Pathogen genetics

The Pathogen genetics programme uses a combination of genotypic and phenotypic approaches to characterise bacteria, eukaryotic parasites (including the malaria parasite and helminths) and viruses that affect human health.

Key aims are to identify the full extent of genetic variation in disease-causing organisms and to identify variants that influence their spread or interaction with human and veterinary hosts. Complementary studies investigate variation in the host that affects interactions with pathogens.

  • Projects - a list of Faculty-led research projects in Pathogen genetics
  • Collaborations and resources - a list of collaborations and resources in Pathogen genetics in which the Sanger Institute plays a leading role

[David Goulding, Genome Research Limited]


* Bacterial genomics and evolution
Nick Thomson's team investigates how variation in bacterial genomes relates to their hosts/niche, changes over time and geography or in response to therapeutic interventions
* Host-microbiota interactions
Trevor Lawley's team studies the host-pathogen interactions that are linked to disease and transmission in experimental murine models and human populations
* Microbial pathogenesis
Gordon Dougan's team elucidates interactions between the host and the pathogen to understand how we respond to infection
* Parasite genomics
Matt Berriman's team uses sequencing to uncover the genomic basis for differences in the biology of strains or species of parasites
* Pathogen genomics
Julian Parkhill's team uses high-throughput sequencing and phenotyping approaches to study the biology and host-interactions of microbial pathogens
* Virus genomics
Paul Kellam's team explores the diversity of DNA and RNA viruses and host-pathogen interactions using next-generation sequencing

Collaborations and resources

* ACT (Artemis Comparison Tool)
A freely available DNA sequence comparison viewer based on the software for Artemis, the genome viewer and annotation tool
* Alien Hunter
Predicts putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs)
* Artemis
A freely available genome viewer and annotation tool that allows visualisation of sequence features and the results of analyses within the context of the sequence, and also its six-frame translation
* Data download
Provides freely available data for the full range of pathogen genomes sequenced at the Sanger Institute
* GeneDB
Provides the latest sequence data and annotation for pathogens sequenced at the Institute and tools to aid the community in accessing and obtaining the maximum value from these data
* Ensembl Genomes
A browser, based on the Ensembl software infrastructure, which allows users to interrogate the genomes of bacteria, protists, fungi, plants and invertebrate metazoa
* MetaHit (Metagenomics of the Human Intestinal Tract)
Aims to understand the role of the human intestinal microbiota in health and disease
* Proteomic mass spectrometry
We solve questions about the biology underlying health and disease by studying molecular pathways and processes in the cell
*Sanger Institute-EBI Single-Cell Genomics Centre
Explores the DNA, RNA and epigenetic features of single cells in order to better understand normal biology and disease
* Sequencing
The Institute harnesses cutting-edge technologies to generate DNA sequence in order to answer questions about biology and disease
* quick link -