{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T00:53:27Z","timestamp":1785372807791,"version":"3.55.0"},"reference-count":67,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2007,8,10]],"date-time":"2007-08-10T00:00:00Z","timestamp":1186704000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.0030151","type":"journal-article","created":{"date-parts":[[2007,8,7]],"date-time":"2007-08-07T12:15:14Z","timestamp":1186488914000},"page":"e151","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":33,"title":["Helicobacter pylori Evolution: Lineage- Specific Adaptations in Homologs of Eukaryotic Sel1-Like Genes"],"prefix":"10.1371","volume":"3","author":[{"given":"Masako","family":"Ogura","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J. Christian","family":"Perez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peer R. E","family":"Mittl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hae-Kyung","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Geidrius","family":"Dailide","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shumin","family":"Tan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yoshiyuki","family":"Ito","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ousman","family":"Secka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daiva","family":"Dailidiene","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kalyani","family":"Putty","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Douglas E","family":"Berg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Awdhesh","family":"Kalia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2007,8,10]]},"reference":[{"key":"pcbi-0030151-b001","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1128\/CMR.00006-06","article-title":"Helicobacter pylori persistence: An overview of interactions between H. pylori and host immune hefenses.","volume":"19","year":"2006","journal-title":"Clin Microbiol Rev"},{"key":"pcbi-0030151-b002","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1128\/CMR.00054-05","article-title":"Pathogenesis of Helicobacter pylori infection.","volume":"19","year":"2006","journal-title":"Clin Microbiol Rev"},{"key":"pcbi-0030151-b003","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1172\/JCI20925","article-title":"Helicobacter pylori persistence: Biology and disease.","volume":"113","year":"2004","journal-title":"J Clin Investigation"},{"key":"pcbi-0030151-b004","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1097\/01.mog.0000194790.51714.f0","article-title":"The role of persistence in Helicobacter pylori pathogenesis.","volume":"22","year":"2006","journal-title":"Curr Opin Gastroenterol"},{"key":"pcbi-0030151-b005","doi-asserted-by":"crossref","first-page":"5137","DOI":"10.1093\/nar\/20.19.5137","article-title":"DNA diversity among clinical isolates of Helicobacter pylori detected by PCR-based RAPD fingerprinting.","volume":"20","year":"1992","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0030151-b006","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1046\/j.1365-2958.1999.01382.x","article-title":"Recombination and clonal groupings within Helicobacter pylori from different geographical regions.","volume":"32","year":"1999","journal-title":"Mol Microbiol"},{"key":"pcbi-0030151-b007","doi-asserted-by":"crossref","first-page":"1582","DOI":"10.1126\/science.1080857","article-title":"Traces of human migrations in Helicobacter pylori populations.","volume":"299","year":"2003","journal-title":"Science"},{"key":"pcbi-0030151-b008","doi-asserted-by":"crossref","first-page":"3210","DOI":"10.1128\/JB.182.11.3210-3218.2000","article-title":"Differences in genotypes of Helicobacter pylori from different human populations.","volume":"182","year":"2000","journal-title":"J Bacteriol"},{"key":"pcbi-0030151-b009","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1126\/science.1098801","article-title":"Functional adaptation of BabA, the H. pylori ABO blood group antigen binding adhesin.","volume":"305","year":"2004","journal-title":"Science"},{"key":"pcbi-0030151-b010","doi-asserted-by":"crossref","first-page":"12619","DOI":"10.1073\/pnas.95.21.12619","article-title":"Free recombination within Helicobacter pylori.","volume":"95","year":"1998","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0030151-b011","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1046\/j.1365-2958.1999.01140.x","article-title":"Emergence of recombinant strains of Helicobacter pylori during human infection.","volume":"31","year":"1999","journal-title":"Mol Microbiol"},{"key":"pcbi-0030151-b012","doi-asserted-by":"crossref","first-page":"15056","DOI":"10.1073\/pnas.251396098","article-title":"Recombination and mutation during long-term gastric colonization by Helicobacter pylori: Estimates of clock rates, recombination size, and minimal age.","volume":"98","year":"2001","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0030151-b013","first-page":"5","article-title":"Prevalence of Helicobacter pylori infection in disorders of the upper gastrointestinal tract in south