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dc.contributor.authorLees, JA
dc.contributor.authorVehkala, M
dc.contributor.authorValimaki, N
dc.contributor.authorHarris, SR
dc.contributor.authorChewapreecha, C
dc.contributor.authorCroucher, NJ
dc.contributor.authorMarttinen, P
dc.contributor.authorDavies, MR
dc.contributor.authorSteer, AC
dc.contributor.authorTong, SYC
dc.contributor.authorHonkela, A
dc.contributor.authorParkhill, J
dc.contributor.authorBentley, SD
dc.contributor.authorCorander, J
dc.date.accessioned2021-02-05T01:05:47Z
dc.date.available2021-02-05T01:05:47Z
dc.date.issued2016-09-01
dc.identifierpii: ncomms12797
dc.identifier.citationLees, J. A., Vehkala, M., Valimaki, N., Harris, S. R., Chewapreecha, C., Croucher, N. J., Marttinen, P., Davies, M. R., Steer, A. C., Tong, S. Y. C., Honkela, A., Parkhill, J., Bentley, S. D. & Corander, J. (2016). Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes. NATURE COMMUNICATIONS, 7 (1), https://doi.org/10.1038/ncomms12797.
dc.identifier.issn2041-1723
dc.identifier.urihttp://hdl.handle.net/11343/260268
dc.description.abstractBacterial genomes vary extensively in terms of both gene content and gene sequence. This plasticity hampers the use of traditional SNP-based methods for identifying all genetic associations with phenotypic variation. Here we introduce a computationally scalable and widely applicable statistical method (SEER) for the identification of sequence elements that are significantly enriched in a phenotype of interest. SEER is applicable to tens of thousands of genomes by counting variable-length k-mers using a distributed string-mining algorithm. Robust options are provided for association analysis that also correct for the clonal population structure of bacteria. Using large collections of genomes of the major human pathogens Streptococcus pneumoniae and Streptococcus pyogenes, SEER identifies relevant previously characterized resistance determinants for several antibiotics and discovers potential novel factors related to the invasiveness of S. pyogenes. We thus demonstrate that our method can answer important biologically and medically relevant questions.
dc.languageEnglish
dc.publisherNATURE PUBLISHING GROUP
dc.titleSequence element enrichment analysis to determine the genetic basis of bacterial phenotypes
dc.typeJournal Article
dc.identifier.doi10.1038/ncomms12797
melbourne.affiliation.departmentPaediatrics (RCH)
melbourne.affiliation.departmentMicrobiology and Immunology
melbourne.affiliation.facultyMedicine, Dentistry & Health Sciences
melbourne.source.titleNature Communications
melbourne.source.volume7
melbourne.source.issue1
dc.rights.licenseCC BY
melbourne.elementsid1100297
melbourne.contributor.authorDavies, Mark
melbourne.contributor.authorSteer, Andrew
dc.identifier.eissn2041-1723
melbourne.accessrightsOpen Access


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