The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Inference of Bacterial Microevolution Using Multilocus Sequence Data
Open accessAbstract
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 pattern of inheritance. The key assumption of our model is that recombination events introduce a constant rate of substitutions to a contiguous region of sequence. The method is applicable both to multilocus sequence typing (MLST) data from a few loci and to alignments of multiple bacterial genomes. It can be used to decide whether a subset of isolates share common ancestry, to estimate the age of the common ancestor, and hence to address a variety of epidemiological and ecological questions that hinge on the pattern of bacterial spread. It should also be useful in associating particular genetic events with the changes in phenotype that they cause. We show that the model outperforms existing methods of subdividing recombinogenic bacteria using MLST data and provide examples from Salmonella and Bacillus. The software used in this article, ClonalFrame, is available from http://bacteria.stats.ox.ac.uk/.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
A tutorial on hidden Markov models and selected applications in speech recognition
Rabiner, L. R. (1989) · Proceedings of the IEEE · doi:10.1109/5.18626 · Cited by 22,743
Evolution of Protein Molecules
JUKES, T. H., & CANTOR, C. R. (1969) · Mammalian Protein Metabolism · doi:10.1016/b978-1-4832-3211-9.50009-7 · Cited by 11,032
Relaxed Phylogenetics and Dating with Confidence
Drummond, A. J., Ho, S. Y. W., Phillips, M. J., & Rambaut, A. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040088 · Cited by 6,463
Mauve: Multiple alignment of conserved genomic sequence with rearrangements
Darling, A. C. E., Mau, B., Blattner, F. R., & Perna, N. T. (2004) · Genome Research · doi:10.1101/gr.2289704 · Cited by 4,949
Lateral gene transfer and the nature of bacterial innovation
Ochman, H., Lawrence, J. G., & Groisman, E. A. (2000) · Nature · doi:10.1038/35012500 · Cited by 3,816
Smith, J. M., Smith, N. H., O'Rourke, M., & Spratt, B. G. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.10.4384 · Cited by 1,802
Cited by
progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
Darling, A. E., Mau, B., & Perna, N. T. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011147 · Cited by 3,848
Croucher, N. J., Page, A. J., Connor, T. R., Delaney, A. J., Keane, J. A., Bentley, S. D., Parkhill, J., & Harris, S. R. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1196 · Cited by 2,741
BIGSdb: Scalable analysis of bacterial genome variation at the population level
Jolley, K. A., & Maiden, M. C. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-595 · Cited by 2,368
The population genetics of commensal Escherichia coli
Tenaillon, O., Skurnik, D., Picard, B., & Denamur, E. (2010) · Nature Reviews Microbiology · doi:10.1038/nrmicro2298 · Cited by 1,533
The microbiome of uncontacted Amerindians
Clemente, J. C., Pehrsson, E. C., Blaser, M. J., Sandhu, K., Gao, Z., Wang, B., Magris, M., Hidalgo, G., Contreras, M., Noya-Alarcón, Ó., et al. (2015) · Science Advances · doi:10.1126/sciadv.1500183 · Cited by 851
Metadata
- Authors
- Didelot, X., & Falush, D.
- Venue
- Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-03-01
- Volume
- 175
- Issue
- 3
- Pages
- 1251-1266
- ISSN
- 0016-6731 (ISSN-L)
- 1943-2631
- OpenAlex
- W2157991545
- Cited by
- 645
- References
- 6
- FWCI
- 9.70
- Type
- journal article
- Language
- en
- Open access
- bronze
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Inference of Bacterial Microevolution Using Multilocus Sequence Data. https://app.cochat.ai/papers/10.1534/genetics.106.063305
- The paper
- Didelot, X., & Falush, D. (2007). Inference of Bacterial Microevolution Using Multilocus Sequence Data. Genetics. https://doi.org/10.1534/genetics.106.063305
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
