Inferring genomic flux in bacteria (2009)
Didelot, Xavier, Darling, Aaron, Falush, Daniel
Acquisition and loss of genetic material are essential forces in bacterial microevolution. They have been repeatedly linked with adaptation of lineages to new lifestyles, and in particular,...
SimMLST: simulation of multi-locus sequence typing data under a neutral model (2009)
Didelot, Xavier, Lawson, Daniel, Falush, Daniel
Summary: Multi-locus sequence typing (MLST) is a widely used method of characterization of bacterial isolates. It has been applied to over 50 000 isolates in over 50 different species. Here, we...
An African origin for the intimate association between humans and Helicobacter pylori (2007)
Linz, Bodo, Balloux, Francois, Moodley, Yoshan, Manica, Andrea, Liu, Hua, Roumagnac, Philippe, ...
Infection of the stomach by Helicobacter pylori is ubiquitous among humans. However, although H. pylori strains from different geographic areas are associated with clear phylogeographic...
An African origin for the intimate association between humans and Helicobacter pylori (2007)
Linz, Bodo, Balloux, Francois, Moodley, Yoshan, Manica, Andrea, Liu, Hua, Roumagnac, Philippe, ...
Infection of the stomach by Helicobacter pylori is ubiquitous among humans. However, although H. pylori strains from different geographic areas are associated with clear phylogeographic...
An African origin for the intimate association between humans and Helicobacter pylori (2007)
Linz, Bodo, Balloux, François, Moodley, Yoshan, Manica, Andrea, Liu, Hua, Roumagnac, Philippe, ...
Didelot, Xavier, Achtman, Mark, Parkhill, Julian, Thomson, Nicholas R., Falush, Daniel
All Salmonella can cause disease but severe systemic infections are primarily caused by a few lineages. Paratyphi A and Typhi are the deadliest human restricted serovars, responsible for ∼600,000...
Mismatch induced speciation in Salmonella: model and data (2006)
Falush, Daniel, Torpdahl, Mia, Didelot, Xavier, Conrad, Donald F., Wilson, Daniel J., Achtman, Mark
Sex and virulence in Escherichia coli: an evolutionary perspective (2006)
Wirth, Thierry, Falush, Daniel, Lan, Ruiting, Colles, Frances, Mensa, Patience, Wieler, Lothar H., ...
Pathogenic Escherichia coli cause over 160 million cases of dysentery and one million deaths per year, whereas non-pathogenic E. coli constitute part of the normal intestinal flora of healthy mammals...
Xavier Didelot, Daniel Falush, Key Words, Daniel Falush
We describe a model-based method for using multilocus sequence data to infer the clonal relation-ships of bacteria and the chromosomal position of homologous recombination events that disrupt a...
Didelot, Xavier, Achtman, Mark, Parkhill, Julian, Thomson, Nicholas R., Falush, Daniel
All Salmonella can cause disease but severe systemic infections are primarily caused by a few lineages. Paratyphi A and Typhi are the deadliest human restricted serovars, responsible for ∼600,000...
Wirth,Thierry, Wang,Xiaoyan, Linz,Bodo, Novick,Richard P., Lum,J. Koji, Blaser,Martin, ...
The history of mankind remains one of the most challenging fields of study. However, the emergence of anatomically modern humans has been so recent that only a few genetically informative...
Langbehn,Douglas R., Brinkman,Ryan R., Falush,Daniel, Paulsen,Jane S., Hayden,M. R.
Huntington's disease (HD) is a neurodegenerative disorder caused by an unstable CAG repeat. For patients at risk, participating in predictive testing and learning of having CAG expansion, a major...
Falush,Daniel, Stephens,Matthew, Pritchard,Jonathan K.
We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci....
Traces of human migrations in Helicobacter pylori populations (2003)
Falush,Daniel, Wirth,Thierry, Linz,Bodo, Pritchard,Jonathan K., Stephens,Matthew, Kidd,Mark, ...
Helicobacter pylori, a chronic gastric pathogen of human beings, can be divided into seven populations and subpopulations with distinct geographical distributions. These modern populations derive...
Traces of human migrations in Helicobacter pylori populations (2003)
Falush, Daniel, Wirth, Thierry, Linz, Bodo, Pritchard, Jonathan K., Stephens, Matthew, Kidd, Mark, ...
