-
1
-
-
0033591290
-
Helicobacter pylori virulence and genetic geography
-
Covacci A, Telford JL, Del GG, et al. Helicobacter pylori virulence and genetic geography. Science 1999;284:1328-33.
-
(1999)
Science
, vol.284
, pp. 1328-1333
-
-
Covacci, A.1
Telford, J.L.2
Del, G.G.3
-
2
-
-
0037057683
-
Helicobacter pylori infection
-
Suerbaum S, Michetti P. Helicobacter pylori infection. N Engl J Med 2002;347:1175-86.
-
(2002)
N Engl J Med
, vol.347
, pp. 1175-1186
-
-
Suerbaum, S.1
Michetti, P.2
-
3
-
-
0035909914
-
Recombination and mutation during long-term gastric colonization by Helicobacter pylori: Estimates of clock rates, recombination size, and minimal age
-
Falush D, Kraft C, Taylor NS, 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 2001;98:15056-61.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 15056-15061
-
-
Falush, D.1
Kraft, C.2
Taylor, N.S.3
-
4
-
-
77957331293
-
Microevolution of Helicobacter pylori during prolonged infection of single hosts and within families
-
Morelli G, Didelot X, Kusecek B, et al. Microevolution of Helicobacter pylori during prolonged infection of single hosts and within families. PLoS Genet 2010;6: e1001036.
-
(2010)
PLoS Genet
, vol.6
, pp. e1001036
-
-
Morelli, G.1
Didelot, X.2
Kusecek, B.3
-
5
-
-
79953187986
-
Helicobacter pylori genome evolution during human infection
-
Kennemann L, Didelot X, Aebischer T, et al. Helicobacter pylori genome evolution during human infection. Proc Natl Acad Sci USA 2011;108:5033-8.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 5033-5038
-
-
Kennemann, L.1
Didelot, X.2
Aebischer, T.3
-
6
-
-
84882750416
-
Genomic evolution and transmission of Helicobacter pylori in two South African families
-
Didelot X, Nell S, Yang I, et al. Genomic evolution and transmission of Helicobacter pylori in two South African families. Proc Natl Acad Sci USA 2013;110:13880-5.
-
(2013)
Proc Natl Acad Sci USA
, vol.110
, pp. 13880-13885
-
-
Didelot, X.1
Nell, S.2
Yang, I.3
-
7
-
-
57049164377
-
Mosaic DNA imports with interspersions of recipient sequence after natural transformation of Helicobacter pylori
-
Kulick S, Moccia C, Didelot X, et al. Mosaic DNA imports with interspersions of recipient sequence after natural transformation of Helicobacter pylori. PLoS One 2008;3:e3797.
-
(2008)
PLoS One
, vol.3
, pp. e3797
-
-
Kulick, S.1
Moccia, C.2
Didelot, X.3
-
8
-
-
63449095763
-
Natural transformation of helicobacter pylori involves the integration of short DNA fragments interrupted by gaps of variable size
-
Lin EA, Zhang XS, Levine SM, et al. Natural transformation of helicobacter pylori involves the integration of short DNA fragments interrupted by gaps of variable size. PLoS Pathog 2009;5:e1000337.
-
(2009)
PLoS Pathog
, vol.5
, pp. e1000337
-
-
Lin, E.A.1
Zhang, X.S.2
Levine, S.M.3
-
9
-
-
84860539116
-
The nucleotide excision repair (NER) system of Helicobacter pylori: Role in mutation prevention and chromosomal import patterns after natural transformation
-
Moccia C, Krebes J, Kulick S, et al. The nucleotide excision repair (NER) system of Helicobacter pylori: role in mutation prevention and chromosomal import patterns after natural transformation. BMC Microbiol 2012;12:67.
