{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T07:11:37Z","timestamp":1790838697089,"version":"4.1.0"},"reference-count":60,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2016,10,4]],"date-time":"2016-10-04T00:00:00Z","timestamp":1475539200000},"content-version":"vor","delay-in-days":2334,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,10,1]]},"DOI":"10.1093\/nar\/gkq378","type":"journal-article","created":{"date-parts":[[2010,5,17]],"date-time":"2010-05-17T22:24:24Z","timestamp":1274135064000},"page":"6089-6101","source":"Crossref","is-referenced-by-count":159,"title":["Strain-specific genes of Helicobacter pylori: genome evolution driven by a novel type IV secretion system and genomic island transfer"],"prefix":"10.1093","volume":"38","author":[{"given":"Wolfgang","family":"Fischer","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lukas","family":"Windhager","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefanie","family":"Rohrer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthias","family":"Zeiller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arno","family":"Karnholz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Reinhard","family":"Hoffmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ralf","family":"Zimmer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rainer","family":"Haas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2010,5,15]]},"reference":[{"key":"key\n\t\t\t\t20170720162423_B1","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1016\/j.mib.2008.09.006","article-title":"Comparative genomics: the bacterial pan-genome","volume":"11","author":"Tettelin","year":"2008","journal-title":"Curr. Opin. Microbiol."},{"key":"key\n\t\t\t\t20170720162423_B2","doi-asserted-by":"crossref","first-page":"1175","DOI":"10.1056\/NEJMra020542","article-title":"Helicobacter pylori infection","volume":"347","author":"Suerbaum","year":"2002","journal-title":"N. Engl. J. Med."},{"key":"key\n\t\t\t\t20170720162423_B3","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","author":"Tomb","year":"1997","journal-title":"Nature"},{"key":"key\n\t\t\t\t20170720162423_B4","doi-asserted-by":"crossref","first-page":"e1000180","DOI":"10.1371\/journal.ppat.1000180","article-title":"Horizontal versus familial transmission of Helicobacter pylori","volume":"4","author":"Schwarz","year":"2008","journal-title":"PLoS Pathog."},{"key":"key\n\t\t\t\t20170720162423_B5","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1038\/nrmicro1658","article-title":"Helicobacter pylori evolution and phenotypic diversification in a changing host","volume":"5","author":"Suerbaum","year":"2007","journal-title":"Nat. Rev. Microbiol."},{"key":"key\n\t\t\t\t20170720162423_B6","doi-asserted-by":"crossref","first-page":"1582","DOI":"10.1126\/science.1080857","article-title":"Traces of human migrations in Helicobacter pylori populations","volume":"299","author":"Falush","year":"2003","journal-title":"Science"},{"key":"key\n\t\t\t\t20170720162423_B7","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1038\/nature05562","article-title":"An African origin for the intimate association between humans and Helicobacter pylori","volume":"445","author":"Linz","year":"2007","journal-title":"Nature"},{"key":"key\n\t\t\t\t20170720162423_B8","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1086\/315173","article-title":"Quasispecies development of Helicobacter pylori observed in paired isolates obtained years apart from the same host","volume":"181","author":"Kuipers","year":"2000","journal-title":"J. Infect. Dis."},{"key":"key\n\t\t\t\t20170720162423_B9","doi-asserted-by":"crossref","first-page":"14625","DOI":"10.1073\/pnas.251551698","article-title":"Helicobacter pylori genetic diversity within the gastric niche of a single human host","volume":"98","author":"Israel","year":"2001","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"key\n\t\t\t\t20170720162423_B10","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","author":"Kang","year":"2006","journal-title":"Nat. Rev. Microbiol."},{"key":"key\n\t\t\t\t20170720162423_B11","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","author":"Alm","year":"1999","journal-title":"Nature"},{"key":"key\n\t\t\t\t20170720162423_B12","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","author":"Oh","year":"2006","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"key\n\t\t\t\t20170720162423_B13","doi-asserted-by":"crossref","first-page":"e43","DOI":"10.1371\/journal.pgen.0010043","article-title":"Gain and loss of multiple genes during the evolution of Helicobacter pylori","volume":"1","author":"Gressmann","year":"2005","journal-title":"PLoS Genet."