The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database
Open accessAbstract
The Pseudomonas Genome Database (http://www.pseudomonas.com) is well known for the application of community-based annotation approaches for producing a high-quality Pseudomonas aeruginosa PAO1 genome annotation, and facilitating whole-genome comparative analyses with other Pseudomonas strains. To aid analysis of potentially thousands of complete and draft genome assemblies, this database and analysis platform was upgraded to integrate curated genome annotations and isolate metadata with enhanced tools for larger scale comparative analysis and visualization. Manually curated gene annotations are supplemented with improved computational analyses that help identify putative drug targets and vaccine candidates or assist with evolutionary studies by identifying orthologs, pathogen-associated genes and genomic islands. The database schema has been updated to integrate isolate metadata that will facilitate more powerful analysis of genomes across datasets in the future. We continue to place an emphasis on providing high-quality updates to gene annotations through regular review of the scientific literature and using community-based approaches including a major new Pseudomonas community initiative for the assignment of high-quality gene ontology terms to genes. As we further expand from thousands of genomes, we plan to provide enhancements that will aid data visualization and analysis arising from whole-genome comparative studies including more pan-genome and population-based approaches.
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Shen, M., Zhang, H., Shen, W., Zou, Z., Lu, S., Li, G., He, X., Agnello, M., Shi, W., Hu, F., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky160 · Cited by 76
Towards robust Pseudomonas cell factories to harbour novel biosynthetic pathways
Bitzenhofer, N. L., Kruse, L., Thies, S., Wynands, B., Lechtenberg, T., Rönitz, J., Kozaeva, E., Wirth, N. T., Eberlein, C., Jaeger, K.-E., et al. (2021) · Essays in Biochemistry · doi:10.1042/ebc20200173 · Cited by 75
Evidence for Selection in the Abundant Accessory Gene Content of a Prokaryote Pangenome
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Gerovac, M., Wicke, L., Chihara, K., Schneider, C., Lavigne, R., & Vogel, J. (2021) · mBio · doi:10.1128/mbio.03454-20 · Cited by 40
Kin selection for cooperation in natural bacterial populations
Belcher, L. J., Dewar, A. E., Ghoul, M., & West, S. A. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2119070119 · Cited by 36
Chawla, R., Klupt, S., Patsalo, V., Williamson, J. R., & Racki, L. R. (2022) · mBio · doi:10.1128/mbio.02463-21 · Cited by 23
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Low, K. E., Gheorghita, A. A., Tammam, S. D., Whitfield, G. B., Li, Y. E., Riley, L. M., Weadge, J. T., Caldwell, S. J., Chong, P. A., Walvoort, M. T. C., et al. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2023.105314 · Cited by 11
Sun, Y., Li, J., Huang, J., Li, S., Li, Y., Lu, B., & Deng, X. (2025) · eLife · doi:10.7554/elife.96172.3 · Cited by 6
Coordinated regulation of chemotaxis and resistance to copper by CsoR in Pseudomonas putida
He, M., Tao, Y., Mu, K., Feng, H., Fan, Y., Liu, T., Huang, Q., Xiao, Y., & Chen, W. (2025) · eLife · doi:10.7554/elife.100914 · Cited by 1
Arnoux, J. (2026) · Thèse de doctorat, Université Paris-Saclay / PPanGGOLiN · doi:10.70675/eee354d9zf63dz48ebz9444zd1809f8fb74d
Metadata
- Authors
- Winsor, G. L., Griffiths, E. J., Lo, R., Dhillon, B. K., Shay, J. A., & Brinkman, F. S. L.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-11-17
- Volume
- 44
- Issue
- D1
- Pages
- D646-D653
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2179324586
- Cited by
- 1,050
- References
- 1
- FWCI
- 24.57
- Type
- journal article
- Language
- en
- Open access
- gold
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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