India.","volume":"11","year":"1998","journal-title":"Natl Med J India"},{"key":"pcbi-0030151-b014","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1111\/j.1523-5378.2005.00304.x","article-title":"Geographic pathology of Helicobacter pylori gastritis.","volume":"10","year":"2005","journal-title":"Helicobacter"},{"key":"pcbi-0030151-b015","doi-asserted-by":"crossref","first-page":"1328","DOI":"10.1126\/science.284.5418.1328","article-title":"Helicobacter pylori virulence and genetic geography.","volume":"284","year":"1999","journal-title":"Science"},{"key":"pcbi-0030151-b016","unstructured":"WrightS 1977 Evolution and the genetics of populations Chicago The University of Chicago Press"},{"key":"pcbi-0030151-b017","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1038\/ng1202-569","article-title":"Biological and biomedical implications of the co-evolution of pathogens and their hosts.","volume":"32","year":"2002","journal-title":"Nat Genet"},{"key":"pcbi-0030151-b018","doi-asserted-by":"crossref","first-page":"14428","DOI":"10.1073\/pnas.222375399","article-title":"Biological activity of the Helicobacter pylori virulence factor CagA is determined by variation in the tyrosine phosphorylation sites.","volume":"99","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0030151-b019","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1146\/annurev.pathol.1.110304.100125","article-title":"The pathogenesis of Helicobacter pylori induced gastro-duodenal diseases.","volume":"1","year":"2006","journal-title":"Annu Rev Pathol: Mech Dis"},{"key":"pcbi-0030151-b020","doi-asserted-by":"crossref","first-page":"2274","DOI":"10.1128\/JCM.37.7.2274-2279.1999","article-title":"Relationship between Helicobacter pylori iceA, cagA, and vacA Status and clinical outcome: Studies in four different countries.","volume":"37","year":"1999","journal-title":"J Clin Microbiol"},{"key":"pcbi-0030151-b021","doi-asserted-by":"crossref","first-page":"1710","DOI":"10.1128\/JCM.35.7.1710-1714.1997","article-title":"Analysis and typing of the vacA gene from cagA-positive strains of Helicobacter pylori isolated in Japan.","volume":"35","year":"1997","journal-title":"J Clin Microbiol"},{"key":"pcbi-0030151-b022","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1086\/515601","article-title":"Prevalence of vacuolating cytotoxin production and distribution of distinct vacA alleles in Helicobacter pylori from China.","volume":"178","year":"1998","journal-title":"J Infect Dis"},{"key":"pcbi-0030151-b023","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1016\/0966-842X(93)90047-U","article-title":"Helicobacter pylori: Microbiology of a \u201cslow\u201d bacterial infection.","volume":"1","year":"1993","journal-title":"Trends Microbiol"},{"key":"pcbi-0030151-b024","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1126\/science.1069076","article-title":"Helicobacter pylori SabA adhesin in persistent infection and chronic inflammation.","volume":"297","year":"2002","journal-title":"Science"},{"key":"pcbi-0030151-b025","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1002\/jcp.20574","article-title":"SEL1L a multifaceted protein playing a role in tumor progression.","volume":"208","year":"2006","journal-title":"J Cellular Physiol"},{"key":"pcbi-0030151-b026","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.cellsig.2006.05.034","article-title":"Sel1-like repeat proteins in signal transduction.","volume":"19","year":"2007","journal-title":"Cellular Signalling"},{"key":"pcbi-0030151-b027","doi-asserted-by":"crossref","first-page":"17693","DOI":"10.1074\/jbc.M001869200","article-title":"The cysteine-rich Protein A from Helicobacter pylori is a beta-lactamase.","volume":"275","year":"2000","journal-title":"J Biol Chem"},{"key":"pcbi-0030151-b028","doi-asserted-by":"crossref","first-page":"542","DOI":"10.1128\/CDLI.10.4.542-545.2003","article-title":"Detection of high titers of antibody against Helicobacter cysteine-rich proteins A, B, C, and E in Helicobacter pylori\u2013infected individuals.","volume":"10","year":"2003","journal-title":"Clin Diagn Lab Immunol"},{"key":"pcbi-0030151-b029","doi-asserted-by":"crossref","first-page":"5107","DOI":"10.1128\/JB.181.16.5107-5110.1999","article-title":"Identification of a novel penicillin-binding protein from Helicobacter pylori.","volume":"181","year":"1999","journal-title":"J Bacteriol"},{"key":"pcbi-0030151-b030","doi-asserted-by":"crossref","first-page":"4732","DOI":"10.1128\/IAI.73.8.4732-4742.2005","article-title":"Characterization of the Helicobacter pylori cysteine-rich protein A as a T-helper cell type 1 polarizing agent.","volume":"73","year":"2005","journal-title":"Infect Immun"},{"key":"pcbi-0030151-b031","doi-asserted-by":"crossref","first-page":"4713","DOI":"10.1128\/IAI.67.9.4713-4719.1999","article-title":"Isolation of recombinant Protective Helicobacter pylori antigens.","volume":"67","year":"1999","journal-title":"Infect Immun"},{"key":"pcbi-0030151-b032","unstructured":"GraurDLiW-H 2000 Fundamentals of molecular evolution Sunderland (Massachusetts) Sinauer