-
1
-
-
43849089834
-
Microbial diversity and the genetic nature of microbial species
-
Achtman, M. and Wagner, M. (2008) Microbial diversity and the genetic nature of microbial species. Nature Reviews Microbiology, 6 (6), 431-440.
-
(2008)
Nature Reviews Microbiology
, vol.6
, Issue.6
, pp. 431-440
-
-
Achtman, M.1
Wagner, M.2
-
2
-
-
56849114851
-
Seasonality and outbreak of a predominant Streptococcus pneumoniae serotype 1 clone from The Gambia: expansion of ST217 hypervirulent clonal complex in West Africa
-
Antonio, M., Hakeem, I., Awine, T. et al. (2008) Seasonality and outbreak of a predominant Streptococcus pneumoniae serotype 1 clone from The Gambia: expansion of ST217 hypervirulent clonal complex in West Africa. BMC Microbiology, 8 (1), 198.
-
(2008)
BMC Microbiology
, vol.8
, Issue.1
, pp. 198
-
-
Antonio, M.1
Hakeem, I.2
Awine, T.3
-
3
-
-
0031762222
-
Streptococcal emm types associated with T-agglutination types and the use of conserved emm gene restriction fragment patterns for subtyping group A streptococci
-
Beall, B., Facklam, R.R., Elliott, J.A. et al. (1998) Streptococcal emm types associated with T-agglutination types and the use of conserved emm gene restriction fragment patterns for subtyping group A streptococci. Journal of Medical Microbiology, 47 (10), 893-898.
-
(1998)
Journal of Medical Microbiology
, vol.47
, Issue.10
, pp. 893-898
-
-
Beall, B.1
Facklam, R.R.2
Elliott, J.A.3
-
5
-
-
0000116740
-
A method for deducing branching sequences in phylogeny
-
Camin, J.H. and Sokal, R.R. (1965) A method for deducing branching sequences in phylogeny. Evolution, 19 (3), 311-326.
-
(1965)
Evolution
, vol.19
, Issue.3
, pp. 311-326
-
-
Camin, J.H.1
Sokal, R.R.2
-
6
-
-
27744601905
-
Assessment of band-based similarity coefficients for automatic type and subtype classification of microbial isolates analyzed by pulsed-field gel electrophoresis
-
Carriço, J., Pinto, F.R., Simas, C. et al. (2005) Assessment of band-based similarity coefficients for automatic type and subtype classification of microbial isolates analyzed by pulsed-field gel electrophoresis. Journal of Clinical Microbiology, 43 (11), 5483-5490.
-
(2005)
Journal of Clinical Microbiology
, vol.43
, Issue.11
, pp. 5483-5490
-
-
Carriço, J.1
Pinto, F.R.2
Simas, C.3
-
7
-
-
33746255226
-
Illustration of a common framework for relating multiple typing methods by application to macrolide-resistant Streptococcus pyogenes
-
Carriço, J.A., Silva-Costa, C., Melo-Cristino, J. et al. (2006) Illustration of a common framework for relating multiple typing methods by application to macrolide-resistant Streptococcus pyogenes. Journal of Clinical Microbiology, 44 (7), 2524-2532.
-
(2006)
Journal of Clinical Microbiology
, vol.44
, Issue.7
, pp. 2524-2532
-
-
Carriço, J.A.1
Silva-Costa, C.2
Melo-Cristino, J.3
-
8
-
-
77952247101
-
Effects of environmental stress on stability of tandem repeats in Escherichia coli O157:H7
-
Cooley, M.B., Carychao, D., Nguyen, K. et al. (2010) Effects of environmental stress on stability of tandem repeats in Escherichia coli O157:H7. Applied and Environmental Microbiology, 76 (10), 3398-3400.
-
(2010)
Applied and Environmental Microbiology
, vol.76
, Issue.10
, pp. 3398-3400
-
-
Cooley, M.B.1
Carychao, D.2
Nguyen, K.3
-
9
-
-
0000250265
-
Measures of the amount of ecologic association between species
-
Dice, L. (1945) Measures of the amount of ecologic association between species. Ecology, 26 (3), 297-302.
-
(1945)
Ecology
, vol.26
, Issue.3
, pp. 297-302
-
-
Dice, L.1
-
10
-
-
38649110663
-
BEAST: Bayesian evolutionary analysis by sampling trees
-
Drummond, A.J. and Rambaut, A. (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.