-
(2012)
BMC Microbiol
, vol.12
, pp. 67
-
-
Moccia, C.1
Krebes, J.2
Kulick, S.3
-
10
-
-
84863338394
-
Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease
-
Young BC, Golubchik T, Batty EM, et al. Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease. Proc Natl Acad Sci USA 2012;109:4550-5.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, pp. 4550-4555
-
-
Young, B.C.1
Golubchik, T.2
Batty, E.M.3
-
11
-
-
84877034258
-
Within-host evolution of Staphylococcus aureus during asymptomatic carriage
-
Golubchik T, Batty EM, Miller RR, et al Within-host evolution of Staphylococcus aureus during asymptomatic carriage. PLoS One 2013;8:e61319.
-
(2013)
PLoS One
, vol.8
, pp. e61319
-
-
Golubchik, T.1
Batty, E.M.2
Miller, R.R.3
-
12
-
-
75649124547
-
De novo assembly of human genomes with massively parallel short read sequencing
-
Li R, Zhu H, Ruan J, et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010;20:265-72.
-
(2010)
Genome Res
, vol.20
, pp. 265-272
-
-
Li, R.1
Zhu, H.2
Ruan, J.3
-
13
-
-
43149115851
-
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
-
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008;18:821-9.
-
(2008)
Genome Res
, vol.18
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
-
14
-
-
40549120596
-
The RAST Server: Rapid annotations using subsystems technology
-
Aziz RK, Bartels D, Best AA, et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008;9:75.
-
(2008)
BMC Genomics
, vol.9
, pp. 75
-
-
Aziz, R.K.1
Bartels, D.2
Best, A.A.3
-
15
-
-
34250665888
-
RNAmmer: Consistent and rapid annotation of ribosomal RNA genes
-
Lagesen K, Hallin P, Rodland EA, et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007;35:3100-8.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 3100-3108
-
-
Lagesen, K.1
Hallin, P.2
Rodland, E.A.3
-
16
-
-
23144460836
-
The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs
-
Schattner P, Brooks AN, Lowe TM. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 2005;33:W686-9.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. W686-W689
-
-
Schattner, P.1
Brooks, A.N.2
Lowe, T.M.3
-
17
-
-
77956193448
-
ProgressiveMauve: Multiple genome alignment with gene gain, loss and rearrangement
-
Darling AE, Mau B, Perna NT. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 2010;5:e11147.
-
(2010)
PLoS One
, vol.5
, pp. e11147
-
-
Darling, A.E.1
Mau, B.2
Perna, N.T.3
-
18
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406-25.
-
(1987)
Mol Biol Evol
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
19
-
-
34249027580
-
Inference of bacterial microevolution using multilocus sequence data
-
Didelot X, Falush D. Inference of bacterial microevolution using multilocus sequence data. Genetics 2007;175:1251-66.
-
(2007)
Genetics
, vol.175
, pp. 1251-1266
-
-
Didelot, X.1
Falush, D.2
-
20
-
-
59649113973
-
Evolution of pathogenicity in the Bacillus cereus group
-
Didelot X, Barker M, Falush D, et al. Evolution of pathogenicity in the Bacillus cereus group. Syst Appl Microbiol 2009;32:81-90.
-
(2009)
Syst Appl Microbiol
, vol.32
, pp. 81-90
-
-
Didelot, X.1
Barker, M.2
Falush, D.3
-
21
-
-
79960935954
-
Recombination and population structure in Salmonella enterica
-
Didelot X, Bowden R, Street T, et al. Recombination and population structure in Salmonella enterica. PLoS Genet 2011;7:e1002191.
-
(2011)
PLoS Genet
, vol.7
, pp. e1002191
-
-
Didelot, X.1
Bowden, R.2
Street, T.3
-
22
-
-
84873085208
-
Progressive genome-wide introgression in agricultural Campylobacter coli
-
Sheppard SK, Didelot X, Jolley KA, et al. Progressive genome-wide introgression in agricultural Campylobacter coli. Mol Ecol 2013;22:1051-64.
-
(2013)
Mol Ecol
, vol.22
, pp. 1051-1064
-
-
Sheppard, S.K.1
Didelot, X.2
Jolley, K.A.3
-
23
-
-
79955883801
-
Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes
-
Kawai M, Furuta Y, Yahara K, et al. Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes. BMC Microbiol 2011;11:104.
