The DOI matches its Crossref record; 60 of the 60 references it cites were found in a registry or an index.
panX: pan-genome analysis and exploration
Open accessAbstract
Horizontal transfer, gene loss, and duplication result in dynamic bacterial genomes shaped by a complex mixture of different modes of evolution. Closely related strains can differ in the presence or absence of many genes, and the total number of distinct genes found in a set of related isolates-the pan-genome-is often many times larger than the genome of individual isolates. We have developed a pipeline that efficiently identifies orthologous gene clusters in the pan-genome. This pipeline is coupled to a powerful yet easy-to-use web-based visualization for interactive exploration of the pan-genome. The visualization consists of connected components that allow rapid filtering and searching of genes and inspection of their evolutionary history. For each gene cluster, panX displays an alignment, a phylogenetic tree, maps mutations within that cluster to the branches of the tree and infers gain and loss of genes on the core-genome phylogeny. PanX is available at pangenome.de. Custom pan-genomes can be visualized either using a web server or by serving panX locally as a browser-based application.
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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
The confluence of big data and evolutionary genome mining for the discovery of natural products
Chevrette, M. G., Gavrilidou, A., Mantri, S., Selem-Mojica, N., Ziemert, N., & Barona-Gómez, F. (2021) · Natural Product Reports · doi:10.1039/d1np00013f · Cited by 66
Evidence for Selection in the Abundant Accessory Gene Content of a Prokaryote Pangenome
Whelan, F. J., Hall, R. J., & McInerney, J. O. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab139 · Cited by 46
Dewar, A. E., Thomas, J. L., Scott, T. W., Wild, G., Griffin, A. S., West, S. A., & Ghoul, M. (2021) · Nature Ecology & Evolution · doi:10.1038/s41559-021-01573-2 · Cited by 44
Godfroid, M., Dagan, T., & Kupczok, A. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy143 · Cited by 37
Metadata
- Authors
- Ding, W., Baumdicker, F., & Neher, R. A.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-10-25
- Volume
- 46
- Issue
- 1
- Pages
- e5-e5
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2949102320
- Cited by
- 300
- References
- 60
- FWCI
- 8.44
- Type
- journal article
- Language
- en
- Open access
- gold
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