-
(2007)
BMC Evolutionary Biology
, vol.7
, pp. 214
-
-
Drummond, A.J.1
Rambaut, A.2
-
12
-
-
0037188519
-
The evolutionary history of methicillin-resistant Staphylococcus aureus (MRSA)
-
Enright, M.C. (2002) The evolutionary history of methicillin-resistant Staphylococcus aureus (MRSA). Proceedings of the National Academy of Sciences, 99 (11), 7687-7692.
-
(2002)
Proceedings of the National Academy of Sciences
, vol.99
, Issue.11
, pp. 7687-7692
-
-
Enright, M.C.1
-
13
-
-
0031764441
-
A multilocus sequence typing scheme for Streptococcus pneumoniae: identification of clones associated with serious invasive disease
-
Enright, M. and Spratt, B.G. (1998) A multilocus sequence typing scheme for Streptococcus pneumoniae: identification of clones associated with serious invasive disease. Microbiology, 144 (11), 3049-3060.
-
(1998)
Microbiology
, vol.144
, Issue.11
, pp. 3049-3060
-
-
Enright, M.1
Spratt, B.G.2
-
14
-
-
0035793056
-
Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenetic consequences
-
Feil, E.J., Holmes, E.C., Bessen, D.E. et al. (2001) Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenetic consequences. Proceedings of the National Academy of Sciences, 98 (1), 182-187.
-
(2001)
Proceedings of the National Academy of Sciences
, vol.98
, Issue.1
, pp. 182-187
-
-
Feil, E.J.1
Holmes, E.C.2
Bessen, D.E.3
-
15
-
-
1342304133
-
eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data
-
Feil, E.J., Li, B.C., Aanensen, D.M. et al. (2004) eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. Journal of Bacteriology, 186 (5), 1518-1530.
-
(2004)
Journal of Bacteriology
, vol.186
, Issue.5
, pp. 1518-1530
-
-
Feil, E.J.1
Li, B.C.2
Aanensen, D.M.3
-
16
-
-
0019797407
-
Evolutionary trees from DNA sequences: a maximum likelihood approach
-
Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17 (6), 368-376.
-
(1981)
Journal of Molecular Evolution
, vol.17
, Issue.6
, pp. 368-376
-
-
Felsenstein, J.1
-
18
-
-
67650093575
-
Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach
-
Francisco, A.P., Bugalho, M., Ramirez, M. and Carriço, J.A. (2009) Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach. BMC Bioinformatics, 10 (1), 152.
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.1
, pp. 152
-
-
Francisco, A.P.1
Bugalho, M.2
Ramirez, M.3
Carriço, J.A.4
-
19
-
-
84865286374
-
PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods
-
Francisco, A.P., Vaz, C., Monteiro, P.T. et al. (2012) PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods. BMC Bioinformatics, 13 (1), 87.
-
(2012)
BMC Bioinformatics
, vol.13
, Issue.1
, pp. 87
-
-
Francisco, A.P.1
Vaz, C.2
Monteiro, P.T.3
-
20
-
-
22944480859
-
Spoligotyping and Mycobacterium tuberculosis
-
Gori, A., Bandera, A., Marchetti, G. et al. (2005) Spoligotyping and Mycobacterium tuberculosis. Emerging Infectious Diseases, 11 (8), 1242.
-
(2005)
Emerging Infectious Diseases
, vol.11
, Issue.8
, pp. 1242
-
-
Gori, A.1
Bandera, A.2
Marchetti, G.3
-
21
-
-
0034757959
-
Determining confidence intervals when measuring genetic diversity and the discriminatory abilities of typing methods for microorganisms
-
Grundmann, H., Hori, S. and Tanner, G. (2001) Determining confidence intervals when measuring genetic diversity and the discriminatory abilities of typing methods for microorganisms. Journal of Clinical Microbiology, 39 (11), 4190-4192.
-
(2001)
Journal of Clinical Microbiology
, vol.39
, Issue.11
, pp. 4190-4192
-
-
Grundmann, H.1
Hori, S.2
Tanner, G.3
-
22
-
-
32944456498
-
Phylogenetic analysis as a tool in molecular epidemiology of infectious diseases
-
Hall, B.G. and Barlow, M. (2006) Phylogenetic analysis as a tool in molecular epidemiology of infectious diseases. Annals of Epidemiology, 16 (3), 157-169.
-
(2006)
Annals of Epidemiology
, vol.16
, Issue.3
, pp. 157-169
-
-
Hall, B.G.1
Barlow, M.2
-
23
-
-
84943817322
-
Error detecting and error correcting codes
-
Hamming, R.W. (1950) Error detecting and error correcting codes. Bell System Technical Journal, 29 (2), 147-160.