-
(2011)
BMC Microbiol
, vol.11
, pp. 104
-
-
Kawai, M.1
Furuta, Y.2
Yahara, K.3
-
24
-
-
2942538300
-
Versatile and open software for comparing large genomes
-
Kurtz S, Phillippy A, Delcher AL, et al. Versatile and open software for comparing large genomes. Genome Biol 2004;5:R12.
-
(2004)
Genome Biol
, vol.5
, pp. R12
-
-
Kurtz, S.1
Phillippy, A.2
Delcher, A.L.3
-
25
-
-
33846032295
-
A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: Convergence or divergence by homologous recombination?
-
Didelot X, Achtman M, Parkhill J, et al. A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: convergence or divergence by homologous recombination? Genome Res 2007;17:61-8.
-
(2007)
Genome Res
, vol.17
, pp. 61-68
-
-
Didelot, X.1
Achtman, M.2
Parkhill, J.3
-
26
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
-
27
-
-
75549086595
-
REBASE- a database for DNA restriction and modifi cation: Enzymes, genes and genomes
-
Roberts RJ, Vincze T, Posfai J, et al. REBASE- a database for DNA restriction and modifi cation: enzymes, genes and genomes. Nucleic Acids Res 2010;38: D234-6.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. D234-D236
-
-
Roberts, R.J.1
Vincze, T.2
Posfai, J.3
-
28
-
-
0031082807
-
Corrected identity of isolates of Helicobacter pylori reference strain NCTC11637
-
Akopyants NS, Jiang Q, Taylor DE, et al. Corrected identity of isolates of Helicobacter pylori reference strain NCTC11637. Helicobacter 1997;2:48-52.
-
(1997)
Helicobacter
, vol.2
, pp. 48-52
-
-
Akopyants, N.S.1
Jiang, Q.2
Taylor, D.E.3
-
29
-
-
79952198319
-
Resistance of Helicobacter pylori to antibiotics from 2000 to 2009 in Shanghai
-
Sun QJ, Liang X, Zheng Q, et al. Resistance of Helicobacter pylori to antibiotics from 2000 to 2009 in Shanghai. World J Gastroenterol 2010;16:5118-21.
-
(2010)
World J Gastroenterol
, vol.16
, pp. 5118-5121
-
-
Sun, Q.J.1
Liang, X.2
Zheng, Q.3
-
30
-
-
84879435191
-
Antibiotic resistance of Helicobacter pylori isolated in the Southeast Coastal Region of China
-
Su P, Li Y, Li H, et al. Antibiotic resistance of Helicobacter pylori isolated in the Southeast Coastal Region of China. Helicobacter 2013;18:274-9.
-
(2013)
Helicobacter
, vol.18
, pp. 274-279
-
-
Su, P.1
Li, Y.2
Li, H.3
-
31
-
-
0030835739
-
The complete genome sequence of the gastric pathogen Helicobacter pylori
-
Tomb JF, White O, Kerlavage AR, et al. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 1997;388:539-47.
-
(1997)
Nature
, vol.388
, pp. 539-547
-
-
Tomb, J.F.1
White, O.2
Kerlavage, A.R.3
-
32
-
-
0037423837
-
Traces of human migrations in Helicobacter pylori populations
-
Falush D, Wirth T, Linz B, et al. Traces of human migrations in Helicobacter pylori populations. Science 2003;299:1582-5.
-
(2003)
Science
, vol.299
, pp. 1582-1585
-
-
Falush, D.1
Wirth, T.2
Linz, B.3
-
33
-
-
0032733829
-
The relative contributions of recombination and mutation to the divergence of clones of Neisseria meningitidis
-
Feil EJ, Maiden MC, Achtman M, et al. The relative contributions of recombination and mutation to the divergence of clones of Neisseria meningitidis. Mol Biol Evol 1999;16:1496-502.
