The DOI matches its Crossref record; 104 of the 104 references it cites were found in a registry or an index.
Inferring Horizontal Gene Transfer
Open accessAbstract
Horizontal or Lateral Gene Transfer (HGT or LGT) is the transmission of portions of genomic DNA between organisms through a process decoupled from vertical inheritance. In the presence of HGT events, different fragments of the genome are the result of different evolutionary histories. This can therefore complicate the investigations of evolutionary relatedness of lineages and species. Also, as HGT can bring into genomes radically different genotypes from distant lineages, or even new genes bearing new functions, it is a major source of phenotypic innovation and a mechanism of niche adaptation. For example, of particular relevance to human health is the lateral transfer of antibiotic resistance and pathogenicity determinants, leading to the emergence of pathogenic lineages. Computational identification of HGT events relies upon the investigation of sequence composition or evolutionary history of genes. Sequence composition-based ("parametric") methods search for deviations from the genomic average, whereas evolutionary history-based ("phylogenetic") approaches identify genes whose evolutionary history significantly differs from that of the host species. The evaluation and benchmarking of HGT inference methods typically rely upon simulated genomes, for which the true history is known. On real data, different methods tend to infer different HGT events, and as a result it can be difficult to ascertain all but simple and clear-cut HGT events.
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
Inferring the historical patterns of biological evolution
Pagel, M. (1999) · Nature · doi:10.1038/44766 · Cited by 5,200
Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference
Shimodaira, H., & Hasegawa, M. (1999) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026201 · Cited by 4,237
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
Evolutionary divergence and convergence in proteins.
ZUCKERKANDL, E., & PAULING, L. (1965) · Evolving Genes and Proteins · doi:10.1016/b978-1-4832-2734-4.50017-6 · Cited by 3,020
An approximately unbiased test of phylogenetic tree selection
Shimodaira, H. (2002) · Systematic Biology · doi:10.1080/10635150290069913 · Cited by 2,791
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D., & Yeates, T. O. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.8.4285 · Cited by 1,585
Welch, R. A., Burland, V., Plunkett, G., Redford, P., Roesch, P., Rasko, D., Buckles, E. L., Liou, S.-R., Boutin, A., Hackett, J., et al. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.252529799 · Cited by 1,531
Nelson, K. E., Clayton, R. A., Gill, S. R., Gwinn, M. L., Dodson, R. J., Haft, D. H., Hickey, E. K., Peterson, J. D., Nelson, W. C., Ketchum, K. A., et al. (1999) · Nature · doi:10.1038/20601 · Cited by 1,502
The Significance of Pneumococcal Types
Griffith, F. (1928) · Journal of Hygiene · doi:10.1017/s0022172400031879 · Cited by 1,344
Bryson, V., & Vogel, H. J. (1965) · Science · doi:10.1126/science.147.3653.68 · Cited by 1,341
Cited by
Widen, S. A., Bes, I. C., Koreshova, A., Pliota, P., Krogull, D., & Burga, A. (2023) · Science · doi:10.1126/science.ade0705 · Cited by 78
Phosphonate production by marine microbes: exploring new sources and potential function
Acker, M., Hogle, S. L., Berube, P. M., Hackl, T., Coe, A., Stepanauskas, R., Chisholm, S. W., & Repeta, D. J. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2113386119 · Cited by 76
Dmitrijeva, M., Tackmann, J., Matias Rodrigues, J. F., Huerta-Cepas, J., Coelho, L. P., & von Mering, C. (2024) · Nature Ecology & Evolution · doi:10.1038/s41559-024-02357-0 · Cited by 72
Integrated Metabolomic–Genomic Workflows Accelerate Microbial Natural Product Discovery
Avalon, N. E., Murray, A. E., & Baker, B. J. (2022) · Analytical Chemistry · doi:10.1021/acs.analchem.2c02245 · Cited by 47
Godfroid, M., Dagan, T., & Kupczok, A. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy143 · Cited by 37
Metadata
- Authors
- Ravenhall, M., Škunca, N., Lassalle, F., & Dessimoz, C.
- Venue
- PLOS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2015-05-28
- Volume
- 11
- Issue
- 5
- Pages
- e1004095
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- OpenAlex
- W1599377382
- Cited by
- 296
- References
- 104
- FWCI
- 9.26
- Type
- journal article
- Language
- en
- Open access
- gold
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: Inferring Horizontal Gene Transfer. https://app.cochat.ai/papers/10.1371/journal.pcbi.1004095
- The paper
- Ravenhall, M., Škunca, N., Lassalle, F., & Dessimoz, C. (2015). Inferring Horizontal Gene Transfer. PLOS Computational Biology. https://doi.org/10.1371/journal.pcbi.1004095
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.