-
(1950)
Bell System Technical Journal
, vol.29
, Issue.2
, pp. 147-160
-
-
Hamming, R.W.1
-
24
-
-
0000006498
-
Diversity and evenness: a unifying notation and its consequences
-
Hill, M. (1973) Diversity and evenness: a unifying notation and its consequences. Ecology, 54 (2), 427-432.
-
(1973)
Ecology
, vol.54
, Issue.2
, pp. 427-432
-
-
Hill, M.1
-
26
-
-
0034849408
-
MRBAYES: Bayesian inference of phylogenetic trees
-
Huelsenbeck, J.P. and Ronquist, F. (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 17 (8), 754-755.
-
(2001)
Bioinformatics
, vol.17
, Issue.8
, pp. 754-755
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
-
27
-
-
0024429456
-
Application of a numerical index of discriminatory power to a comparison of four physiochemical typing methods for Candida albicans
-
Hunter, P. and Fraser, C. (1989) Application of a numerical index of discriminatory power to a comparison of four physiochemical typing methods for Candida albicans. Journal of Clinical Microbiology, 27 (10), 2156-2160.
-
(1989)
Journal of Clinical Microbiology
, vol.27
, Issue.10
, pp. 2156-2160
-
-
Hunter, P.1
Fraser, C.2
-
28
-
-
0001368373
-
Étude comparative de la distribution florale dans une portion des Alpes et des Jura
-
Jaccard, P. (1901) Étude comparative de la distribution florale dans une portion des Alpes et des Jura. Bulletin de la Société Vaudoise des Sciences Naturelles, 37, 547-579.
-
(1901)
Bulletin de la Société Vaudoise des Sciences Naturelles
, vol.37
, pp. 547-579
-
-
Jaccard, P.1
-
29
-
-
70350674995
-
On the shortest spanning subtree of a graph and the traveling salesman problem
-
Kruskal, J.B. (1956) On the shortest spanning subtree of a graph and the traveling salesman problem. Proceedings of the American Mathematical Society, 7 (1), 48-50.
-
(1956)
Proceedings of the American Mathematical Society
, vol.7
, Issue.1
, pp. 48-50
-
-
Kruskal, J.B.1
-
30
-
-
78651168454
-
Epidemiologic characterization of group A streptococci by T-agglutination and M-precipitation tests in the public health laboratory
-
Moody, M.D., Padula, J., Lizana, D. and Hall, C.T. (1965) Epidemiologic characterization of group A streptococci by T-agglutination and M-precipitation tests in the public health laboratory. Health Laboratory Science, 2, 149-162.
-
(1965)
Health Laboratory Science
, vol.2
, pp. 149-162
-
-
Moody, M.D.1
Padula, J.2
Lizana, D.3
Hall, C.T.4
-
33
-
-
44449093013
-
Polyclonal population structure of Streptococcus pneumoniae isolates in Spain carrying mef and mef plus erm(B)
-
de la Pedrosa, E.G.G., Morosini, M.I., van der Linden, M. et al. (2008) Polyclonal population structure of Streptococcus pneumoniae isolates in Spain carrying mef and mef plus erm(B). Antimicrobial Agents and Chemotherapy, 52 (6), 1964-1969.
-
(2008)
Antimicrobial Agents and Chemotherapy
, vol.52
, Issue.6
, pp. 1964-1969
-
-
de la Pedrosa, E.G.G.1
Morosini, M.I.2
van der Linden, M.3
-
34
-
-
58149200162
-
A confidence interval for the Wallace coefficient of concordance and its application to microbial typing methods
-
Pinto, F.R., Melo-Cristino, J. and Ramirez, M. (2008) A confidence interval for the Wallace coefficient of concordance and its application to microbial typing methods. PLoS One, 3 (11), e3696.
-
(2008)
PLoS One
, vol.3
, Issue.11
, pp. e3696
-
-
Pinto, F.R.1
Melo-Cristino, J.2
Ramirez, M.3
-
35
-
-
84950632109
-
Objective criteria for the evaluation of clustering methods
-
Rand, W.M. (1971) Objective criteria for the evaluation of clustering methods. Journal of the American Statistical Association, 66 (336), 846-850.
-
(1971)
Journal of the American Statistical Association
, vol.66
, Issue.336
, pp. 846-850
-
-
Rand, W.M.1
-
37
-
-
84952503562
-
Thirteen ways to look at the correlation coefficient
-
Rodgers, J.L. and Nicewander, W.A. (1988) Thirteen ways to look at the correlation coefficient. American Statistician, 42 (1), 59-66.
