-
1
-
-
84876718480
-
Effect of long-term laboratory propagation on Chlamydia trachomatis genome dynamics
-
Borges, V., Ferreira, R., Nunes, A., Sousa-Uva, M., Abreu, M., Borrego, M. J. & Gomes, J. P. (2013). Effect of long-term laboratory propagation on Chlamydia trachomatis genome dynamics. Infect Genet Evol 17, 23-32.
-
(2013)
Infect Genet Evol
, vol.17
, pp. 23-32
-
-
Borges, V.1
Ferreira, R.2
Nunes, A.3
Sousa-Uva, M.4
Abreu, M.5
Borrego, M.J.6
Gomes, J.P.7
-
2
-
-
33646167864
-
A simple and robust statistical test for detecting the presence of recombination
-
Bruen, T. C., Philippe, H. & Bryant, D. (2006). A simple and robust statistical test for detecting the presence of recombination. Genetics 172, 2665-2681.
-
(2006)
Genetics
, vol.172
, pp. 2665-2681
-
-
Bruen, T.C.1
Philippe, H.2
Bryant, D.3
-
3
-
-
79954468455
-
CDC Grand Rounds: Chlamydia prevention: Challenges and strategies for reducing disease burden and sequelae
-
Centers for Disease Control and Prevention
-
Centers for Disease Control and Prevention (2011). CDC Grand Rounds: Chlamydia prevention: challenges and strategies for reducing disease burden and sequelae. MMWR Morb Mortal Wkly Rep 60, 370-373.
-
(2011)
MMWR Morb Mortal Wkly Rep
, vol.60
, pp. 370-373
-
-
-
4
-
-
70249142557
-
Predicting phenotype and emerging strains among Chlamydia trachomatis infections
-
other authors
-
Dean, D., Bruno, W. J., Wan, R., Gomes, J. P., Devignot, S., Mehari, T., de Vries, H. J., Morré, S. A., Myers, G. & other authors (2009). Predicting phenotype and emerging strains among Chlamydia trachomatis infections. Emerg Infect Dis 15, 1385-1394.
-
(2009)
Emerg Infect Dis
, vol.15
, pp. 1385-1394
-
-
Dean, D.1
Bruno, W.J.2
Wan, R.3
Gomes, J.P.4
Devignot, S.5
Mehari, T.6
de Vries, H.J.7
Morré, S.A.8
Myers, G.9
-
5
-
-
4644334497
-
Tetracycline resistance in Chlamydia suis mediated by genomic islands inserted into the chlamydial inv-like gene
-
Dugan, J., Rockey, D. D., Jones, L. & Andersen, A. A. (2004). Tetracycline resistance in Chlamydia suis mediated by genomic islands inserted into the chlamydial inv-like gene. Antimicrob Agents Chemother 48, 3989-3995.
-
(2004)
Antimicrob Agents Chemother
, vol.48
, pp. 3989-3995
-
-
Dugan, J.1
Rockey, D.D.2
Jones, L.3
Andersen, A.A.4
-
6
-
-
0033837307
-
Quantitative Chlamydia trachomatis cultures: Correlation of chlamydial inclusion-forming units with serovar, age, sex, and race
-
Eckert, L. O., Suchland, R. J., Hawes, S. E. & Stamm, W. E. (2000). Quantitative Chlamydia trachomatis cultures: correlation of chlamydial inclusion-forming units with serovar, age, sex, and race. J Infect Dis 182, 540-544.
-
(2000)
J Infect Dis
, vol.182
, pp. 540-544
-
-
Eckert, L.O.1
Suchland, R.J.2
Hawes, S.E.3
Stamm, W.E.4
-
7
-
-
3042565597
-
Recombination in the genome of Chlamydia trachomatis involving the polymorphic membrane protein C gene relative to ompA and evidence for horizontal gene transfer
-
Gomes, J. P., Bruno, W. J., Borrego, M. J. & Dean, D. (2004). Recombination in the genome of Chlamydia trachomatis involving the polymorphic membrane protein C gene relative to ompA and evidence for horizontal gene transfer. J Bacteriol 186, 4295-4306.