-
(1999)
Mol Biol Evol
, vol.16
, pp. 1496-1502
-
-
Feil, E.J.1
Maiden, M.C.2
Achtman, M.3
-
34
-
-
84865231395
-
Transforming clinical microbiology with bacterial genome sequencing
-
Didelot X, Bowden R, Wilson DJ, et al. Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet 2012;13:601-12.
-
(2012)
Nat Rev Genet
, vol.13
, pp. 601-612
-
-
Didelot, X.1
Bowden, R.2
Wilson, D.J.3
-
35
-
-
77954143123
-
Impact of recombination on bacterial evolution
-
Didelot X, Maiden MC. Impact of recombination on bacterial evolution. Trends Microbiol 2010;18:315-22.
-
(2010)
Trends Microbiol
, vol.18
, pp. 315-322
-
-
Didelot, X.1
Maiden, M.C.2
-
36
-
-
0033812744
-
Restriction-modifi cation system differences in Helicobacter pylori are a barrier to interstrain plasmid transfer
-
Ando T, Xu Q, Torres M, et al. Restriction-modifi cation system differences in Helicobacter pylori are a barrier to interstrain plasmid transfer. Mol Microbiol 2000;37:1052-65.
-
(2000)
Mol Microbiol
, vol.37
, pp. 1052-1065
-
-
Ando, T.1
Xu, Q.2
Torres, M.3
-
37
-
-
79955968392
-
Characterisation of the genes encoding resistance to metronidazole (rdxA and frxA) and clarithromycin (the 23S-rRNA genes) in South African isolates of Helicobacter pylori
-
Tanih NF, Ndip LM, Ndip RN. Characterisation of the genes encoding resistance to metronidazole (rdxA and frxA) and clarithromycin (the 23S-rRNA genes) in South African isolates of Helicobacter pylori. Ann Trop Med Parasitol 2011;105:251-9.
-
(2011)
Ann Trop Med Parasitol
, vol.105
, pp. 251-259
-
-
Tanih, N.F.1
Ndip, L.M.2
Ndip, R.N.3
-
38
-
-
84874058094
-
Antimicrobial susceptibility and resistance patterns among Helicobacter pylori strains from The Gambia, West Africa
-
Secka O, Berg DE, Antonio M, et al. Antimicrobial susceptibility and resistance patterns among Helicobacter pylori strains from The Gambia, West Africa. Antimicrob Agents Chemother 2013;57:1231-7.
-
(2013)
Antimicrob Agents Chemother
, vol.57
, pp. 1231-1237
-
-
Secka, O.1
Berg, D.E.2
Antonio, M.3
-
39
-
-
0033983312
-
Quasispecies development of Helicobacter pylori observed in paired isolates obtained years apart from the same host
-
Kuipers EJ, Israel DA, Kusters JG, et al. Quasispecies development of Helicobacter pylori observed in paired isolates obtained years apart from the same host. J Infect Dis 2000;181:273-82.
-
(2000)
J Infect Dis
, vol.181
, pp. 273-282
-
-
Kuipers, E.J.1
Israel, D.A.2
Kusters, J.G.3
-
40
-
-
79959354608
-
Genomes of two chronological isolates (Helicobacter pylori 2017 and 2018) of the West African Helicobacter pylori strain 908 obtained from a single patient
-
Avasthi TS, Devi SH, Taylor TD, et al. Genomes of two chronological isolates (Helicobacter pylori 2017 and 2018) of the West African Helicobacter pylori strain 908 obtained from a single patient. J Bacteriol 2011;193:3385-6.