-
(1988)
American Statistician
, vol.42
, Issue.1
, pp. 59-66
-
-
Rodgers, J.L.1
Nicewander, W.A.2
-
38
-
-
33745136790
-
Multilocus sequence typing scheme for Enterococcus faecalis reveals hospital-adapted genetic complexes in a background of high rates of recombination
-
Ruiz-Garbajosa, P., Bonten, M.J., Robinson, D.A. et al. (2006) Multilocus sequence typing scheme for Enterococcus faecalis reveals hospital-adapted genetic complexes in a background of high rates of recombination. Journal of Clinical Microbiology, 44 (6), 2220-2228.
-
(2006)
Journal of Clinical Microbiology
, vol.44
, Issue.6
, pp. 2220-2228
-
-
Ruiz-Garbajosa, P.1
Bonten, M.J.2
Robinson, D.A.3
-
39
-
-
0023375195
-
The neighbor-joining method: a new method for reconstructing phylogenetic trees
-
Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4 (4), 406-425.
-
(1987)
Molecular Biology and Evolution
, vol.4
, Issue.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
40
-
-
3843099223
-
Multiple-locus variable-number tandem repeat analysis of Dutch Bordetella pertussis strains reveals rapid genetic changes with clonal expansion during the late 1990s
-
Schouls, L.M., van der Heide, H.G., Vauterin, L. et al. (2004) Multiple-locus variable-number tandem repeat analysis of Dutch Bordetella pertussis strains reveals rapid genetic changes with clonal expansion during the late 1990s. Journal of Bacteriology, 186 (16), 5496-5505.
-
(2004)
Journal of Bacteriology
, vol.186
, Issue.16
, pp. 5496-5505
-
-
Schouls, L.M.1
van der Heide, H.G.2
Vauterin, L.3
-
41
-
-
80355145041
-
Adjusted Wallace coefficient as a measure of congruence between typing methods
-
Severiano, A., Pinto, F.R., Ramirez, M. and Carriço, J.A. (2011a) Adjusted Wallace coefficient as a measure of congruence between typing methods. Journal of Clinical Microbiology, 49 (11), 3997-4000.
-
(2011)
Journal of Clinical Microbiology
, vol.49
, Issue.11
, pp. 3997-4000
-
-
Severiano, A.1
Pinto, F.R.2
Ramirez, M.3
Carriço, J.A.4
-
42
-
-
79956190902
-
Evaluation of jackknife and bootstrap for defining confidence intervals for pairwise agreement measures
-
Severiano, A., Carriço, J.A., Robinson, D.A. et al. (2011b) Evaluation of jackknife and bootstrap for defining confidence intervals for pairwise agreement measures. PLoS One, 6 (5), e19539.
-
(2011)
PLoS One
, vol.6
, Issue.5
, pp. e19539
-
-
Severiano, A.1
Carriço, J.A.2
Robinson, D.A.3
-
43
-
-
84940644968
-
A mathematical theory of communication
-
Shannon, C. (1948) A mathematical theory of communication. The Bell System Technical Journal, 27 (1), 379-423.
-
(1948)
The Bell System Technical Journal
, vol.27
, Issue.1
, pp. 379-423
-
-
Shannon, C.1
-
44
-
-
33344464667
-
Measurement of diversity
-
Simpson, E. (1949) Measurement of diversity. Nature, 163 (4148), 688.
-
(1949)
Nature
, vol.163
, Issue.4148
, pp. 688
-
-
Simpson, E.1
-
46
-
-
0034539018
-
Population structure and evolutionary dynamics of pathogenic bacteria
-
Smith, J.M., Feil, E.J. and Smith, N.H. (2000) Population structure and evolutionary dynamics of pathogenic bacteria. BioEssays, 22 (12), 1115-1122.
-
(2000)
BioEssays
, vol.22
, Issue.12
, pp. 1115-1122
-
-
Smith, J.M.1
Feil, E.J.2
Smith, N.H.3
-
47
-
-
79951958974
-
Cross-species spread of SCCmec IV subtypes in staphylococci
-
Smyth, D.S., Wong, A. and Robinson, D.A. (2010) Cross-species spread of SCCmec IV subtypes in staphylococci. Infection, Genetics and Evolution, 11 (2), 446-453.
-
(2010)
Infection, Genetics and Evolution
, vol.11
, Issue.2
, pp. 446-453
-
-
Smyth, D.S.1
Wong, A.2
Robinson, D.A.3
-
48
-
-
0029498868
-
Thirty years of numerical taxonomy
-
Sneath, P.H.A. (1995) Thirty years of numerical taxonomy. Systematic Biology, 44 (3), 281-298.
