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 pathogenesis
Trevor Lawley's team studies the host-pathogen interactions that are linked to disease and transmission in experimental murine models and human populations
*Cell surface signalling laboratory
Gavin Wright's team aims to discover entirely new signalling pathways by identifying novel cell surface receptor-ligand pairs
* Malaria programme: Billker group
Oliver Billker's team elucidates the molecular and cell biology of malaria parasites to understand their development and transmission
* Malaria programme: Kwiatkowski group
Dominic Kwiatkowski's team investigates biological consequences of natural variation in the human and Plasmodium genomes
* Malaria programme: Rayner group
Julian Rayner's team investigates the interactions between Plasmodium falciparum and human red blood cells
* 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
* LookSeq
A web-based application for alignment visualisation, browsing and analysis of genome sequence data
* MalariaGEN
A consortium of researchers across the globe that aims to integrate the latest genomic and epidemiological knowledge and technology to enable greater understanding of malaria
* MapSeg/pf
A database of genome variation in the malaria parasite Plasmodium falciparum in populations around the world
* MetaHit (Metagenomics of the Human Intestinal Tract)
Aims to understand the role of the human intestinal microbiota in health and disease
* MRC Centre for Genomics and Global Health (CGGH)
The CGGH accelerates the translation of large-scale genomic data into meaningful information and effective tools to combat infectious diseases endemic in the developing world
* 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 -