-
(2004)
J Bacteriol
, vol.186
, pp. 4295-4306
-
-
Gomes, J.P.1
Bruno, W.J.2
Borrego, M.J.3
Dean, D.4
-
8
-
-
33845965685
-
Evolution of Chlamydia trachomatis diversity occurs by widespread interstrain recombination involving hotspots
-
Gomes, J. P., Bruno, W. J., Nunes, A., Santos, N., Florindo, C., Borrego, M. J. & Dean, D. (2007). Evolution of Chlamydia trachomatis diversity occurs by widespread interstrain recombination involving hotspots. Genome Res 17, 50-60.
-
(2007)
Genome Res
, vol.17
, pp. 50-60
-
-
Gomes, J.P.1
Bruno, W.J.2
Nunes, A.3
Santos, N.4
Florindo, C.5
Borrego, M.J.6
Dean, D.7
-
9
-
-
84859326308
-
Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing
-
other authors
-
Harris, S. R., Clarke, I. N., Seth-Smith, H. M., Solomon, A. W., Cutcliffe, L. T., Marsh, P., Skilton, R. J., Holland, M. J., Mabey, D. & other authors (2012). Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing. Nat Genet 44, 413-419, S1.
-
(2012)
Nat Genet
, vol.44
-
-
Harris, S.R.1
Clarke, I.N.2
Seth-Smith, H.M.3
Solomon, A.W.4
Cutcliffe, L.T.5
Marsh, P.6
Skilton, R.J.7
Holland, M.J.8
Mabey, D.9
-
10
-
-
36448948250
-
Extending assembly of short DNA sequences to handle error
-
Jeck, W. R., Reinhardt, J. A., Baltrus, D. A., Hickenbotham, M. T., Magrini, V., Mardis, E. R., Dangl, J. L. & Jones, C. D. (2007). Extending assembly of short DNA sequences to handle error. Bioinformatics 23, 2942-2944.
-
(2007)
Bioinformatics
, vol.23
, pp. 2942-2944
-
-
Jeck, W.R.1
Reinhardt, J.A.2
Baltrus, D.A.3
Hickenbotham, M.T.4
Magrini, V.5
Mardis, E.R.6
Dangl, J.L.7
Jones, C.D.8
-
11
-
-
77952738479
-
Genome sequencing of recent clinical Chlamydia trachomatis strains identifies loci associated with tissue tropism and regions of apparent recombination
-
Jeffrey, B. M., Suchland, R. J., Quinn, K. L., Davidson, J. R., Stamm, W. E. & Rockey, D. D. (2010). Genome sequencing of recent clinical Chlamydia trachomatis strains identifies loci associated with tissue tropism and regions of apparent recombination. Infect Immun 78, 2544-2553.
-
(2010)
Infect Immun
, vol.78
, pp. 2544-2553
-
-
Jeffrey, B.M.1
Suchland, R.J.2
Quinn, K.L.3
Davidson, J.R.4
Stamm, W.E.5
Rockey, D.D.6
-
12
-
-
84879101284
-
Genomic and phenotypic characterization of in vitrogenerated Chlamydia trachomatis recombinants
-
Jeffrey, B.M., Suchland, R. J., Eriksen, S. G., Sandoz, K. M. & Rockey, D. D. (2013). Genomic and phenotypic characterization of in vitrogenerated Chlamydia trachomatis recombinants. BMCMicrobiol 13, 142.
-
(2013)
BMCMicrobiol
, vol.13
, pp. 142
-
-
Jeffrey, B.M.1
Suchland, R.J.2
Eriksen, S.G.3
Sandoz, K.M.4
Rockey, D.D.5
-
13
-
-
79957467989
-
Interplay of recombination and selection in the genomes of Chlamydia trachomatis
-
Joseph, S. J., Didelot, X., Gandhi, K., Dean, D. & Read, T. D. (2011). Interplay of recombination and selection in the genomes of Chlamydia trachomatis. Biol Direct 6, 28.
-
(2011)
Biol Direct
, vol.6
, pp. 28
-
-
Joseph, S.J.1
Didelot, X.2
Gandhi, K.3
Dean, D.4
Read, T.D.5
-
14
-
-
0037100671
-
MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
-
Katoh, K., Misawa, K., Kuma, K. & Miyata, T. (2002). MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30, 3059-3066.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 3059-3066
-
-
Katoh, K.1
Misawa, K.2
Kuma, K.3
Miyata, T.4
-
15
-
-
68049142320
-
Multiple alignment of DNA sequences with MAFFT
-
Katoh, K., Asimenos, G. & Toh, H. (2009). Multiple alignment of DNA sequences with MAFFT. Methods Mol Biol 537, 39-64.