-
(2011)
J Bacteriol
, vol.193
, pp. 3385-3386
-
-
Avasthi, T.S.1
Devi, S.H.2
Taylor, T.D.3
-
41
-
-
0035807814
-
Helicobacter pylori genetic diversity within the gastric niche of a single human host
-
Israel DA, Salama N, Krishna U, et al. Helicobacter pylori genetic diversity within the gastric niche of a single human host. Proc Natl Acad Sci USA 2001;98:14625-30.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 14625-14630
-
-
Israel, D.A.1
Salama, N.2
Krishna, U.3
-
42
-
-
0029760575
-
Multiple strain colonization and metronidazole resistance in Helicobacter pylori-infected patients: Identi fication from sequential and multiple biopsy specimens
-
Jorgensen M, Daskalopoulos G, Warburton V, et al . Multiple strain colonization and metronidazole resistance in Helicobacter pylori-infected patients: identi fication from sequential and multiple biopsy specimens. J Infect Dis 1996;174:631-5.
-
(1996)
J Infect Dis
, vol.174
, pp. 631-635
-
-
Jorgensen, M.1
Daskalopoulos, G.2
Warburton, V.3
-
43
-
-
0035120651
-
Helicobacter pylori genotypes are associated with clinical outcome in Portuguese patients and show a high prevalence of infections with multiple strains
-
Figueiredo C, Van Doorn LJ, Nogueira C, et al. Helicobacter pylori genotypes are associated with clinical outcome in Portuguese patients and show a high prevalence of infections with multiple strains. Scand J Gastroenterol 2001;36:128-35.
-
(2001)
Scand J Gastroenterol
, vol.36
, pp. 128-135
-
-
Figueiredo, C.1
Van Doorn, L.J.2
Nogueira, C.3
-
44
-
-
84865411410
-
Multiple infection and microdiversity among Helicobacter pylori isolates in a single host in India
-
Patra R, Chattopadhyay S, De R, et al. Multiple infection and microdiversity among Helicobacter pylori isolates in a single host in India. PLoS One 2012;7:e43370.
-
(2012)
PLoS One
, vol.7
, pp. e43370
-
-
Patra, R.1
Chattopadhyay, S.2
De, R.3
-
46
-
-
1842738286
-
Distinguishing human ethnic groups by means of sequences from Helicobacter pylori: Lessons from Ladakh
-
Wirth T, Wang X, Linz B, et al. Distinguishing human ethnic groups by means of sequences from Helicobacter pylori: lessons from Ladakh. Proc Natl Acad Sci USA 2004;101:4746-51.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 4746-4751
-
-
Wirth, T.1
Wang, X.2
Linz, B.3
-
47
-
-
33847201150
-
An African origin for the intimate association between humans and Helicobacter pylori
-
Linz B, Balloux F, Moodley Y, et al. An African origin for the intimate association between humans and Helicobacter pylori. Nature 2007;445:915-18.
-
(2007)
Nature
, vol.445
, pp. 915-918
-
-
Linz, B.1
Balloux, F.2
Moodley, Y.3
-
48
-
-
58849086252
-
The peopling of the Pacific from a bacterial perspective
-
Moodley Y, Linz B, Yamaoka Y, et al. The peopling of the Pacific from a bacterial perspective. Science 2009;323:527-30.
-
(2009)
Science
, vol.323
, pp. 527-530
-
-
Moodley, Y.1
Linz, B.2
Yamaoka, Y.3
-
49
-
-
84877749743
-
Chromosome painting in silico in a bacterial species reveals fine population structure
-
Yahara K, Furuta Y, Oshima K, et al. Chromosome painting in silico in a bacterial species reveals fine population structure. Mol Biol Evol 2013;30: 1454-64.
-
(2013)
Mol Biol Evol
, vol.30
, pp. 1454-1464
-
-
Yahara, K.1
Furuta, Y.2
Oshima, K.3
-
50
-
-
33750107653
-
Bacterial populations as perfect gases: Genomic integrity and diversi fi cation tensions in Helicobacter pylori
-
Kang J, Blaser MJ. Bacterial populations as perfect gases: genomic integrity and diversi fi cation tensions in Helicobacter pylori. Nat Rev Microbiol 2006;4:826-36.
-
(2006)
Nat Rev Microbiol
, vol.4
, pp. 826-836
-
-
Kang, J.1
Blaser, M.J.2
|