-
1
-
-
33847201150
-
An African origin for the intimate association between humans and Helicobacter pylori
-
Linz, B. et al. An African origin for the intimate association between humans and Helicobacter pylori. Nature 445, 915-918 (2007).
-
(2007)
Nature
, vol.445
, pp. 915-918
-
-
Linz, B.1
-
2
-
-
84863692086
-
Age of the association between Helicobacter pylori and man
-
Moodley, Y. et al. Age of the association between Helicobacter pylori and man. PLoS Pathog. 8, e1002693 (2012).
-
(2012)
PLoS Pathog.
, vol.8
-
-
Moodley, Y.1
-
3
-
-
33750107653
-
Bacterial populations as perfect gases: Genomic integrity and diversification tensions in Helicobacter pylori
-
DOI 10.1038/nrmicro1528, PII NRMICRO1528
-
Kang, J. & Blaser, M. J. Bacterial populations as perfect gases: genomic integrity and diversification tensions in Helicobacter pylori. Nat. Rev. Microbiol. 4, 826-836 (2006). (Pubitemid 44593949)
-
(2006)
Nature Reviews Microbiology
, vol.4
, Issue.11
, pp. 826-836
-
-
Kang, J.1
Blaser, M.J.2
-
4
-
-
77957331293
-
Microevolution of Helicobacter pylori during prolonged infection of single hosts and within families
-
Morelli, G. et al. Microevolution of Helicobacter pylori during prolonged infection of single hosts and within families. PLoS Genet. 6, e1001036 (2010).
-
(2010)
PLoS Genet.
, vol.6
-
-
Morelli, G.1
-
5
-
-
79953187986
-
Helicobacter pylori genome evolution during human infection
-
Kennemann, L. et al. Helicobacter pylori genome evolution during human infection. Proc. Natl Acad. Sci. USA 108, 5033-5038 (2011).
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 5033-5038
-
-
Kennemann, L.1
-
6
-
-
84882750416
-
Genomic evolution and transmission of Helicobacter pylori in two South African families
-
Didelot, X. et al. Genomic evolution and transmission of Helicobacter pylori in two South African families. Proc. Natl Acad. Sci. USA 110, 13880-13885 (2013).
-
(2013)
Proc. Natl Acad. Sci. USA
, vol.110
, pp. 13880-13885
-
-
Didelot, X.1
-
7
-
-
0037423837
-
Traces of human migrations in Helicobacter pylori populations
-
DOI 10.1126/science.1080857
-
Falush, D. et al. Traces of human migrations in Helicobacter pylori populations. Science 299, 1582-1585 (2003). (Pubitemid 36297709)
-
(2003)
Science
, vol.299
, Issue.5612
, pp. 1582-1585
-
-
Falush, D.1
Wirth, T.2
Linz, B.3
Pritchard, J.K.4
Stephens, M.5
Kidd, M.6
Blaser, M.J.7
Graham, D.Y.8
Vacher, S.9
Perez-Perez, G.I.10
Yamaoka, Y.11
Megraud, F.12
Otto, K.13
Reichard, U.14
Katzowitsch, E.15
Wang, X.16
Achtman, M.17
Suerbaum, S.18
-
8
-
-
58849086252
-
The peopling of the Pacific from a bacterial perspective
-
Moodley, Y. et al. The peopling of the Pacific from a bacterial perspective. Science 323, 527-530 (2009).
-
(2009)
Science
, vol.323
, pp. 527-530
-
-
Moodley, Y.1
-
9
-
-
34249276425
-
Gain and loss of multiple genes during the evolution of Helicobacter pylori
-
Gressmann, H. et al. Gain and loss of multiple genes during the evolution of Helicobacter pylori. PLoS Genet. 1, e43 (2005).
-
(2005)
PLoS Genet.