-
(2009)
Methods Mol Biol
, vol.537
, pp. 39-64
-
-
Katoh, K.1
Asimenos, G.2
Toh, H.3
-
16
-
-
55549097836
-
Mapping short DNA sequencing reads and calling variants using mapping quality scores
-
Li, H., Ruan, J. & Durbin, R. (2008). Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18, 1851-1858.
-
(2008)
Genome Res
, vol.18
, pp. 1851-1858
-
-
Li, H.1
Ruan, J.2
Durbin, R.3
-
17
-
-
5344244656
-
-
R Development Core Team. Vienna: R Foundation for Statistical Computing
-
R Development Core Team (2008). R: A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing.
-
(2008)
R: A Language and Environment for Statistical Computing
-
-
-
18
-
-
84877118112
-
Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture
-
other authors
-
Seth-Smith, H. M., Harris, S. R., Skilton, R. J., Radebe, F. M., Golparian, D., Shipitsyna, E., Duy, P. T., Scott, P., Cutcliffe, L. T. & other authors (2013). Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture. Genome Res 23, 855-866.
-
(2013)
Genome Res
, vol.23
, pp. 855-866
-
-
Seth-Smith, H.M.1
Harris, S.R.2
Skilton, R.J.3
Radebe, F.M.4
Golparian, D.5
Shipitsyna, E.6
Duy, P.T.7
Scott, P.8
Cutcliffe, L.T.9
-
19
-
-
84855193674
-
Hypervirulent Chlamydia trachomatis clinical strain is a recombinant between lymphogranuloma venereum (L(2) and D lineages
-
e00045-11
-
Somboonna, N., Wan, R., Ojcius, D. M., Pettengill, M. A., Joseph, S. J., Chang, A., Hsu, R., Read, T. D. & Dean, D. (2011). Hypervirulent Chlamydia trachomatis clinical strain is a recombinant between lymphogranuloma venereum (L(2) and D lineages. MBio 2, e00045-11.
-
(2011)
MBio
, vol.2
-
-
Somboonna, N.1
Wan, R.2
Ojcius, D.M.3
Pettengill, M.A.4
Joseph, S.J.5
Chang, A.6
Hsu, R.7
Read, T.D.8
Dean, D.9
-
20
-
-
84855934660
-
In vitro recombinants of antibiotic-resistant Chlamydia trachomatis strains have statistically more breakpoints than clinical recombinants for the same sequenced loci and exhibit selection at unexpected loci
-
Srinivasan, T., Bruno, W. J., Wan, R., Yen, A., Duong, J. & Dean, D. (2012). In vitro recombinants of antibiotic-resistant Chlamydia trachomatis strains have statistically more breakpoints than clinical recombinants for the same sequenced loci and exhibit selection at unexpected loci. J Bacteriol 194, 617-626.
-
(2012)
J Bacteriol
, vol.194
, pp. 617-626
-
-
Srinivasan, T.1
Bruno, W.J.2
Wan, R.3
Yen, A.4
Duong, J.5
Dean, D.6
-
21
-
-
0032561496
-
Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis
-
other authors
-
Stephens, R. S., Kalman, S., Lammel, C., Fan, J., Marathe, R., Aravind, L., Mitchell, W., Olinger, L., Tatusov, R. L. & other authors (1998). Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science 282, 754-759.
-
(1998)
Science
, vol.282
, pp. 754-759
-
-
Stephens, R.S.1
Kalman, S.2
Lammel, C.3
Fan, J.4
Marathe, R.5
Aravind, L.6
Mitchell, W.7
Olinger, L.8
Tatusov, R.L.9
-
22
-
-
77956626598
-
Frameshift mutations in a single novel virulence factor alter the in vivo pathogenicity of Chlamydia trachomatis for the female murine genital tract
-
other authors
-
Sturdevant, G. L., Kari, L., Gardner, D. J., Olivares-Zavaleta, N., Randall, L. B., Whitmire, W. M., Carlson, J. H., Goheen, M. M., Selleck, E. M. & other authors (2010). Frameshift mutations in a single novel virulence factor alter the in vivo pathogenicity of Chlamydia trachomatis for the female murine genital tract. Infect Immun 78, 3660-3668.