},{"key":"key\n\t\t\t\t20170720162423_B14","first-page":"115","article-title":"Type IV secretion systems in Helicobacter pylori","volume-title":"Helicobacter pylori. Molecular Genetics and Cellular Biology","author":"Fischer","year":"2008"},{"key":"key\n\t\t\t\t20170720162423_B15","doi-asserted-by":"crossref","first-page":"2755","DOI":"10.1128\/JB.184.10.2755-2766.2002","article-title":"Characterization of two cryptic Helicobacter pylori plasmids: a putative source for horizontal gene transfer and gene shuffling","volume":"184","author":"Hofreuter","year":"2002","journal-title":"J. Bacteriol."},{"key":"key\n\t\t\t\t20170720162423_B16","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1046\/j.1365-2958.2001.02502.x","article-title":"Natural transformation competence in Helicobacter pylori is mediated by the basic components of a type IV secretion system","volume":"41","author":"Hofreuter","year":"2001","journal-title":"Mol. Microbiol."},{"key":"key\n\t\t\t\t20170720162423_B17","doi-asserted-by":"crossref","first-page":"3764","DOI":"10.1128\/JB.185.13.3764-3772.2003","article-title":"Cluster of type IV secretion genes in Helicobacter pylori's plasticity zone","volume":"185","author":"Kersulyte","year":"2003","journal-title":"J. Bacteriol."},{"key":"key\n\t\t\t\t20170720162423_B18","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20170720162423_B19","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/1471-2105-4-21","article-title":"EasyGene \u2013 a prokaryotic gene finder that ranks ORFs by statistical significance","volume":"4","author":"Larsen","year":"2003","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170720162423_B20","doi-asserted-by":"crossref","first-page":"2607","DOI":"10.1093\/nar\/29.12.2607","article-title":"GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions","volume":"29","author":"Besemer","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720162423_B21","doi-asserted-by":"crossref","first-page":"1622","DOI":"10.1093\/bioinformatics\/bth137","article-title":"Development of joint application strategies for two microbial gene finders","volume":"20","author":"McHardy","year":"2004","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170720162423_B22","doi-asserted-by":"crossref","first-page":"1704","DOI":"10.1093\/nar\/gkg250","article-title":"A revised annotation and comparative analysis of Helicobacter pylori genomes","volume":"31","author":"Boneca","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720162423_B23","doi-asserted-by":"crossref","first-page":"3497","DOI":"10.1093\/nar\/gkg500","article-title":"Multiple sequence alignment with the Clustal series of programs","volume":"31","author":"Chenna","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720162423_B24","volume-title":"Molecular Cloning. A Laboratory Manual","author":"Sambrook","year":"2001","edition":"3rd edn"},{"key":"key\n\t\t\t\t20170720162423_B25","doi-asserted-by":"crossref","first-page":"5908","DOI":"10.1128\/AEM.01135-06","article-title":"Contraselectable streptomycin susceptibility determinant for genetic manipulation and analysis of Helicobacter pylori","volume":"72","author":"Dailidiene","year":"2006","journal-title":"Appl. Environ. Microbiol."},{"key":"key\n\t\t\t\t20170720162423_B26","doi-asserted-by":"crossref","first-page":"753","DOI":"10.1111\/j.1365-2958.1993.tb01618.x","article-title":"Aflagellated mutants of Helicobacter pylori generated by genetic transformation of naturally competent strains using transposon shuttle mutagenesis","volume":"8","author":"Haas","year":"1993","journal-title":"Mol. Microbiol."},{"key":"key\n\t\t\t\t20170720162423_B27","doi-asserted-by":"crossref","first-page":"777","DOI":"10.1128\/JB.186.3.777-784.2004","article-title":"The RecA protein of Helicobacter pylori requires a posttranslational modification for full activity","volume":"186","author":"Fischer","year":"2004","journal-title":"J. Bacteriol."},{"key":"key\n\t\t\t\t20170720162423_B28","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1111\/j.1365-2958.1994.tb01019.x","article-title":"Genetic analysis of the Helicobacter pylori vacuolating cytotoxin: structural similarities with IgA protease type of exported protein","volume":"12(2)","author":"Schmitt","year":"1994","journal-title":"Mol. Microbiol."},{"key":"key\n\t\t\t\t20170720162423_B29","doi-asserted-by":"crossref","first-page":"1497","DOI":"10.1126\/science.287.5457.1497","article-title":"Translocation of Helicobacter pylori CagA into gastric epithelial cells by type IV secretion","volume":"287","author":"Odenbreit","year":"2000","journal-title":"Science"},{"key":"key\n\t\t\t\t20170720162423_B30","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/1471-2164-10-3","article-title":"Genome sequence analysis of Helicobacter pylori strains associated with gastric ulceration and gastric cancer","volume":"10","author":"McClain","year":"2009","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t20170720162423_B31","doi-asserted-by":"crossref","first-page":"2740","DOI":"10.1073\/pnas.051612298","article-title":"Comparative