, vol.1
-
-
Gressmann, H.1
-
10
-
-
33845674063
-
A paradigm for direct stress-induced mutation in prokaryotes
-
DOI 10.1096/fj.06-6209com
-
Kang, J. M., Iovine, N. M. & Blaser, M. J. A paradigm for direct stress-induced mutation in prokaryotes. FASEB J. 20, 2476-2485 (2006). (Pubitemid 44953820)
-
(2006)
FASEB Journal
, vol.20
, Issue.14
, pp. 2476-2485
-
-
Kang, J.M.1
Iovine, N.M.2
Blaser, M.J.3
-
11
-
-
0035807814
-
Helicobacter pylori genetic diversity within the gastric niche of a single human host
-
DOI 10.1073/pnas.251551698
-
Israel, D. A. et al. Helicobacter pylori genetic diversity within the gastric niche of a single human host. Proc. Natl Acad. Sci. USA 98, 14625-14630 (2001). (Pubitemid 33121442)
-
(2001)
Proceedings of the National Academy of Sciences of the United States of America
, vol.98
, Issue.25
, pp. 14625-14630
-
-
Israel, D.A.1
Salama, N.2
Krishna, U.3
Rieger, U.M.4
Atherton, J.C.5
Falkow, S.6
Peek Jr., R.M.7
-
12
-
-
0035909914
-
Recombination and mutation during long-term gastric colonization by Helicobacter pylori: Estimates of clock rates, recombination size, and minimal age
-
DOI 10.1073/pnas.251396098
-
Falush, D. et al. Recombination and mutation during long-term gastric colonization by Helicobacter pylori: Estimates of clock rates, recombination size and minimal age. Proc. Natl Acad. Sci. USA 98, 15056-15061 (2001). (Pubitemid 34013968)
-
(2001)
Proceedings of the National Academy of Sciences of the United States of America
, vol.98
, Issue.26
, pp. 15056-15061
-
-
Falush, D.1
Kraft, C.2
Taylor, N.S.3
Correa, P.4
Fox, J.G.5
Achtman, M.6
Suerbaum, S.7
-
13
-
-
23744448910
-
Pathogen evolution in vivo: Genome dynamics of two isolates obtained 9 years apart from a duodenal ulcer patient infected with a single Helicobacter pylori strain
-
DOI 10.1128/JCM.43.8.4237-4241.2005
-
Prouzet-Mauleon, V. et al. Pathogen evolution in vivo: genome dynamics of two isolates obtained 9 years apart from a duodenal ulcer patient infected with a single Helicobacter pylori strain. J. Clin. Microbiol. 43, 4237-4241 (2005). (Pubitemid 41129737)
-
(2005)
Journal of Clinical Microbiology
, vol.43
, Issue.8
, pp. 4237-4241
-
-
Prouzet-Mauleon, V.1
Hussain, M.A.2
Lamouliatte, H.3
Kauser, F.4
Megraud, F.5
Ahmed, N.6
-
14
-
-
0030017015
-
Transient and persistent experimental infection of nonhuman primates with Helicobacter pylori: Implications for human disease
-
Dubois, A. et al. Transient and persistent experimental infection of nonhuman primates with Helicobacter pylori: implications for human disease. Infect. Immun. 64, 2885-2891 (1996). (Pubitemid 26256120)
-
(1996)
Infection and Immunity
, vol.64
, Issue.8
, pp. 2885-2891
-
-
Dubois, A.1
Berg, D.E.2
Incecik, E.T.3
Fiala, N.4
Heman-Ackah, L.M.5
Perez-Perez, G.I.6
Blaser, M.J.7
-
15
-
-
0034783750
-
Determination of the infectious dose of Helicobacter pylori during primary and secondary infection in rhesus monkeys (Macaca mulatta)
-
DOI 10.1128/IAI.69.11.6887-6892.2001
-
Solnick, J. V. et al. Determination of the infectious dose of Helicobacter pylori during primary and secondary infection in rhesus monkeys (Macaca mulatta). Infect. Immun. 69, 6887-6892 (2001). (Pubitemid 32995448)
-
(2001)
Infection and Immunity
, vol.69
, Issue.11
, pp. 6887-6892
-
-
Solnick, J.V.1
Hansen, L.M.2
Canfield, D.R.3
Parsonnet, J.4
-
16
-
-
23344452848
-
Comparison of Helicobacter pylori virulence gene expression in vitro and in the rhesus macaque
-
DOI 10.1128/IAI.73.8.4895-4904.2005
-
Boonjakuakul, J. K., Canfield, D. R. & Solnick, J. V. Comparison of Helicobacter pylori virulence gene expression in vitro and in the Rhesus macaque. Infect. Immun. 73, 4895-4904 (2005). (Pubitemid 41105646)
-
(2005)
Infection and Immunity
, vol.73
, Issue.8
, pp. 4895-4904
-
-
Boonjakuakul, J.K.1
Canfield, D.R.2
Solnick, J.V.3
-
17
-
-
80055056483
-
Rates of mutation and host transmission for an Escherichia coli clone over 3 years
-
Reeves, P. R. et al. Rates of mutation and host transmission for an Escherichia coli clone over 3 years. PLoS ONE 6, e26907 (2011).
