Gally, David

Richardson, Emily Jane

2014-05-02T11:18:06Z

2014-05-02T11:18:06Z

2013-11-29

Salmonella is one of the most important pathogens of mankind and animals alike, causing several billion pounds worth of damage worldwide each year. We have sequenced, annotated and published 4 genomes of Salmonella of well-defined virulence in farm animals. This provides valuable measures of intraserovar diversity and opportunities to formally link genotypes to phenotypes in target animals. Specifically, we have examined pathway detrition and mutagenesis and linked this to host specificity of the serovars. With the advent of next generation sequencing there has been a boom in genomic sequence submission, and an onslaught of -omics data has ensued. Integrating these different data types is complex and there is little available to visualise this data in the context of its genome. We present GeneBook, a web-based tool that synchronously integrates disparate datasets, displaying a fully annotated genome, enriched with publicly available data and the user's private experiments. It is accessed through a user-friendly interface that allows scientists to interrogate genomic features across multiple, heterogeneous, experiments.

http://hdl.handle.net/1842/8793

en

The University of Edinburgh

Richardson EJ, Limaye B, Inamdar H, et al (2011) Genome sequences of Salmonella enterica serovar Typhimurium, Choleraesuis, Dublin, and Gallinarum strains of well-defined virulence in food-producing animals. J Bacteriol. 193(12):3162-3 [Genome announcement, IF: 3.726)

Richardson EJ, Watson M (2012) The automatic annotation of bacterial genomes. Briefings in Bioinformatics. doi: 10.1093/bib/bbs007 [Review, IF: 9.283]

Salmonella

Next-generation sequencing

Bioinformatics

Next-generation bioinformatics analysis of bacterial genomes, with a focus on serovar host specificity and pathogenicity in Salmonella

Thesis or Dissertation

Doctoral

PhD Doctor of Philosophy