Author

Simon R Harris

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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Microbiology· 2 Bioinformatics· 1 Genetics· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Assay:whole-genome sequencing· 4 Organism:bacteria (other)· 3 Approach:statistical model· 3 Approach:experimental assay· 2 Research Focus:gene regulatory network inference· 2 Research Focus:host-pathogen & immune response· 2 Organism:human· 2 Research Focus:chromatin & epigenetic regulation· 1

Frequent Co-Authors

Julian ParkhilliD· 5 shared Carl Robinson· 2 shared Claire ChewapreechaiD· 2 shared Jukka CoranderiD· 2 shared Karen F Steward· 2 shared Nicholas J Croucher· 2 shared Stephen D Bentley· 2 shared Amelia R. L. Charbonneau· 1 shared

Activity by Year

2015-2017 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 24 mutual co-author links

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5 shared papersMicrobiology

Julian ParkhillORCID

Mutual co-authors in cluster

Author profile →

5 papers

Recent·Most cited

Genomic dissection of an Icelandic epidemic of equine respiratory disease

Sigríður Björnsdóttir, Simon R Harris, Vilhjálmur Svansson, Eggert Gunnarsson, Ólöf Sigurðardóttir, Kristina Gammeljord, Karen F Steward, J Richard Newton, Carl Robinson, Amelia R. L. Charbonneau, Julian Parkhill, Matthew T. G. Holden, Andrew S. Waller

The paper investigates an Icelandic equine respiratory disease epidemic, identifying Streptococcus zooepidemicus clone ST209 as the causative agent and tracing its origin and spread.

mBio · Sep 6, 2017Peer-reviewedMicrobiology

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

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

Circlator: automated circularization of genome assemblies using long sequencing reads

Martin Hunt, Nishadi De Silva, Thomas D Otto, Julian Parkhill, Jacqueline A Keane, Simon R Harris

Circlator automates genome circularization using long reads, accurately circularizing 26 of 27 test sequences from bacteria and other organisms.

Genome Biology · Dec 29, 2015Peer-reviewedBioinformatics

Genome specialization and decay of the strangles pathogen, Streptococcus equi, is driven by persistent infection

Simon R Harris, Carl Robinson, Karen F Steward, Katy S Webb, Romain Paillot, Julian Parkhill, Matthew T G Holden, Andrew S Waller

This study investigates the genome evolution of Streptococcus equi, revealing population replacement and genomic decay linked to its host-restricted lifestyle and persistent carriage in horses.

Genome Research · Sep 1, 2015Peer-reviewedMicrobiology