-
(2011)
PLoS ONE
, vol.6
-
-
Reeves, P.R.1
-
18
-
-
33744814106
-
Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients
-
DOI 10.1073/pnas.0602138103
-
Smith, E. E. et al. Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients. Proc. Natl Acad. Sci. USA 103, 8487-8492 (2006). (Pubitemid 43838482)
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, Issue.22
, pp. 8487-8492
-
-
Smith, E.E.1
Buckley, D.G.2
Wu, Z.3
Saenphimmachak, C.4
Hoffman, L.R.5
D'Argenio, D.A.6
Miller, S.I.7
Ramsey, B.W.8
Speert, D.P.9
Moskowitz, S.M.10
Burns, J.L.11
Kaul, R.12
Olson, M.V.13
-
19
-
-
34547226145
-
Tracking the in vivo evolution of multidrug resistance in Staphylococcus aureus by whole-genome sequencing
-
DOI 10.1073/pnas.0609839104
-
Mwangi, M. M. et al. Tracking the in vivo evolution of multidrug resistance in Staphylococcus aureus by whole-genome sequencing. Proc. Natl Acad. Sci. USA 104, 9451-9456 (2007). (Pubitemid 47185800)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.22
, pp. 9451-9456
-
-
Mwangi, M.M.1
Shang, W.W.2
Zhou, Y.3
Sieradzki, K.4
De Lencastre, H.5
Richardson, P.6
Bruce, D.7
Rubin, E.8
Myers, E.9
Siggia, E.D.10
Tomasz, A.11
-
20
-
-
77954065669
-
A timescale for evolution, population expansion, and spatial spread of an emerging clone of methicillin-resistant Staphylococcus aureus
-
Nubel, U. et al. A timescale for evolution, population expansion, and spatial spread of an emerging clone of methicillin-resistant Staphylococcus aureus. PLoS Pathog. 6, e1000855 (2010).
-
(2010)
PLoS Pathog.
, vol.6
-
-
Nubel, U.1
-
21
-
-
75649084906
-
Evolution of MRSA during hospital transmission and intercontinental spread
-
Harris, S. R. et al. Evolution of MRSA during hospital transmission and intercontinental spread. Science 327, 469-474 (2010).
-
(2010)
Science
, vol.327
, pp. 469-474
-
-
Harris, S.R.1
-
22
-
-
58449126084
-
The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria
-
Moran, N. A., McLaughlin, H. J. & Sorek, R. The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria. Science 323, 379-382 (2009).
-
(2009)
Science
, vol.323
, pp. 379-382
-
-
Moran, N.A.1
McLaughlin, H.J.2
Sorek, R.3
-
23
-
-
84859192030
-
Ultrafast Evolution and Loss of CRISPRs Following a Host Shift in a Novel Wildlife Pathogen Mycoplasma gallisepticum
-
Delaney, N. F. et al. Ultrafast Evolution and Loss of CRISPRs Following a Host Shift in a Novel Wildlife Pathogen, Mycoplasma gallisepticum. PLoS Genet. 8, e1002511 (2012).
-
(2012)
PLoS Genet.