genomics of the restriction-modification systems in Helicobacter pylori","volume":"98","author":"Lin","year":"2001","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"key\n\t\t\t\t20170720162423_B32","doi-asserted-by":"crossref","first-page":"e6859","DOI":"10.1371\/journal.pone.0006859","article-title":"Helicobacter pylori's plasticity zones are novel transposable elements","volume":"4","author":"Kersulyte","year":"2009","journal-title":"PLoS ONE"},{"key":"key\n\t\t\t\t20170720162423_B33","doi-asserted-by":"crossref","first-page":"e6531","DOI":"10.1371\/journal.pone.0006531","article-title":"The dif\/Xer recombination systems in proteobacteria","volume":"4","author":"Carnoy","year":"2009","journal-title":"PLoS ONE"},{"key":"key\n\t\t\t\t20170720162423_B34","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1038\/nature06248","article-title":"Bacterial pathogenomics","volume":"449","author":"Pallen","year":"2007","journal-title":"Nature"},{"key":"key\n\t\t\t\t20170720162423_B35","doi-asserted-by":"crossref","first-page":"1455","DOI":"10.1371\/journal.pcbi.0030151","article-title":"Helicobacter pylori evolution: lineage- specific adaptations in homologs of eukaryotic Sel1-like genes","volume":"3","author":"Ogura","year":"2007","journal-title":"PLoS. Comput. Biol."},{"key":"key\n\t\t\t\t20170720162423_B36","doi-asserted-by":"crossref","first-page":"13950","DOI":"10.1073\/pnas.0506758102","article-title":"Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial \u201cpan-genome\u201d","volume":"102","author":"Tettelin","year":"2005","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"key\n\t\t\t\t20170720162423_B37","doi-asserted-by":"crossref","first-page":"R103","DOI":"10.1186\/gb-2007-8-6-r103","article-title":"Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains","volume":"8","author":"Hogg","year":"2007","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t20170720162423_B38","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1186\/1471-2164-10-385","article-title":"Microbial comparative pan-genomics using binomial mixture models","volume":"10","author":"Snipen","year":"2009","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t20170720162423_B39","doi-asserted-by":"crossref","first-page":"e1000128","DOI":"10.1371\/journal.pgen.1000128","article-title":"Dynamics of genome rearrangement in bacterial populations","volume":"4","author":"Darling","year":"2008","journal-title":"PLoS Genet."},{"key":"key\n\t\t\t\t20170720162423_B40","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1007\/s00239-005-0192-2","article-title":"Selection for chromosome architecture in bacteria","volume":"62","author":"Hendrickson","year":"2006","journal-title":"J. Mol. Evol."},{"key":"key\n\t\t\t\t20170720162423_B41","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1038\/79918","article-title":"Genome rearrangement by replication-directed translocation","volume":"26","author":"Tillier","year":"2000","journal-title":"Nat. Genet."},{"key":"key\n\t\t\t\t20170720162423_B42","doi-asserted-by":"crossref","first-page":"1219","DOI":"10.1093\/oxfordjournals.molbev.a026212","article-title":"Analysis of long repeats in bacterial genomes reveals alternative evolutionary mechanisms in Bacillus subtilis and other competent prokaryotes","volume":"16","author":"Rocha","year":"1999","journal-title":"Mol. Biol. Evol."},{"key":"key\n\t\t\t\t20170720162423_B43","doi-asserted-by":"crossref","first-page":"13579","DOI":"10.1073\/pnas.1735481100","article-title":"Extensive repetitive DNA facilitates prokaryotic genome plasticity","volume":"100","author":"Aras","year":"2003","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"key\n\t\t\t\t20170720162423_B44","doi-asserted-by":"crossref","first-page":"2802","DOI":"10.1093\/molbev\/msm215","article-title":"The repertoire of minimal mobile elements in the Neisseria species and evidence that these are involved in horizontal gene transfer in other bacteria","volume":"24","author":"Snyder","year":"2007","journal-title":"Mol. Biol. Evol."},{"key":"key\n\t\t\t\t20170720162423_B45","doi-asserted-by":"crossref","first-page":"e1000337","DOI":"10.1371\/journal.ppat.1000337","article-title":"Natural transformation of Helicobacter pylori involves the integration of short DNA fragments interrupted by gaps of variable size","volume":"5","author":"Lin","year":"2009","journal-title":"PLoS Pathog."},{"key":"key\n\t\t\t\t20170720162423_B46","doi-asserted-by":"crossref","first-page":"1052","DOI":"10.1046\/j.1365-2958.2000.02049.x","article-title":"Restriction-modification system differences in Helicobacter pylori are a barrier to interstrain plasmid transfer","volume":"37","author":"Ando","year":"2000","journal-title":"Mol. Microbiol."