Academic Experience 

2019-present  Principle Investigator, Shanghai Institute of Immunity and Infection, CAS 

2014-2019   MRC Senior Research Fellow

05-07.2014  Project Professor, University of Tokyo

2010-2014   Senior Scientist, Max Planck Institute for Evolutionary Anthropology, Leipzig

2008-2010   Senior Research Fellow, Department of Microbiology, University College Cork

2003-2007   Wellcome Trust Career Development Fellow, Department of Statistics, University of Oxford

2000-2003   Postdoc, Max Planck Institute for Infection Biology, Berlin

1998-2000   Japan Society for the Promotion of Science Fellow, Department of Mathematical Biology, Kyushu University

Education

BA, Cambridge, Mathematics.
PhD University College London, Genetics

Research highlights during my career include:

The most powerful method to extract ancestry information from DNA sequence data (chromosome painting/fine STRUCTURE, refs 5,7 and 8 below).

The first bacterial genome wide association study (ref 6 below).

The first bacterial genome wide epistasis scan (ref 9).

The first hidden markov model in population genetics (the linkage model of STRUCTURE, ref 1).

The first method to infer bacterial evolution incorporating recombination and mutation (ClonalFrame, ref 4)

The research group currently focuses on four themes:

Helicobacter pylori – life on the edge of chaos.

H. pylori is an important member of the human microbiota for several reasons, including its role in gastric cancer and its well-studied interaction with the human immune system during chronic infection. It also accumulates and reassorts genetic variation at an exceptionally high rate. We are assembling thousands of genome from across the world, including high and low disease incidence regions in China in order to understand its evolution from multiple perspectives and to make the organism a model system for population genetics.

Epistasis and fitness landscapes in natural bacterial populations.

Bacteria face a wide diversity of challenges in the natural environment, many of which are difficult to study in the laboratory. We are developing tools to reveal fitness interactions between loci and the diversity of strategies used by bacteria in the same species.  There is a particular focus on highly recombining species, including Vibrio parahaemolyticus and H. pylori that recombine at high rates, which give the richest epistasis signals.

Comparative genomics of bacteria

For the first time, we have genome date from of 1000s of strains from 100s of different bacterial species. We are building an evolutionarily annotated database in order to understand how evolutionary and ecological factors combine to determine the pattern of diversity in different species.

Community composition dynamics from metagenomics data

The microbiota of the human digestive tract is a diverse, important and increasingly well-studied community. But the rules governing community composition and its evolution over time are far from being understood. Together with other research groups from the Centre for Microbes Development and Health http://www.shanghaipasteur.cas.cn/CMDH, we will investigate how different species interact with each other and their host.