, vol.8
-
-
Delaney, N.F.1
-
24
-
-
33846630062
-
Temporal trends in gonococcal population genetics in a high prevalence urban community
-
DOI 10.1016/j.meegid.2006.11.003, PII S1567134806001249
-
Perez-Losada, M. et al. Temporal trends in gonococcal population genetics in a high prevalence urban community. Infect. Genet. Evol. 7, 271-278 (2007). (Pubitemid 46177951)
-
(2007)
Infection, Genetics and Evolution
, vol.7
, Issue.2
, pp. 271-278
-
-
Perez-Losada, M.1
Crandall, K.A.2
Zenilman, J.3
Viscidi, R.P.4
-
25
-
-
58449131619
-
Rapid evolution and the importance of recombination to the gastroenteric pathogen Campylobacter jejuni
-
Wilson, D. J. et al. Rapid evolution and the importance of recombination to the gastroenteric pathogen Campylobacter jejuni. Mol. Biol. Evol. 26, 385-397 (2009).
-
(2009)
Mol. Biol. Evol.
, vol.26
, pp. 385-397
-
-
Wilson, D.J.1
-
26
-
-
0036147047
-
Rates of molecular evolution in RNA viruses: A quantitative phylogenetic analysis
-
DOI 10.1007/s00239-001-0064-3
-
Jenkins, G. M. et al. Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis. J. Mol. Evol. 54, 156-165 (2002). (Pubitemid 34076343)
-
(2002)
Journal of Molecular Evolution
, vol.54
, Issue.2
, pp. 156-165
-
-
Jenkins, G.M.1
Rambaut, A.2
Pybus, O.G.3
Holmes, E.C.4
-
27
-
-
53849133821
-
Evolutionary history and phylogeography of human viruses
-
Holmes, E. C. Evolutionary history and phylogeography of human viruses. Annu. Rev. Microbiol. 62, 307-328 (2008).
-
(2008)
Annu. Rev. Microbiol.
, vol.62
, pp. 307-328
-
-
Holmes, E.C.1
-
28
-
-
1242319255
-
Modification of Helicobacter pylori outer membrane protein expression during experimental infection of rhesus macaques
-
DOI 10.1073/pnas.0308573100
-
Solnick, J. V. et al. Modification of Helicobacter pylori outer membrane protein expression during experimental infection of rhesus macaques. Proc. Natl Acad. Sci. USA 101, 2106-2111 (2004). (Pubitemid 38229022)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.7
, pp. 2106-2111
-
-
Solnick, J.V.1
Hansen, L.M.2
Salama, N.R.3
Boonjakuakul, J.K.4
Syvanen, M.5
-
29
-
-
77950240220
-
Expression of the BabA adhesin during experimental infection with Helicobacter pylori
-
Styer, C. M. et al. Expression of the BabA adhesin during experimental infection with Helicobacter pylori. Infect. Immun. 78, 1593-1600 (2010).
-
(2010)
Infect. Immun.
, vol.78
, pp. 1593-1600
-
-
Styer, C.M.1
-
30
-
-
84878017920
-
Functional plasticity in the type IV secretion system of Helicobacter pylori
-
Barrozo, R. M. et al. Functional plasticity in the type IV secretion system of Helicobacter pylori. PLoS Pathog. 9, e1003189 (2013).
-
(2013)
PLoS Pathog.
, vol.9
-
-
Barrozo, R.M.1
-
31
-
-
84892409308
-
Helicobacter pylori genomic microevolution during naturally occurring transmission between adults
-
Linz, B. et al. Helicobacter pylori genomic microevolution during naturally occurring transmission between adults. PLoS ONE 8, e82187 (2013).
-
(2013)
PLoS ONE
, vol.8
-
-
Linz, B.1
-
32
-
-
48249087613
-
Correlation of T cell response and bacterial clearance in human volunteers challenged with Helicobacter pylori revealed by randomised controlled vaccination with Ty21a-based Salmonella vaccines
-
Aebischer, T. et al. Correlation of T cell response and bacterial clearance in human volunteers challenged with Helicobacter pylori revealed by randomised controlled vaccination with Ty21a-based Salmonella vaccines. Gut 57, 1065-1072 (2008).
