The DOI matches its Crossref record; 43 of the 43 references it cites were found in a registry or an index.
The impact of prophages on bacterial chromosomes
Open accessAbstract
Summary: Prophages were automatically localized in se‐quenced bacterial genomes by a simple semantic script leading to the identification of 190 prophages in 115 investigated genomes. The distribution of prophages with respect to presence or absence in a given bacterial species, the location and orientation of the prophages on the replichore was not homogeneous. In bacterial pathogens, prophages are particularly prominent. They frequently encoded virulence genes and were major contributors to the genetic individuality of the strains. However, some commensal and free‐living bacteria also showed prominent prophage contributions to the bacterial genomes. Lysogens containing multiple sequence‐related prophages can experience rearrangements of the bacterial genome across prophages, leading to prophages with new gene constellations. Transfer RNA genes are the preferred chromosomal integration sites, and a number of prophages also carry tRNA genes. Prophage integration into protein coding sequences can lead to either gene disruption or new proteins. The phage repressor, immunity and lysogenic conversion genes are frequently transcribed from the prophage. The expression of the latter is sometimes integrated into control circuits linking prophages, the lysogenic bacterium and its animal host. Prophages are apparently as easily acquired as they are lost from the bacterial chromosome. Fixation of prophage genes seems to be restricted to those with functions that have been co‐opted by the bacterial host.
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
Whole genome sequencing of meticillin-resistant Staphylococcus aureus
Kuroda, M., Ohta, T., Uchiyama, I., Baba, T., Yuzawa, H., Kobayashi, I., Cui, L., Oguchi, A., Aoki, K.-I., Nagai, Y., et al. (2001) · The Lancet · doi:10.1016/s0140-6736(00)04403-2 · Cited by 1,961
Phylogenetic Classification and the Universal Tree
Doolittle, W. F. (1999) · Science · doi:10.1126/science.284.5423.2124 · Cited by 1,888
Comparative Genomics of Listeria Species
Glaser, P., Frangeul, L., Buchrieser, C., Rusniok, C., Amend, A., Baquero, F., Berche, P., Bloecker, H., Brandt, P., Chakraborty, T., et al. (2001) · Science · doi:10.1126/science.1063447 · Cited by 1,504
Genome and virulence determinants of high virulence community-acquired MRSA
Baba, T., Takeuchi, F., Kuroda, M., Yuzawa, H., Aoki, K.-I., Oguchi, A., Nagai, Y., Iwama, N., Asano, K., Naimi, T., et al. (2002) · The Lancet · doi:10.1016/s0140-6736(02)08713-5 · Cited by 1,370
Gene expression in Pseudomonas aeruginosa biofilms
Whiteley, M., Bangera, M. G., Bumgarner, R. E., Parsek, M. R., Teitzel, G. M., Lory, S., & Greenberg, E. P. (2001) · Nature · doi:10.1038/35101627 · Cited by 1,183
Prophages and bacterial genomics: what have we learned so far?
Casjens, S. (2003) · Molecular Microbiology · doi:10.1046/j.1365-2958.2003.03580.x · Cited by 896
Canchaya, C., Proux, C., Fournous, G., Bruttin, A., & Brüssow, H. (2003) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.67.2.238-276.2003 · Cited by 646
Self-citationGenome Sequence of Yersinia pestis KIM
Deng, W., Burland, V., Plunkett, G., Boutin, A., Mayhew, G. F., Liss, P., Perna, N. T., Rose, D. J., Mau, B., Zhou, S., et al. (2002) · Journal of Bacteriology · doi:10.1128/jb.184.16.4601-4611.2002 · Cited by 540
Brüssow, H., & Hendrix, R. W. (2002) · Cell · doi:10.1016/s0092-8674(01)00637-7 · Cited by 507
Self-citationTettelin, H., Masignani, V., Cieslewicz, M. J., Eisen, J. A., Peterson, S., Wessels, M. R., Paulsen, I. T., Nelson, K. E., Margarit, I., Read, T. D., et al. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.182380799 · Cited by 500
Cited by
Lysogeny in nature: mechanisms, impact and ecology of temperate phages
Howard-Varona, C., Hargreaves, K. R., Abedon, S. T., & Sullivan, M. B. (2017) · The ISME Journal · doi:10.1038/ismej.2017.16 · Cited by 894
Viral dark matter and virus–host interactions resolved from publicly available microbial genomes
Roux, S., Hallam, S. J., Woyke, T., & Sullivan, M. B. (2015) · eLife · doi:10.7554/elife.08490 · Cited by 478
Pervasive domestication of defective prophages by bacteria
Bobay, L.-M., Touchon, M., & Rocha, E. P. C. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1405336111 · Cited by 384
Detecting genomic islands using bioinformatics approaches
Langille, M. G. I., Hsiao, W. W. L., & Brinkman, F. S. L. (2010) · Nature Reviews Microbiology · doi:10.1038/nrmicro2350 · Cited by 279
Bikel, S., Valdez-Lara, A., Cornejo-Granados, F., Rico, K., Canizales-Quinteros, S., Soberón, X., Del Pozo-Yauner, L., & Ochoa-Leyva, A. (2015) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2015.06.001 · Cited by 263
Metadata
- Authors
- Canchaya, C., Fournous, G., & Brüssow, H.
- Venue
- Molecular Microbiology
- Publisher
- Wiley
- Published
- 2004-06-04
- Volume
- 53
- Issue
- 1
- Pages
- 9-18
- ISSN
- 0950-382X (ISSN-L)
- 1365-2958
- OpenAlex
- W2135614314
- Cited by
- 373
- References
- 43
- FWCI
- 14.90
- 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: The impact of prophages on bacterial chromosomes. https://app.cochat.ai/papers/10.1111/j.1365-2958.2004.04113.x
- The paper
- Canchaya, C., Fournous, G., & Brüssow, H. (2004). The impact of prophages on bacterial chromosomes. Molecular Microbiology. https://doi.org/10.1111/j.1365-2958.2004.04113.x
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.