Associates"},{"key":"pcbi-0030151-b033","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1016\/S0959-437X(02)00348-9","article-title":"Inference of selection from multiple species alignments.","volume":"12","year":"2002","journal-title":"Curr Opin Genetics Development"},{"key":"pcbi-0030151-b034","unstructured":"GillespieJH 1991 The causes and consequences of molecular evolution New York Oxford University Press"},{"key":"pcbi-0030151-b035","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1093\/genetics\/155.1.431","article-title":"Codon-substitution models for heterogeneous selection pressure at amino acid sites.","volume":"155","year":"2000","journal-title":"Genetics"},{"key":"pcbi-0030151-b036","doi-asserted-by":"crossref","first-page":"908","DOI":"10.1093\/oxfordjournals.molbev.a004148","article-title":"Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages.","volume":"19","year":"2002","journal-title":"Mol Biol Evol"},{"key":"pcbi-0030151-b037","doi-asserted-by":"crossref","first-page":"992","DOI":"10.1128\/jb.184.4.992-1002.2002","article-title":"Transposable Element ISHp608 of Helicobacter pylori: Nonrandom geographic distribution, functional organization, and insertion specificity.","volume":"184","year":"2002","journal-title":"J Bacteriol"},{"key":"pcbi-0030151-b038","doi-asserted-by":"crossref","first-page":"13108","DOI":"10.1073\/pnas.95.22.13108","article-title":"PCR-based subtractive hybridization and differences in gene content among strains of Helicobacter pylori.","volume":"95","year":"1998","journal-title":"Proc Natl Acad Sci"},{"key":"pcbi-0030151-b039","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1038\/41483","article-title":"The complete genome sequence of the gastric pathogen Helicobacter pylori.","volume":"388","year":"1997","journal-title":"Nature"},{"key":"pcbi-0030151-b040","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1038\/16495","article-title":"Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori.","volume":"397","year":"1999","journal-title":"Nature"},{"key":"pcbi-0030151-b041","doi-asserted-by":"crossref","first-page":"9999","DOI":"10.1073\/pnas.0603784103","article-title":"The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: Evolution during disease progression.","volume":"103","year":"2006","journal-title":"Proc Natl Acad Sci"},{"key":"pcbi-0030151-b042","article-title":"Who ate whom? Adaptive Helicobacter genomic changes that accompanied a host jump from early humans to large felines.","volume":"2","year":"2006","journal-title":"PLoS Genetics"},{"key":"pcbi-0030151-b043","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1128\/JB.186.2.356-365.2004","article-title":"Helicobacter acinonychis: Genetic and rodent infection studies of a Helicobacter pylori\u2013like Gastric pathogen of cheetahs and other big cats.","volume":"186","year":"2004","journal-title":"J Bacteriol"},{"key":"pcbi-0030151-b044","doi-asserted-by":"crossref","first-page":"7901","DOI":"10.1073\/pnas.1332093100","article-title":"The complete genome sequence of the carcinogenic bacterium Helicobacter hepaticus.","volume":"100","year":"2003","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0030151-b045","doi-asserted-by":"crossref","first-page":"11690","DOI":"10.1073\/pnas.1932838100","article-title":"Complete genome sequence and analysis of Wolinella succinogenes.","volume":"100","year":"2003","journal-title":"Proc Natl Acad Sci"},{"key":"pcbi-0030151-b046","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1126\/science.290.5494.1151","article-title":"The evolutionary fate and consequences of duplicate genes.","volume":"290","year":"2000","journal-title":"Science"},{"key":"pcbi-0030151-b047","doi-asserted-by":"crossref","first-page":"17319","DOI":"10.1073\/pnas.0608309103","article-title":"Multiple pathways of selected gene amplification during adaptive mutation.","volume":"103","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0030151-b048","doi-asserted-by":"crossref","first-page":"7687","DOI":"10.1128\/JB.187.22.7687-7695.2005","article-title":"Diverse phenotypes resulting from polyphosphate kinase gene (ppk1) inactivation in different strains of Helicobacter pylori.","volume":"187","year":"2005","journal-title":"J Bacteriol"},{"key":"pcbi-0030151-b049","doi-asserted-by":"crossref","first-page":"1076","DOI":"10.1038\/nm1097-1076","article-title":"Gastrogenomic delights: A movable feast.","volume":"3","year":"1997","journal-title":"Nat Med"},{"key":"pcbi-0030151-b050","doi-asserted-by":"crossref","first-page":"826","DOI":"10.1038\/nrmicro1528","article-title":"Bacterial populations as perfect gases: Genomic integrity and diversification tensions in Helicobacter pylori.","volume":"4","year":"2006","journal-title":"Nat Rev Micro"},{"key":"pcbi-0030151-b051","doi-asserted-by":"crossref","first-page":"568","DOI":"10.1093\/oxfordjournals.molbev.a025957","article-title":"Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution.","volume":"15","year":"1998","journal-title":"Mol Biol