Falush,Daniel, Kraft,Christian, Taylor,Nancy S., Correa,Pelayo, Fox,James G., Achtman,Mark, ...
The bacterium Helicobacter pylori colonizes the gastric mucosa of half of the human population, resulting in chronic gastritis, ulcers, and cancer. We sequenced ten gene fragments from pairs of...
Falush, Daniel, Kraft, Christian, Taylor, Nancy S., Correa, Pelayo, Fox, James G., Achtman, Mark, ...
Zhu, Peixuan, Van Der Ende, Arie, Falush, Daniel, Brieske, Norbert, Morelli, Giovanna, Linz, Bodo, ...
The genetic variability at six polymorphic loci was examined within a global collection of 502 isolates of subgroup III, serogroup A Neisseria meningitidis. Nine “genoclouds” were identified,...
Falush, Daniel, Kraft, Christian, Taylor, Nancy S., Correa, Pelayo, Fox, James G., Achtman, Mark, ...
The bacterium Helicobacter pylori colonizes the gastric mucosa of half of the human population, resulting in chronic gastritis, ulcers, and cancer. We sequenced ten gene fragments from pairs of...
Wirth, Thierry, Wang, Xiaoyan, Linz, Bodo, Novick, Richard P., Lum, J. Koji, Blaser, Martin, ...
The history of mankind remains one of the most challenging fields of study. However, the emergence of anatomically modern humans has been so recent that only a few genetically informative...
Sequence Typing and Comparison of Population Biology of Campylobacter coli and Campylobacter jejuni
Dingle, Kate E., Colles, Frances M., Falush, Daniel, Maiden, Martin C. J.
A multilocus sequence typing (MLST) scheme that uses the same loci as a previously described system for Campylobacter jejuni was developed for Campylobacter coli. The C. coli-specific primers were...
Falush, Daniel, Almqvist, Elisabeth W., Brinkmann, Ryan R., Iwasa, Yoh, Hayden, Michael R.
We describe a new approach for analysis of the epidemiology of progressive genetic disorders that quantifies the rate of progression of the disease in the population by measuring the mutational flow....
Genomic Changes during Chronic Helicobacter pylori Infection
Kraft, Christian, Stack, Allison, Josenhans, Christine, Niehus, Eike, Dietrich, Guido, Correa, Pelayo, ...
The gastric pathogen Helicobacter pylori shows tremendous genetic variability within human populations, both in gene content and at the sequence level. We investigated how this variability arises by...
Falush, Daniel, Stephens, Matthew, Pritchard, Jonathan K
We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci....
Sex and virulence in Escherichia coli: an evolutionary perspective
Wirth, Thierry, Falush, Daniel, Lan, Ruiting, Colles, Frances, Mensa, Patience, Wieler, Lothar H, ...
Pathogenic Escherichia coli cause over 160 million cases of dysentery and one million deaths per year, whereas non-pathogenic E. coli constitute part of the normal intestinal flora of healthy mammals...
Zhu, Peixuan, Van Der Ende, Arie, Falush, Daniel, Brieske, Norbert, Morelli, Giovanna, Linz, Bodo, ...
The genetic variability at six polymorphic loci was examined within a global collection of 502 isolates of subgroup III, serogroup A Neisseria meningitidis. Nine “genoclouds” were identified,...
Falush, Daniel, Kraft, Christian, Taylor, Nancy S., Correa, Pelayo, Fox, James G., Achtman, Mark, ...
The bacterium Helicobacter pylori colonizes the gastric mucosa of half of the human population, resulting in chronic gastritis, ulcers, and cancer. We sequenced ten gene fragments from pairs of...
Wirth, Thierry, Wang, Xiaoyan, Linz, Bodo, Novick, Richard P., Lum, J. Koji, Blaser, Martin, ...
The history of mankind remains one of the most challenging fields of study. However, the emergence of anatomically modern humans has been so recent that only a few genetically informative...
Sequence Typing and Comparison of Population Biology of Campylobacter coli and Campylobacter jejuni
Dingle, Kate E., Colles, Frances M., Falush, Daniel, Maiden, Martin C. J.