-
(2010)
Infect Immun
, vol.78
, pp. 3660-3668
-
-
Sturdevant, G.L.1
Kari, L.2
Gardner, D.J.3
Olivares-Zavaleta, N.4
Randall, L.B.5
Whitmire, W.M.6
Carlson, J.H.7
Goheen, M.M.8
Selleck, E.M.9
-
23
-
-
0026075022
-
Simplified microtiter cell culture method for rapid immunotyping of Chlamydia trachomatis
-
Suchland, R. J. & Stamm, W. E. (1991). Simplified microtiter cell culture method for rapid immunotyping of Chlamydia trachomatis. J Clin Microbiol 29, 1333-1338.
-
(1991)
J Clin Microbiol
, vol.29
, pp. 1333-1338
-
-
Suchland, R.J.1
Stamm, W.E.2
-
24
-
-
0033985761
-
Isolates of Chlamydia trachomatis that occupy nonfusogenic inclusions lack IncA, a protein localized to the inclusion membrane
-
Suchland, R. J., Rockey, D. D., Bannantine, J. P. & Stamm, W. E. (2000). Isolates of Chlamydia trachomatis that occupy nonfusogenic inclusions lack IncA, a protein localized to the inclusion membrane. Infect Immun 68, 360-367.
-
(2000)
Infect Immun
, vol.68
, pp. 360-367
-
-
Suchland, R.J.1
Rockey, D.D.2
Bannantine, J.P.3
Stamm, W.E.4
-
25
-
-
0344838680
-
Longitudinal assessment of infecting serovars of Chlamydia trachomatis in Seattle public health clinics: 1988-1996
-
Suchland, R. J., Eckert, L. O., Hawes, S. E. & Stamm, W. E. (2003). Longitudinal assessment of infecting serovars of Chlamydia trachomatis in Seattle public health clinics: 1988-1996. Sex Transm Dis 30, 357-361.
-
(2003)
Sex Transm Dis
, vol.30
, pp. 357-361
-
-
Suchland, R.J.1
Eckert, L.O.2
Hawes, S.E.3
Stamm, W.E.4
-
26
-
-
57349113738
-
Identification of concomitant infection with Chlamydia trachomatis IncA-negative mutant and wild-type strains by genomic, transcriptional, and biological characterizations
-
Suchland, R. J., Jeffrey, B. M., Xia, M., Bhatia, A., Chu, H. G., Rockey, D. D. & Stamm, W. E. (2008). Identification of concomitant infection with Chlamydia trachomatis IncA-negative mutant and wild-type strains by genomic, transcriptional, and biological characterizations. Infect Immun 76, 5438-5446.
-
(2008)
Infect Immun
, vol.76
, pp. 5438-5446
-
-
Suchland, R.J.1
Jeffrey, B.M.2
Xia, M.3
Bhatia, A.4
Chu, H.G.5
Rockey, D.D.6
Stamm, W.E.7
-
27
-
-
80053440375
-
Development of a transformation system for Chlamydia trachomatis: Restoration of glycogen biosynthesis by acquisition of a plasmid shuttle vector
-
Wang, Y., Kahane, S., Cutcliffe, L. T., Skilton, R. J., Lambden, P. R. & Clarke, I. N. (2011). Development of a transformation system for Chlamydia trachomatis: restoration of glycogen biosynthesis by acquisition of a plasmid shuttle vector. PLoS Pathog 7, e1002258.
-
(2011)
PLoS Pathog
, vol.7
-
-
Wang, Y.1
Kahane, S.2
Cutcliffe, L.T.3
Skilton, R.J.4
Lambden, P.R.5
Clarke, I.N.6
-
28
-
-
0024492598
-
Protective monoclonal antibodies to Chlamydia trachomatis serovar-and serogroup-specific major outer membrane protein determinants
-
Zhang, Y. X., Stewart, S. J. & Caldwell, H. D. (1989). Protective monoclonal antibodies to Chlamydia trachomatis serovar-and serogroup-specific major outer membrane protein determinants. Infect Immun 57, 636-638.
-
(1989)
Infect Immun
, vol.57
, pp. 636-638
-
-
Zhang, Y.X.1
Stewart, S.J.2
Caldwell, H.D.3
|