Evol"},{"key":"pcbi-0030151-b052","doi-asserted-by":"crossref","first-page":"7508","DOI":"10.1128\/JB.186.22.7508-7520.2004","article-title":"Evolutionary dynamics of insertion sequences in Helicobacter pylori.","volume":"186","year":"2004","journal-title":"J Bacteriol"},{"key":"pcbi-0030151-b053","doi-asserted-by":"crossref","first-page":"1686","DOI":"10.1093\/oxfordjournals.molbev.a003991","article-title":"Phylogenetic evidence for frequent positive selection and recombination in the meningococcal surface antigen PorB.","volume":"19","year":"2002","journal-title":"Mol Biol Evol"},{"key":"pcbi-0030151-b054","doi-asserted-by":"crossref","first-page":"1229","DOI":"10.1093\/genetics\/164.3.1229","article-title":"Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites.","volume":"164","year":"2003","journal-title":"Genetics"},{"key":"pcbi-0030151-b055","doi-asserted-by":"crossref","first-page":"1464","DOI":"10.1158\/1055-9965.EPI-05-0095","article-title":"Intestinal helminthiasis in Colombian children promotes a Th2 response to Helicobacter pylori: Possible implications for gastric carcinogenesis.","volume":"14","year":"2005","journal-title":"Cancer Epidemiol Biomarkers Prev"},{"key":"pcbi-0030151-b056","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1016\/j.micinf.2005.05.017","article-title":"Helicobacter pylori and Schistosoma japonicum co-infection in a Chinese population: Helminth infection alters humoral responses to H. pylori and serum pepsinogen I\/II ratio.","volume":"8","year":"2006","journal-title":"Microbes Infection"},{"key":"pcbi-0030151-b057","doi-asserted-by":"crossref","first-page":"10187","DOI":"10.1074\/jbc.M108993200","article-title":"The crystal structure of Helicobacter pylori cysteine-rich protein B reveals a novel fold for a penicillin-binding protein.","volume":"277","year":"2002","journal-title":"J Biol Chem"},{"key":"pcbi-0030151-b058","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1016\/j.jmb.2004.04.055","article-title":"The crystal structure of Helicobacter cysteine-rich protein C at 2.0 A resolution: Similar peptide-binding sites in TPR and SEL1-like repeat proteins.","volume":"340","year":"2004","journal-title":"J Mol Biol"},{"key":"pcbi-0030151-b059","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1038\/nrg1838","article-title":"An integrated view of protein evolution.","volume":"7","year":"2006","journal-title":"Nat Rev Genet"},{"key":"pcbi-0030151-b060","doi-asserted-by":"crossref","first-page":"14878","DOI":"10.1073\/pnas.232565499","article-title":"Dobzhansky-Muller incompatibilities in protein evolution.","volume":"99","year":"2002","journal-title":"Proc Natl Acad Sci"},{"key":"pcbi-0030151-b061","doi-asserted-by":"crossref","first-page":"1323","DOI":"10.1534\/genetics.104.037259","article-title":"The coupon collector and the suppressor mutation: Estimating the number of compensatory mutations by maximum likelihood.","volume":"170","year":"2005","journal-title":"Genetics"},{"key":"pcbi-0030151-b062","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1093\/genetics\/143.1.237","article-title":"The Caenorhabditis elegans sel-1 gene, a negative regulator of lin-12 and glp-1, encodes a predicted extracellular protein.","volume":"143","year":"1996","journal-title":"Genetics"},{"key":"pcbi-0030151-b063","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1016\/j.gene.2003.10.021","article-title":"Identification of a region within SEL1L protein required for tumour growth inhibition.","volume":"326","year":"2004","journal-title":"Gene"},{"key":"pcbi-0030151-b064","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1007\/s10120-002-0203-6","article-title":"The epidemiology of gastric cancer.","volume":"5","year":"2002","journal-title":"Gastric Cancer"},{"key":"pcbi-0030151-b065","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1038\/35001088","article-title":"The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences.","volume":"403","year":"2000","journal-title":"Nature"},{"key":"pcbi-0030151-b066","article-title":"Major structural differences and novel potential virulence mechanisms from the genomes of multiple Campylobacter Species.","volume":"3","year":"2005","journal-title":"PLoS Biology"},{"key":"pcbi-0030151-b067","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1093\/oxfordjournals.molbev.a025634","article-title":"Excess amino acid polymorphism in mitochondrial DNA: Contrasts among genes from Drosophila, mice, and humans.","volume":"13","year":"1996","journal-title":"Mol Biol Evol"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.0030151","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,8,21]],"date-time":"2021-08-21T09:22:52Z","timestamp":1629537772000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.0030151"}},"subtitle":[],"editor":[{"given":"Jonathan A","family":"Eisen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2007,8,10]]},"references-count":67,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2007,8,10]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.0030151","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,8,10]]}}}