Wellcome Sanger Institute

Genomics of Pneumonia, Meningitis and Neonatal Sepsis

Parasites and Microbes

We study variation in the genomes of major bacterial pathogens to understand their evolution in the context of disease and aymptomatic carriage with a view to informing strategies for treatment and prevention.

The Bentley Group website

Our people

Group lead

Professor Stephen D. Bentley

Principal Staff Scientist and Team Leader

Using bacterial pathogen genomics to understand patterns of colonisation, transmission and genetic associations with disease. Focus on pathogens associated with respiratory infection and particularly those which have a major disease burden in resource-poor settings.

Core team

Dr Dorota Jamrozy

Principal Bioinformatician

Dr Stephanie Wai-U Lo

Translational Science Lead / Senior Scientific Manager

Neil MacAlasdair

PhD Student

Previous core team members

Dr Christine J Boinett

Principal Bioinformatician

Dr Claire Chewapreecha

International Fellow, MORU Mahidol Oxford Tropical Medicine Research Unit

John Lees

Former PhD Student at the Sanger Institute

The following were also members of this team:

Alison Maguire
Jyothish Bhai
Ebrima Bojang
Feyruz Yalcin
Nicholas Croucher
Gareth Peat

Associated research

Collaborations

Collaboration

Global Pneumococcal Sequencing Project

A worldwide genomic survey of the impact of vaccination on the pathogen population

Collaboration

JUNO: A global genomic survey of Streptococcus agalactiae

JUNO project is a global genomic surveillance study of Streptococcus agalactiae with the central aim of informing disease intervention strategies.

Tools & software

Tool

FastBAPS

A fast solution to cluster genetic sequences

Tool

Pairsnp

Obtians pairwise SNP distance matrices from multiple sequence alignments

Tool

Panaroo

A Bacterial Pangenome Analysis Pipeline

Tool

PopPUNK

A tool for clustering genomes

Tool

SEER and PYSEER

Seuqence enrichment analyis used in Genome Wide Association studies (GWAS)

Tool

Gubbins

Genealogies Unbiased By recomBinations In Nucleotide Sequences

Related groups

Science group

Parasites and Microbes Informatics

Parasites and Microbes

The Parasites and Microbes Informatics team develop and maintain software applications and systems to support the research activities of the Parasites ...

Science group

Thomson Group

Bacterial genomics and evolution

The bacterial genomics and evolution team focuses primarily on using whole-genome sequencing approaches to study the patterns and drivers for historical ...

Science group

Aanensen Group

Genomic Epidemiology of Infectious Diseases

Our mission is to inform control strategies and interventions on a local, national and international scale. Our group consists of a ...

Wellcome Sanger Institute

Programmes and Facilities

Programme

Parasites and Microbes

We use genomics to study important problems in infectious disease, with a strong desire to develop and refine tools for disease ...

Partners

We work with the following groups

External

Genomics of Pneumonia, Meningitis and Neonatal Sepsis

Our people

Group lead

Professor Stephen D. Bentley

Core team

Dr Dorota Jamrozy

Dr Stephanie Wai-U Lo

Neil MacAlasdair

Previous core team members

Dr Christine J Boinett

Dr Claire Chewapreecha

John Lees

Associated research

Global Pneumococcal Sequencing Project

JUNO: A global genomic survey of Streptococcus agalactiae

FastBAPS

Pairsnp

Panaroo

PopPUNK

SEER and PYSEER

Gubbins

Related groups

Parasites and Microbes Informatics

Thomson Group

Aanensen Group

Programmes and Facilities

Parasites and Microbes

Partners

The Bill and Melinda Gates Foundation

Wellcome Trust

Jukka Corrander