Bayesian modeling of recombination events in bacterial populations (2008)
Marttinen, Pekka, Baldwin, Adam, Hanage, William P, Dowson, Chris, Mahenthiralingam, Eshwar, Corander, Jukka
Abstract Background We consider the discovery of recombinant segments jointly with their origins within multilocus DNA sequences from bacteria representing heterogeneous populations of fairly closely...
Assessing the reliability of eBURST using simulated populations with known ancestry (2007)
Turner, Katherine ME, Hanage, William P, Fraser, Christophe, Connor, Thomas R, Spratt, Brian G
Abstract Background The program eBURST uses multilocus sequence typing data to divide bacterial populations into groups of closely related strains (clonal complexes), predicts the founding genotype...
Matthew C. Fisher, William P. Hanage, Sybren De Hoog, Elizabeth Johnson, Michael D. Smith, Nicholas J. White, ...
Long-distance dispersal in microbial eukaryotes has been shown to result in the establishment of populations on continental and global scales. Such “ubiquitous dispersal” has been claimed to be a...
Fuzzy species among recombinogenic bacteria (2005)
Hanage, William P, Fraser, Christophe, Spratt, Brian G
Abstract Background It is a matter of ongoing debate whether a universal species concept is possible for bacteria. Indeed, it is not clear whether closely related isolates of bacteria typically form...
Hanage, William P., Auranen, Kari, Syrjänen, Ritva, Herva, Elja, Mäkelä, P. Helena, Kilpi, Terhi, ...
The relative abilities of pneumococcal serotypes and strains (clones) to cause acute otitis media (AOM) were investigated by comparing the serotypes and genotypes of pneumococci recovered from cases...
Feil, Edward J., Li, Bao C., Aanensen, David M., Hanage, William P., Spratt, Brian G.
The introduction of multilocus sequence typing (MLST) for the precise characterization of isolates of bacterial pathogens has had a marked impact on both routine epidemiological surveillance and...
Invasiveness of Serotypes and Clones of Streptococcus pneumoniae among Children in Finland
Hanage, William P., Kaijalainen, Tarja H., Syrjänen, Ritva K., Auranen, Kari, Leinonen, Maija, Mäkelä, P. Helena, ...
Streptococcus pneumoniae (the pneumococcus) causes diseases from otitis media to life-threatening invasive infection. The species is extremely antigenically and clonally diverse. We wished to...
Neutral microepidemic evolution of bacterial pathogens
Fraser, Christophe, Hanage, William P., Spratt, Brian G.
Understanding bacterial population genetics is vital for interpreting the response of bacterial populations to selection pressures such as antibiotic treatment or vaccines targeted at only a subset...
Using Multilocus Sequence Data To Define the Pneumococcus
Hanage, William P., Kaijalainen, Tarja, Herva, Elja, Saukkoriipi, Annika, Syrjänen, Ritva, Spratt, Brian G.
We investigated the genetic relationships between serotypeable pneumococci and nonserotypeable presumptive pneumococci using multilocus sequence typing (MLST) and partial sequencing of the...
Fisher, Matthew C, Hanage, William P, De Hoog, Sybren, Johnson, Elizabeth, Smith, Michael D, White, Nicholas J, ...
Long-distance dispersal in microbial eukaryotes has been shown to result in the establishment of populations on continental and global scales. Such “ubiquitous dispersal” has been claimed to be a...
Hanage, William P., Auranen, Kari, Syrjänen, Ritva, Herva, Elja, Mäkelä, P. Helena, Kilpi, Terhi, ...
The relative abilities of pneumococcal serotypes and strains (clones) to cause acute otitis media (AOM) were investigated by comparing the serotypes and genotypes of pneumococci recovered from cases...
Feil, Edward J., Li, Bao C., Aanensen, David M., Hanage, William P., Spratt, Brian G.
The introduction of multilocus sequence typing (MLST) for the precise characterization of isolates of bacterial pathogens has had a marked impact on both routine epidemiological surveillance and...
Invasiveness of Serotypes and Clones of Streptococcus pneumoniae among Children in Finland
Hanage, William P., Kaijalainen, Tarja H., Syrjänen, Ritva K., Auranen, Kari, Leinonen, Maija, Mäkelä, P. Helena, ...
Streptococcus pneumoniae (the pneumococcus) causes diseases from otitis media to life-threatening invasive infection. The species is extremely antigenically and clonally diverse. We wished to...
Neutral microepidemic evolution of bacterial pathogens
Fraser, Christophe, Hanage, William P., Spratt, Brian G.
Understanding bacterial population genetics is vital for interpreting the response of bacterial populations to selection pressures such as antibiotic treatment or vaccines targeted at only a subset...
Using Multilocus Sequence Data To Define the Pneumococcus
Hanage, William P., Kaijalainen, Tarja, Herva, Elja, Saukkoriipi, Annika, Syrjänen, Ritva, Spratt, Brian G.
We investigated the genetic relationships between serotypeable pneumococci and nonserotypeable presumptive pneumococci using multilocus sequence typing (MLST) and partial sequencing of the...
Fisher, Matthew C, Hanage, William P, De Hoog, Sybren, Johnson, Elizabeth, Smith, Michael D, White, Nicholas J, ...
Long-distance dispersal in microbial eukaryotes has been shown to result in the establishment of populations on continental and global scales. Such “ubiquitous dispersal” has been claimed to be a...
Assessing the reliability of eBURST using simulated populations with known ancestry
Turner, Katherine ME, Hanage, William P, Fraser, Christophe, Connor, Thomas R, Spratt, Brian G
Sequences, sequence clusters and bacterial species
Hanage, William P, Fraser, Christophe, Spratt, Brian G
Whatever else they should share, strains of bacteria assigned to the same species should have house-keeping genes that are similar in sequence. Single gene sequences (or rRNA gene sequences) have...
Modelling bacterial speciation
Hanage, William P, Spratt, Brian G, Turner, Katherine M.E, Fraser, Christophe
A central problem in understanding bacterial speciation is how clusters of closely related strains emerge and persist in the face of recombination. We use a neutral Fisher–Wright model in which...
Variation in HIV-1 set-point viral load: Epidemiological analysis and an evolutionary hypothesis
Fraser, Christophe, Hollingsworth, T. Déirdre, Chapman, Ruth, De Wolf, Frank, Hanage, William P.
The natural course of HIV-1 infection is characterized by a high degree of heterogeneity in viral load, not just within patients over time, but also between patients, especially during the...