},{"key":"key\n\t\t\t\t20170720162423_B47","doi-asserted-by":"crossref","first-page":"5391","DOI":"10.1093\/nar\/gkf686","article-title":"Helicobacter pylori interstrain restriction-modification diversity prevents genome subversion by chromosomal DNA from competing strains","volume":"30","author":"Aras","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720162423_B48","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","author":"Falush","year":"2001","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"key\n\t\t\t\t20170720162423_B49","doi-asserted-by":"crossref","first-page":"e3797","DOI":"10.1371\/journal.pone.0003797","article-title":"Mosaic DNA imports with interspersions of recipient sequence after natural transformation of Helicobacter pylori","volume":"3","author":"Kulick","year":"2008","journal-title":"PLoS ONE"},{"key":"key\n\t\t\t\t20170720162423_B50","doi-asserted-by":"crossref","first-page":"3493","DOI":"10.1099\/mic.0.28250-0","article-title":"Conjugative plasmid DNA transfer in Helicobacter pylori mediated by chromosomally encoded relaxase and TraG-like proteins","volume":"151","author":"Backert","year":"2005","journal-title":"Microbiology"},{"key":"key\n\t\t\t\t20170720162423_B51","doi-asserted-by":"crossref","first-page":"2901","DOI":"10.1128\/JB.180.11.2901-2905.1998","article-title":"Evidence for a conjugation-like mechanism of DNA transfer in Helicobacter pylori","volume":"180","author":"Kuipers","year":"1998","journal-title":"J. Bacteriol."},{"key":"key\n\t\t\t\t20170720162423_B52","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1128\/JCM.01456-06","article-title":"Conjugative transfer of chromosomally encoded antibiotic resistance from Helicobacter pylori to Campylobacter jejuni","volume":"45","author":"Oyarzabal","year":"2007","journal-title":"J. Clin. Microbiol."},{"key":"key\n\t\t\t\t20170720162423_B53","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1128\/JB.188.1.249-254.2006","article-title":"Genomic changes during chronic Helicobacter pylori infection","volume":"188","author":"Kraft","year":"2006","journal-title":"J. Bacteriol."},{"key":"key\n\t\t\t\t20170720162423_B54","doi-asserted-by":"crossref","first-page":"R57","DOI":"10.1186\/gb-2003-4-9-r57","article-title":"The source of laterally transferred genes in bacterial genomes","volume":"4","author":"Daubin","year":"2003","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t20170720162423_B55","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1128\/MMBR.00038-08","article-title":"Challenging a paradigm: the role of DNA homology in tyrosine recombinase reactions","volume":"73","author":"Rajeev","year":"2009","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"key\n\t\t\t\t20170720162423_B56","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.tim.2008.11.003","article-title":"Genomic islands are dynamic, ancient integrative elements in bacterial evolution","volume":"17","author":"Boyd","year":"2009","journal-title":"Trends Microbiol."},{"key":"key\n\t\t\t\t20170720162423_B57","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1111\/j.1365-2958.2004.04356.x","article-title":"Genetic recombination and the cell cycle: what we have learned from chromosome dimers","volume":"54","author":"Lesterlin","year":"2004","journal-title":"Mol. Microbiol."},{"key":"key\n\t\t\t\t20170720162423_B58","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1038\/nature00782","article-title":"Filamentous phage integration requires the host recombinases XerC and XerD","volume":"417","author":"Huber","year":"2002","journal-title":"Nature"},{"key":"key\n\t\t\t\t20170720162423_B59","doi-asserted-by":"crossref","first-page":"1704","DOI":"10.1111\/j.1365-2958.2005.04521.x","article-title":"Neisseria gonorrhoeae secretes chromosomal DNA via a novel type IV secretion system","volume":"55","author":"Hamilton","year":"2005","journal-title":"Mol. Microbiol."},{"key":"key\n\t\t\t\t20170720162423_B60","doi-asserted-by":"crossref","first-page":"1519","DOI":"10.1099\/jmm.0.47273-0","article-title":"Evidence that the cytolethal distending toxin locus was once part of a genomic island in the periodontal pathogen Aggregatibacter (Actinobacillus) actinomycetemcomitans strain Y4","volume":"56","author":"Doungudomdacha","year":"2007","journal-title":"J. Med. Microbiol."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/38\/18\/6089\/18782926\/gkq378.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,6,4]],"date-time":"2020-06-04T15:44:22Z","timestamp":1591285462000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article-lookup\/doi\/10.1093\/nar\/gkq378"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,5,15]]},"references-count":60,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2010,5,15]]},"published-print":{"date-parts":[[2010,10,1]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkq378","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.3296956.2984054","asserted-by":"object"}]},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,5,15]]}}}