Imperial College London
Portrait Picture

DrNicholasCroucher

Faculty of Medicine, School of Public Health

Reader in Bacterial Genomics
 
 
 
//

Contact

 

+44 (0)20 7594 3820n.croucher

 
 
//

Location

 

1104Sir Michael Uren HubWhite City Campus

//

Summary

 

Publications

Citation

BibTex format

@article{Lees:2016:10.1038/ncomms12797,
author = {Lees, JA and Vehkala, M and Välimäki, N and Harris, SR and Chewapreecha, C and Croucher, NJ and Marttinen, P and Davies, MR and Steer, AC and Tong, SY and Honkela, A and Parkhill, J and Bentley, SD and Corander, J},
doi = {10.1038/ncomms12797},
journal = {Nature Communications},
title = {Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes},
url = {http://dx.doi.org/10.1038/ncomms12797},
volume = {7},
year = {2016}
}
Download

RIS format (EndNote, RefMan)

TY  - JOUR
AB  - Bacterial 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.
AU  - Lees,JA
AU  - Vehkala,M
AU  - Välimäki,N
AU  - Harris,SR
AU  - Chewapreecha,C
AU  - Croucher,NJ
AU  - Marttinen,P
AU  - Davies,MR
AU  - Steer,AC
AU  - Tong,SY
AU  - Honkela,A
AU  - Parkhill,J
AU  - Bentley,SD
AU  - Corander,J
DO  - 10.1038/ncomms12797
PY  - 2016///
SN  - 2041-1723
TI  - Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes
T2  - Nature Communications
UR  - http://dx.doi.org/10.1038/ncomms12797
UR  - https://www.nature.com/articles/ncomms12797
UR  - http://hdl.handle.net/10044/1/41230
VL  - 7
ER  -
Download