Collaborations

Kat Holt
Monash University, Australia

The group of Kat Holt has built its unique expertise studying the evolutionary epidemiology of ESKAPE pathogens by using latest developments in sequencing technology and bioinformatics, particularly of the Oxford Nanopore Sequencing. We have been collaborating by sharing data and expertise on the genetics of polysaccharide capsules as well as methods to analyse huge collections of bacterial genomes.

Mark Enright
Manchester Metropolitan University, UK

Mark’s group in Manchester are using experimental microbiology and genomics to understand bacteria-phage interactions. Our group is providing bioinformatic expertise to make sense of Mark’s exciting experiments, and sketch next directions for theoretical and experimental work.

Nick R. Thomson
Wellcome Trust Sanger Institute, UK

Nick and his colleagues at the Sanger have a unique ability to map observations from laboratory experiments to processes governing bacterial populations world-wide, and form hypotheses about the key drivers of bacterial evolution. Our group is currently planning to generate and share important datasets to learn about the epidemiology of bacteriophages in the context of antimicrobial resistance in bacteria.

Christophe Fraser
University of Oxford, UK

The group of Christophe Fraser has exceptional track record in using the evolutionary theory to explain key phenomena in pathogen epidemiology, particularly in the fields of HIV research and bacterial diseases. Rafal’s previous interactions with Christophe’s group have resulted in important work on the significance of recombination to bacterial evolution, and in the future we plan to continue the interactions between our group and Christophe’s group at the Big Data Institute in Oxford.

Pekka Marttinen
Aalto University, Finland

Pekka is a statistician who has been very successful applying novel statistical approaches to the field of bacterial genomics. We will be liaising with Pekka’s group to apply machine learning approaches, like deep learning, to deepening our understanding of the microbial world.

Aaron Darling
University of Technology Sydney, Australia

The Darling group at the UTS Sydney has a broad expertise in computational genomics and has previously worked on novel statistical approaches to track bacterial evolution in metagenomes. They are also working on developing new DNA sequencing approaches.

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