A multilocus sequence typing (MLST) scheme that uses the same loci as a previously described system for Campylobacter jejuni was developed for Campylobacter coli. The C. coli-specific primers were...
Falush, Daniel, Almqvist, Elisabeth W., Brinkmann, Ryan R., Iwasa, Yoh, Hayden, Michael R.
We describe a new approach for analysis of the epidemiology of progressive genetic disorders that quantifies the rate of progression of the disease in the population by measuring the mutational flow....
Genomic Changes during Chronic Helicobacter pylori Infection
Kraft, Christian, Stack, Allison, Josenhans, Christine, Niehus, Eike, Dietrich, Guido, Correa, Pelayo, ...
The gastric pathogen Helicobacter pylori shows tremendous genetic variability within human populations, both in gene content and at the sequence level. We investigated how this variability arises by...
Falush, Daniel, Stephens, Matthew, Pritchard, Jonathan K
We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci....
Sex and virulence in Escherichia coli: an evolutionary perspective
Wirth, Thierry, Falush, Daniel, Lan, Ruiting, Colles, Frances, Mensa, Patience, Wieler, Lothar H, ...
Pathogenic Escherichia coli cause over 160 million cases of dysentery and one million deaths per year, whereas non-pathogenic E. coli constitute part of the normal intestinal flora of healthy mammals...
Inference of Bacterial Microevolution Using Multilocus Sequence Data
Didelot, Xavier, Falush, Daniel
We describe a model-based method for using multilocus sequence data to infer the clonal relationships of bacteria and the chromosomal position of homologous recombination events that disrupt a clonal...
Didelot, Xavier, Achtman, Mark, Parkhill, Julian, Thomson, Nicholas R., Falush, Daniel
All Salmonella can cause disease but severe systemic infections are primarily caused by a few lineages. Paratyphi A and Typhi are the deadliest human restricted serovars, responsible for ∼600,000...
Inference of population structure using multilocus genotype data: dominant markers and null alleles
FALUSH, DANIEL, STEPHENS, MATTHEW, PRITCHARD, JONATHAN K
Dominant markers such as amplified fragment length polymorphisms (AFLPs) provide an economical way of surveying variation at many loci. However, the uncertainty about the underlying genotypes...
Mismatch induced speciation in Salmonella: model and data
Falush, Daniel, Torpdahl, Mia, Didelot, Xavier, Conrad, Donald F, Wilson, Daniel J, Achtman, Mark
In bacteria, DNA sequence mismatches act as a barrier to recombination between distantly related organisms and can potentially promote the cohesion of species. We have performed computer simulations...
Inferring Human Colonization History Using a Copying Model
Hellenthal, Garrett, Auton, Adam, Falush, Daniel
Genome-wide scans of genetic variation can potentially provide detailed information on how modern humans colonized the world but require new methods of analysis. We introduce a statistical approach...
Kulick, Stefan, Moccia, Claudia, Didelot, Xavier, Falush, Daniel, Kraft, Christian, Suerbaum, Sebastian
Helicobacter pylori colonizes the gastric mucosa of half of the human population, causing gastritis, ulcers, and cancer. H. pylori is naturally competent for transformation by exogenous DNA, and...
Lin, Edward A., Zhang, Xue-Song, Levine, Steven M., Gill, Steven R., Falush, Daniel, Blaser, Martin J.
Helicobacter pylori are gram-negative bacteria notable for their high level of genetic diversity and plasticity, features that may play a key role in the organism's ability to colonize the human...
Inferring genomic flux in bacteria
Didelot, Xavier, Darling, Aaron, Falush, Daniel
Acquisition and loss of genetic material are essential forces in bacterial microevolution. They have been repeatedly linked with adaptation of lineages to new lifestyles, and in particular,...
Host-associated Genetic Import in Campylobacter jejuni
McCarthy, Noel D., Colles, Frances M., Dingle, Kate E., Bagnall, Mary C., Manning, Georgina, Maiden, Martin C.J., ...
C. jejuni genomes have a host signature that enables attribution of isolates to animal sources.
Toward the Use of Genomics to Study Microevolutionary Change in Bacteria
Bacteria evolve rapidly in response to the environment they encounter. Some environmental changes are experienced numerous times by bacteria from the same population, providing an opportunity to...