Open data visualization and sharing for genomic epidemiology (original) (raw)
CladeI-MPXV genomic diversity from 2018-2024 (DRC)
Eddy et al. 2024.
Mpox in DRC is predominated by clade Ia, exhibiting high genetic diversity. (doi:10.1016/j.cell.2024.10.017)
https://www.cell.com/cell/fulltext/S0092-8674%2824%2901199-1
Tracing the spread of carbapenem-resistant Klebsiella pneumoniae
David S et al. 2019.
Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread. Nature Microbiology 2058-5276. (doi:10.1038/s41564-019-0492-8)
https://www.nature.com/articles/s41564-019-0492-8
Streptococcus pneumoniae PMEN2
Croucher NJ et al. 2014.
Variable recombination dynamics during the emergence, transmission and 'disarming' of a multidrug-resistant pneumococcal clone. BMC Biology 12:49
http://www.ncbi.nlm.nih.gov/pubmed/24957517
West African Ebola epidemic (2013-2016)
Dudas G. et al. 2017.
Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature. 2017 Apr 20;544(7650):309-315. (doi:10.1038/nature22040).
https://pubmed.ncbi.nlm.nih.gov/28405027/
Zika virus in the Americas
Rodrigues Faria, N. et al. 2016.
Zika virus in the Americas: Early epidemiological and genetic findings. Science 352(6283):345-9.
http://science.sciencemag.org/content/352/6283/345.article-info
Y-chromosome Human Phylogeny
Hallast P. et al. 2015.
The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades. Mol Biol Evol 32(3):661
http://www.ncbi.nlm.nih.gov/pubmed/25468874
Vibrio cholerae
Mutreja A. et al. 2011.
Evidence for several waves of global transmission in the seventh cholera pandemic. Nature 477:462
http://www.ncbi.nlm.nih.gov/pubmed/21866102
Staphylococcus aureus ST239
Harris S. et al. 2010.
Evolution of MRSA during hospital transmission and intercontinental spread.
http://www.ncbi.nlm.nih.gov/pubmed/20093474
Yersinia enterocolitica
Reuter S. et al. 2015.
Directional gene flow and ecological separation in Yersinia enterocolitica. M Gen 1(3): doi:10.1099/mgen.0.000030.
http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000030
Salmonella Typhi
Wong V. et al. 2015.
Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intra-continental transmission events. Nature Genetics 47(6):632