-
(2008)
Gut
, vol.57
, pp. 1065-1072
-
-
Aebischer, T.1
-
33
-
-
0031741116
-
Procedure guideline for carbon-14-urea breath test
-
Balon, H. et al. Procedure guideline for carbon-14-urea breath test. J. Nucl. Med. 39, 2012-2014 (1998). (Pubitemid 28518909)
-
(1998)
Journal of Nuclear Medicine
, vol.39
, Issue.11
, pp. 2012-2014
-
-
Balon, H.1
Gold, C.A.2
Dworkin, H.J.3
McCormick, V.A.4
Freitas, J.E.5
Smith, W.J.M.6
-
34
-
-
24044455869
-
Genome sequencing in microfabricated high-density picolitre reactors
-
DOI 10.1038/nature03959, PII N03959
-
Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376-380 (2005). (Pubitemid 41613494)
-
(2005)
Nature
, vol.437
, Issue.7057
, pp. 376-380
-
-
Margulies, M.1
Egholm, M.2
Altman, W.E.3
Attiya, S.4
Bader, J.S.5
Bemben, L.A.6
Berka, J.7
Braverman, M.S.8
Chen, Y.-J.9
Chen, Z.10
Dewell, S.B.11
Du, L.12
Fierro, J.M.13
Gomes, X.V.14
Godwin, B.C.15
He, W.16
Helgesen, S.17
Ho, C.H.18
Irzyk, G.P.19
Jando, S.C.20
Alenquer, M.L.I.21
Jarvie, T.P.22
Jirage, K.B.23
Kim, J.-B.24
Knight, J.R.25
Lanza, J.R.26
Leamon, J.H.27
Lefkowitz, S.M.28
Lei, M.29
Li, J.30
Lohman, K.L.31
Lu, H.32
Makhijani, V.B.33
McDade, K.E.34
McKenna, M.P.35
Myers, E.W.36
Nickerson, E.37
Nobile, J.R.38
Plant, R.39
Puc, B.P.40
Ronan, M.T.41
Roth, G.T.42
Sarkis, G.J.43
Simons, J.F.44
Simpson, J.W.45
Srinivasan, M.46
Tartaro, K.R.47
Tomasz, A.48
Vogt, K.A.49
Volkmer, G.A.50
Wang, S.H.51
Wang, Y.52
Weiner, M.P.53
Yu, P.54
Begley, R.F.55
Rothberg, J.M.56
more..
-
35
-
-
40549120596
-
The RAST Server: Rapid annotations using subsystems technology
-
Aziz, R. K. et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9, 75 (2008).
-
(2008)
BMC Genomics
, vol.9
, pp. 75
-
-
Aziz, R.K.1
-
36
-
-
80054913451
-
FLASH: Fast length adjustment of short reads to improve genome assemblies
-
Magoc, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957-2963 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 2957-2963
-
-
Magoc, T.1
Salzberg, S.L.2
-
37
-
-
75249099173
-
InGAP: An integrated next-generation genome analysis pipeline
-
Qi, J. et al. inGAP: an integrated next-generation genome analysis pipeline. Bioinformatics 26, 127-129 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 127-129
-
-
Qi, J.1
-
38
-
-
13244252363
-
GenomeViz: Visualizing microbial genomes
-
Ghai, R., Hain, T. & Chakraborty, T. GenomeViz: visualizing microbial genomes. BMC Bioinformatics 5, 198 (2004).
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 198
-
-
Ghai, R.1
Hain, T.2
Chakraborty, T.3
-
39
-
-
24044433279
-
ACT: The Artemis comparison tool
-
DOI 10.1093/bioinformatics/bti553
-
Carver, T. J. et al. ACT: the Artemis Comparison Tool. Bioinformatics 21, 3422-3423 (2005). (Pubitemid 41222448)
-
(2005)
Bioinformatics
, vol.21
, Issue.16
, pp. 3422-3423
-
-
Carver, T.J.1
Rutherford, K.M.2
Berriman, M.3
Rajandream, M.-A.4
Barrell, B.G.5
Parkhill, J.6
-
40
-
-
0030305457
-
R: A language for data analysis and graphics
-
Ihaka, R. & Gentleman, R. R: A language for data analysis and graphics. J. Comput. Graph. Stat. 5, 299-314 (1996).
-
(1996)
J. Comput. Graph. Stat.
, vol.5
, pp. 299-314
-
-
Ihaka, R.1
Gentleman, R.2
|