Author

Stephen D Bentley

Wellcome Sanger Institute

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Genomics· 3 Genetics· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 4 Assay:whole-genome sequencing· 4 Organism:bacteria (other)· 2 Research Focus:differential expression· 1 Research Focus:gene regulatory network inference· 1 Organism:human· 1 Research Focus:variant calling· 1 Research Focus:variant effect prediction· 1

Frequent Co-Authors

Julian ParkhilliD· 3 shared Nicholas J Croucher· 3 shared Claire ChewapreechaiD· 2 shared Jukka CoranderiD· 2 shared Simon R Harris· 2 shared Alex Alderton· 1 shared Aminu S Jahun· 1 shared Ana S Manso· 1 shared

Activity by Year

2016-2021 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 20 mutual co-author links

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3 shared papersGenomics

Julian ParkhillORCID

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Author profile →

4 papers

Recent·Most cited

Patterns of within-host genetic diversity in SARS-CoV-2

Gerry Tonkin-Hill, Iñigo Martincorena, Roberto Amato, Andrew R J Lawson, Moritz Gerstung, Ian Johnston, David K Jackson, Naomi R Park, Stefanie V Lensing, Michael A Quail, Sónia Gonçalves, Cristina Ariani, Michael Spencer Chapman, William L Hamilton, Luke W Meredith, , Dominic Kwiatkowski

This study analyzes within-host genetic diversity in 1,181 SARS-CoV-2 samples, finding high mutation rates, strand asymmetries, and purifying selection, with implications for transmission chain reconstruction.

eLife · Aug 13, 2021Peer-reviewedGenomics

Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis

Marcin J Skwark, Nicholas J Croucher, Santeri Puranen, Claire Chewapreecha, Maiju Pesonen, Yingying Xu, Paul Turner, Simon R Harris, Julian Parkhill, Stephen D Bentley, Erik Aurell, Jukka Corander

This paper introduces genomeDCA, a statistical method to identify epistatic interactions in Streptococcus pneumoniae genomes, revealing networks of resistance, virulence, and core genes.

PLOS Genetics · Feb 16, 2017Peer-reviewedGenetics

Large scale genomic analysis shows no evidence for repeated pathogen adaptation during the invasive phase of bacterial meningitis in humans

John Lees, Philip H. C. Kremer, Ana S Manso, Nicholas J Croucher, Bart Ferwerda, Mercedes Valls Serón, Marco R Oggioni, Julian Parkhill, Matthjis C Brouwer, Arie van der Ende, Diederik van de Beek, Stephen D Bentley

This study analyzes genomic variation in meningitis pathogens to determine if adaptation occurs during the invasive phase, finding no evidence of such adaptation for four species.

bioRxiv · Aug 17, 2016Genomics

Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes

John A Lees, Minna Vehkala, Niko Välimäki, Simon R Harris, Claire Chewapreecha, Nicholas J Croucher, Pekka Marttinen, Mark R Davies, Andrew C Steer, Stephen Y C Tong, Antti Honkela, Julian Parkhill, Stephen D Bentley, Jukka Corander

This paper introduces SEER, a statistical method to identify sequence elements associated with bacterial phenotypes, demonstrating its application in discovering antibiotic resistance and invasiveness factors in Streptococcus species.

bioRxiv · Mar 2, 2016Genomics