Postdoctoral Programme in Evolutionary and Epidemiological Dynamics

Intro

Applications are now open for SEED Postdoctoral Fellowships

The Sanger Epidemiological and Evolutionary Dynamics (SEED) Postdoctoral Programme offers the chance to develop and implement innovative methods for analysis of large-scale genomic datasets to address fundamental problems concerning the evolution, transmission dynamics and control of major infectious diseases.

SEED Fellowships are based within the Parasite and Microbes Programme at the Wellcome Sanger Institute. Each project is co-supervised by an Associate Faculty member and a Sanger Group Leader, and where appropriate there can be more than two supervisors.  By linking projects to both Associate and Core Faculty, we bring together a supervisory team comprising world leaders in genomics, infectious disease epidemiology and mathematical modelling.

This Postdoctoral Programme provides many opportunities for international collaboration.  The Wellcome Genome Campus has a large critical mass of scientific expertise with well-equipped facilities and an active seminar programme.

SEED Projects for 2021

Predefined projects

You may select one or more projects that interest you from those listed below. The three-year fellowships will be awarded after a competitive selection process, with applications being linked to specific projects defined in advance of the application deadline. Please apply via our job site.

Self-proposed projects

You are welcome to propose a project of your own.  This would need to be co-supervised by at least one member of our Associate Faculty members and a Sanger Group Leader in the Sanger Parasites and Microbes Programme.  Please submit a brief outline proposal (approximately 500-1000 words) to the Group Leader and Associate Faculty member who you would like to work with via SEEDfellowship@sanger.ac.uk.  They will need to approve your proposal before you submit the application. Once approved, please apply via our job site.

Potential supervisors for SEED Fellowship:

Dominic Kwiatkowski

Wellcome Sanger Institute

Mara Lawniczak

Wellcome Sanger Institute

Matthew Berriman

Wellcome Sanger Institute

Trevor Lawley

Wellcome Sanger Institute

Nicholas Thomson

Wellcome Sanger Institute

Stephen Bentley

Wellcome Sanger Institute

Jeffrey Barrett

Wellcome Sanger Institute

Caroline Buckee

Harvard TH Chan School of Public Health

Caroline Colijn

Simon Fraser University

Jukka Corander

University of Oslo

Christophe Fraser

University of Oxford Big Data Institute

Marc Lipsitch

Harvard TH Chan School of Public Health

Predefined projects for 2021

Inference for large-scale transmission models

Potential Supervisors: Jukka Corander, Nicholas ThomsonStephen Bentley, Christophe Fraser and Caroline Colijn

Inference for large-scale transmission simulator models to estimate parameters of epidemiological/evolutionary interest, and to test intervention policies in silico under uncertainty.

Read the project description 

Genomic epidemiology for SARS-CoV-2: sooner and later

Potential Supervisors: Caroline Colijn, Christophe Fraser, Marc Lipsitch, Dominic Kwiatkowski, and Jeffrey Barrett  

Project to establish the immediate-term genomic epidemiology for SARS-CoV-2, including its use in real time, and the longer-term integrated modelling and genomic surveillance to detect increased transmission, monitor for emerging potential vaccine escape strains and to monitor for impacts of selection.

Read the project description

Respiratory microbiome analytics

Potential Supervisors: Jukka Corander, Trevor Lawley, and Stephen Bentley

The work will exploit data from large gut microbiome studies (and pilot respiratory microbiome studies) to inform the development of simulations representing equivalent scenarios in the respiratory microbiome that will be used to test potential analytical approaches.

Read the project description

Spatiotemporal Genomics in Anopheles mosquitoes

Potential Supervisors: Caroline Colijn, Dominic Kwiatkowski, and Mara Lawniczak

Examine demographic and evolutionary patterns across the entire genome, although insecticide resistance will be a major focus of our analysis both for its practical importance and because it provides a remarkable opportunity to study the evolution of an animal species under intense selective pressure and in near real time.

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Surveillance of human and environmental drivers of cholera in Bangladesh 

Potential Supervisors: Caroline Buckee and Nicholas Thomson

Build on a successful collaboration with partners in Bangladesh prior to, and during, the COVID-19 epidemic, to develop new approaches to cholera surveillance. We are currently building our capacity to conduct distributed genomic capacity using MinION nanopore sequencing approaches – which have successfully been deployed to analyze SARS-COV-2 genomes this year – to conduct surveillance of Vibrio cholerae and other water-borne pathogens in environmental samples.

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Genomic approaches to the evolutionary dynamics of malaria drug resistance

Potential Supervisors: Caroline Buckee, Caroline Colijn, Christophe Fraser and Dominic Kwiatkowski

Develop analytical approaches to utilise longitudinal genomic data to gain novel insights into the evolutionary, epidemiological and demographic processes that determine the emergence and spread of antimalarial drug resistance.

Read the project description