-
(1995)
Systematic Biology
, vol.44
, Issue.3
, pp. 281-298
-
-
Sneath, P.H.A.1
-
50
-
-
0000825481
-
A statistical method for evaluating systematic relationships
-
Sokal, R.R. and Michener, C.D. (1958) A statistical method for evaluating systematic relationships. University of Kansas Science Bulletin, 38, 1409-1438.
-
(1958)
University of Kansas Science Bulletin
, vol.38
, pp. 1409-1438
-
-
Sokal, R.R.1
Michener, C.D.2
-
51
-
-
0002471149
-
The comparison of dendrograms by objective methods
-
Sokal, R.R. and Rohlf, F. (1962) The comparison of dendrograms by objective methods. Taxon, 11 (2), 33-40.
-
(1962)
Taxon
, vol.11
, Issue.2
, pp. 33-40
-
-
Sokal, R.R.1
Rohlf, F.2
-
52
-
-
0002965815
-
The proof and measurement of association between two things
-
Spearman, C. (1904) The proof and measurement of association between two things. The American Journal of Psychology, 15 (1), 72-101.
-
(1904)
The American Journal of Psychology
, vol.15
, Issue.1
, pp. 72-101
-
-
Spearman, C.1
-
53
-
-
34249745345
-
Assessing the reliability of eBURST using simulated populations with known ancestry
-
Turner, K.M., Hanage, W.P., Fraser, C. et al. (2007) Assessing the reliability of eBURST using simulated populations with known ancestry. BMC Microbiology, 7 (1), 30.
-
(2007)
BMC Microbiology
, vol.7
, Issue.1
, pp. 30
-
-
Turner, K.M.1
Hanage, W.P.2
Fraser, C.3
-
54
-
-
33846200897
-
-
(ed E. Stackebrandt), Springer-Verlag, New York
-
Vauterin, L. and Vauterin, P. (2006) Integrated databasing and analysis, in Molecular Identification, Systematics, and Population Structure of Prokaryotes (ed E. Stackebrandt), Springer-Verlag, New York, pp. 141-217.
-
(2006)
Integrated databasing and analysis, in Molecular Identification, Systematics, and Population Structure of Prokaryotes
, pp. 141-217
-
-
Vauterin, L.1
Vauterin, P.2
-
55
-
-
0027478539
-
Penicillin-resistant Streptococcus pneumoniae strains recovered in Houston: identification and molecular characterization of multiple clones
-
Versalovic, J., Kapur, V., Mason, E.O., Jr et al. (1993) Penicillin-resistant Streptococcus pneumoniae strains recovered in Houston: identification and molecular characterization of multiple clones. The Journal of Infectious Diseases, 167 (4), 850-856.
-
(1993)
The Journal of Infectious Diseases
, vol.167
, Issue.4
, pp. 850-856
-
-
Versalovic, J.1
Kapur, V.2
Mason, E.O.3
-
56
-
-
33846661637
-
Mutations, mutation rates, and evolution at the hypervariable VNTR loci of Yersinia pestis
-
Vogler, A., Keys, C.E., Allender, C. et al. (2007) Mutations, mutation rates, and evolution at the hypervariable VNTR loci of Yersinia pestis. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 616 (1-2), 145-158.
-
(2007)
Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
, vol.616
, Issue.1-2
, pp. 145-158
-
-
Vogler, A.1
Keys, C.E.2
Allender, C.3
-
57
-
-
84945923591
-
A method for comparing two hierarchical clusterings: comment
-
Wallace, D.L. (1983) A method for comparing two hierarchical clusterings: comment. Journal of the American Statistical Association, 78 (383), 569-576.
-
(1983)
Journal of the American Statistical Association
, vol.78
, Issue.383
, pp. 569-576
-
-
Wallace, D.L.1
-
58
-
-
0001587384
-
On the abstract properties of linear dependence
-
Whitney, H. (1935) On the abstract properties of linear dependence. American Journal of Mathematics, 57 (3), 509-533.
-
(1935)
American Journal of Mathematics
, vol.57
, Issue.3
, pp. 509-533
-
-
Whitney, H.1
-
59
-
-
0034111151
-
The direction of microsatellite mutations is dependent upon allele length
-
Xu, X., Peng, M. and Fang, Z. (2000) The direction of microsatellite mutations is dependent upon allele length. Nature Genetics, 24 (4), 396-399.
-
(2000)
Nature Genetics
, vol.24
, Issue.4
, pp. 396-399
-
-
Xu, X.1
Peng, M.2
Fang, Z.3
|