"Mol. Syst. Biol."},{"key":"B77","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-016-2147-1","article-title":"Vaccination with toxofilin DNA in combination with an alum-monophosphoryl lipid A mixed adjuvant induces significant protective immunity against Toxoplasma gondii.","volume":"17","author":"Song","year":"2017","journal-title":"BMC Infect. Dis."},{"key":"B78","doi-asserted-by":"publisher","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"B79","doi-asserted-by":"publisher","first-page":"5844","DOI":"10.1073\/pnas.1203190109","article-title":"Globally diverse Toxoplasma gondii isolates comprise six major clades originating from a small number of distinct ancestral lineages.","volume":"109","author":"Su","year":"2012","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B80","doi-asserted-by":"publisher","first-page":"W609","DOI":"10.1093\/nar\/gkl315","article-title":"PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments.","volume":"34","author":"Suyama","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"B81","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1093\/genetics\/123.3.585","article-title":"Statistical-method for testing the neutral mutation hypothesis by DNA polymorphism.","volume":"123","author":"Tajima","year":"1989","journal-title":"Genetics"},{"key":"B82","doi-asserted-by":"publisher","first-page":"1776","DOI":"10.1126\/science.1133643","article-title":"A secreted serine-threonine kinase determines virulence in the eukaryotic pathogen Toxoplasma gondii.","volume":"314","author":"Taylor","year":"2006","journal-title":"Science"},{"key":"B83","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1007\/s00239-016-9765-5","article-title":"Finding direction in the search for selection.","volume":"84","author":"Thiltgen","year":"2017","journal-title":"J. Mol. Evol."},{"key":"B84","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1146\/annurev-genet-111212-133526","article-title":"Detecting natural selection in genomic data.","volume":"47","author":"Vitti","year":"2013","journal-title":"Annu. Rev. Genet."},{"key":"B85","doi-asserted-by":"publisher","first-page":"7446","DOI":"10.1073\/pnas.1304322110","article-title":"Hammondia hammondi, an avirulent relative of Toxoplasma gondii, has functional orthologs of known T. gondii virulence genes.","volume":"110","author":"Walzer","year":"2013","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B86","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00321-12","article-title":"Integrated bioinformatic and targeted deletion analyses of the SRS gene superfamily identify SRS29C as a negative regulator of Toxoplasma virulence.","volume":"3","author":"Wasmuth","year":"2012","journal-title":"mBio"},{"key":"B87","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1111\/j.1365-3024.2005.00809.x","article-title":"Protecting babies: vaccine strategies to prevent foetopathy in Neospora caninum-infected cattle.","volume":"28","author":"Williams","year":"2006","journal-title":"Parasite Immunol."},{"key":"B88","doi-asserted-by":"publisher","first-page":"1593","DOI":"10.1128\/iai.69.3.1593-1598.2001","article-title":"Use of a whole genome approach to identify vaccine molecules affording protection against Streptococcus pneumoniae infection.","volume":"69","author":"Wizemann","year":"2001","journal-title":"Infect. Immun."},{"key":"B89","doi-asserted-by":"publisher","DOI":"10.1186\/s13323-015-0023-1","article-title":"Inferring positive selection in humans from genomic data.","volume":"6","author":"Wollstein","year":"2015","journal-title":"Investig. Genet."},{"key":"B90","doi-asserted-by":"publisher","first-page":"306","DOI":"10.1007\/bf00160154","article-title":"Maximum-likelihood phylogenetic estimation from DNA-sequences with variable rates over sites: approximate methods.","volume":"39","author":"Yang","year":"1994","journal-title":"J. Mol. Evol."},{"key":"B91","doi-asserted-by":"publisher","first-page":"1586","DOI":"10.1093\/molbev\/msm088","article-title":"PAML 4: phylogenetic analysis by maximum likelihood.","volume":"24","author":"Yang","year":"2007","journal-title":"Mol. Biol. Evol."},{"key":"B92","doi-asserted-by":"publisher","first-page":"1107","DOI":"10.1093\/molbev\/msi097","article-title":"Bayes empirical Bayes inference of amino acid sites under positive selection.","volume":"22","author":"Yang","year":"2005","journal-title":"Mol. Biol. Evol."},{"key":"B93","doi-asserted-by":"publisher","first-page":"1609","DOI":"10.1586\/14760584.2015.1098539","article-title":"Recent advances in developing vaccines against Toxoplasma gondii: an update.","volume":"14","author":"Zhang","year":"2015","journal-title":"Expert Rev. Vaccines"},{"key":"B94","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-016-1496-0","article-title":"Vaccination with Toxoplasma gondii calcium-dependent protein kinase 6 and rhoptry protein 18 encapsulated in poly(lactide-co-glycolide) microspheres induces long-term protective immunity in mice.","volume":"16","author":"Zhang","year":"2016","journal-title":"BMC Infect. Dis."}],"container-title":["Frontiers in Genetics"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fgene.2018.00332\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,8,29]],"date-time":"2022-08-29T19:53:03Z","timestamp":1661802783000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fgene.2018.00332\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,8,20]]},"references-count":94,"alternative-id":["10.3389\/fgene.2018.00332"],"URL":"https:\/\/doi.org\/10.3389\/fgene.2018.00332","relation":{},"ISSN":["1664-8021"],"issn-type":[{"value":"1664-8021","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,8,20]]},"article-number":"332"}}