Postdoctoral Fellow - Pandemic-scale Phylodynamics

European Molecular Biology Laboratory; Saffron Walden; On-site; GBP 40,000 - 60,000; Full time

Job summary

A leading research institute in the UK seeks a postdoctoral candidate to develop phylodynamic methods for pathogen analysis. Applicants should possess a PhD in a relevant field and strong computational skills, especially in C++ and Python. The successful candidate will prepare genomic datasets and perform analyses as part of a collaborative team. Benefits include generous stipends reviewed annually, supportive career services, and flexible working conditions in a beautiful environment.

Benefits

Generous stipend reviewed yearly

Flexible working arrangements

Private medical insurance

30 days annual leave

On-site gym and library

Visa and relocation support

Qualifications

• PhD degree, preferably in computational or epidemiological subject.
• Strong programming skills in C++ and/or Python.
• Experience in software development in Unix environments.

Responsibilities

• Contribute to develop phylodynamic methods for pathogen evolutionary history.
• Develop massive-scale simulations for testing inference methods.
• Prepare real genomic epidemiological datasets.

Skills

Programming in C++

Programming in Python

Strong computational skills

Proficient in written and spoken English

Ability to work independently and in a team

Education

PhD degree in a relevant subject

Tools

Unix-based environments

Job description

The following is a project led by Nicola De Maio and Nick Goldman at EMBL-EBI. Nicola, who joined EMBL-EBI in 2018 after a postdoctoral fellowship at the University of Oxford, focuses on phylogenetic, phylogeographic, phylodynamic, and population genetic methods. Nick Goldman joined EMBL-EBI as Group Leader in 2002 after post‑doctoral research at the Medical Research Council in London and the University of Cambridge. He has extensive experience developing genetic sequence analysis methods to study evolution and associated algorithms such as multiple sequence alignment, and has recently worked on computational methods to improve the efficiency of next‑generation sequencing technologies. This project is part of a collaboration involving postdoctoral fellow Samuel Martin at EMBL-EBI; PIs Anna Zhukova, Frédéric Lemoine and Sebastian Duchene at Institut Pasteur; and Prof Alice McHardy at the Helmholtz Centre for Infection Research.

Project Overview

The aim of the project is to: 1) develop and benchmark massive-scale phylodynamic methods for inferring, in unprecedented detail, the evolutionary history of a pathogen, the timing of epidemiological events, transmission within and between countries, and the emergence of new pathogen variants; 2) develop methods for massive-scale simulations of pathogen transmission and evolution, to be used for testing, benchmarking, and training phylodynamic inference methods; 3) prepare large-scale real genomic epidemiological datasets and perform their phylodynamic analysis.

Your role

The candidate will contribute to some or all of these tasks, applying mathematical modelling, algorithmic development, programming, and data collection and preparation.

Qualifications

Required qualifications

• (or will soon have) A PhD degree, preferably in a computational, statistical, mathematical, bioinformatic or epidemiological subject.
• Strong computational skills, in particular programming in C++ and/or Python, and experience in software development and Unix-based environments.
• Proficient communication skills in both written and spoken English.
• Demonstrated ability to work both independently and collaboratively with other group members and external collaborators.

Optional qualifications

• Experience of computational genome sequence analysis, especially in phylogenetics or phylodynamics.
• Experience in probabilistic modelling and statistical inference.
• Experience in the development of scalable computational methods and using an HPC.
• Experience developing machine learning methods.
• Experience of computer code optimisation.
• Experience in programming in Java.
• Experience in genomic epidemiology or microbial genomics.

Salary and contract

For individuals who have obtained their PhD, the Year 1 Stipend rate is £3,383.52 per month after tax but excluding pension and insurance contributions. For individuals who are yet to be awarded their PhD, an initial predoctoral rate of £2,436.14 per month is applied after tax but excluding pension and insurance contributions. The contract will start as soon as possible (ideally early in 2026) and conclude at the end of October 2027, for a maximum duration of 22 months.

Professional development support

The EMBL Fellows' Career Service provides support and guidance to predoctoral and postdoctoral fellows across all six EMBL's sites. Working with a dedicated Careers Advisor, this invaluable service will help you to take informed decisions about your career planning both in the short and longer term. Whether your main interest is pursuing a career path in academia, exploring opportunities in industry or an independent venture, the EMBL Fellows' Career Service will provide you with a portfolio of activities and resources to help you.

Why join us

We are located on the Wellcome Genome Campus, alongside other prominent research and biotech organisations, and surrounded by beautiful Cambridgeshire countryside. This is a highly collaborative and inclusive community where our employees enjoy a relaxed atmosphere. We are committed to ensuring our employees feel valued, supported and empowered to reach their professional potential.

Benefits

• Financial incentives: Monthly family and child allowances, generous stipend reviewed yearly, pension scheme, death benefit and unemployment insurances
• Flexible working arrangements including hybrid working patterns
• Private medical insurance for you and your immediate family
• Generous time off: 30 days annual leave per year in addition to public holidays
• Campus life: Free shuttle bus to and from work, on-site library, subsidised on-site gym and cafeteria, casual dress code, extensive sports and social club activities (on campus and remotely)
• Family benefits: On-site nursery (Heidelberg & Hinxton), 10 days of child sick leave, paid maternity & parental leave, holiday clubs on campus and monthly family and child allowances
• Benefits for non-residents: Visa and financial support to relocate if you're overseas

Additional information

• International applicants: We recruit internationally and successful candidates are offered visa exemptions. Read more on our page for international applicants.
• Diversity & Inclusion: At EMBL-EBI, we believe that diverse teams drive innovation and scientific excellence. We encourage applications from candidates of all genders, identities, nationalities, and/or any other diverse backgrounds.
• Job location: All our fellowships are based on-site (for at least part of each week). If you are living overseas, you will receive a generous relocation package to support you.
• EMBL is a signatory of DORA. Find out how we apply DORA principles to our recruitment and performance assessment processes here.
• Watch this video to find out what it's like to be a Postdoc at EMBL-EBI.