Postdoctoral Fellow

About the team/job

The Pathogen Informatics and Modelling group at EMBL-EBI aims to develop innovative approaches to help apply the power of sequencing to controlling pathogen threats. We are interested both in producing methods, and generating biological insights by applying these methods to data from various sources.

Biologically, we are primarily interested in understanding how pathogens transmit, both from the host and pathogen's perspectives. Understanding this process better will help us design and implement more effective interventions (such as next generation vaccines) to interrupt this process.

From a methodological perspective, current approaches are struggling to handle the speed and scale at which sequence data is now being generated. This limits our analysis power, the responsiveness of inference to new data, and ultimately our ambitions for the purposes for which genomes can be used. We also see that not all researchers have the same access to these methods – we aim to lower the barrier to entry and research ways to make methods useful for a range of different purposes (public health, medical microbiology, basic sciences).

Specifically, we work in five overlapping project areas:

• Database-scale analysis of pathogen evolution (including modelling transmssion)
• Methods for real-time genomic epidemiology
• Sequencing within-host diversity
• GPU algorithms for mathematical modelling and bioinformatics
• Democratising bioinformatics

We are growing a diverse, inclusive and collegiate group, and will support members as collaborators with their own independent research interests. 

Your role

This role is a flexible position, primarily to work on modelling projects in the group. Currently these include:

• Linking selection, function and structure in bacterial pathogen genomes.
• Building models which link pathogen evolution (with genomic data) and between-host transmission (with 'classic' epidemiological data).
• Associating genetic and phenotypic variation in bacteria.
• Expanding the range of transmission models in our group, and adding to their software support. We are particularly interested in climate-sensitive pathogens.

To do this, you will use and extend our existing computational methods (implemented in C++ and R, and runnable on GPUs). You will also use modern statistical packages like stan and pyro to make efficient implementations of your models which can be fit to large datasets.

You will have access to a variety of powerful computational resources, and state of the art genomic datasets from research and public health organisations. We will include you as an equal member in ongoing collaborations that you become involved in.

There will also be significant flexibility to design your own projects, where your interests, broadly fit into the group's themes.

You will also be involved in the mentorship of junior group members working on modelling projects. 

You have

• A PhD in a relevant subject (e.g. epidemiology, genomics, statistics).
• Strong experience in at least one programming language such as R, python or Julia.
• Experience designing, implementing, running and fitting mathematical models.
• An interest in applying these techniques to infectious disease transmission.
• Compassion and empathy when working with others, especially from different backgrounds. 

You might also have

• Experience modelling infectious disease transmission.
• Experience using genomic data.
• Experience in a compiled language such as C, C++ or rust.
• Experience using stan, pyro, or a similar statistical inference framework.
• Experience creating software packages.
• Experience maintaining software packages.
• Experience communicating research to a broad range of audiences.
• Experience working collaboratively on code.
• Experience working with other researchers on collaborative modelling projects.
• Your own research interests in infectious diseases.
• Links or collaborations to infectious disease modelling groups. 

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 exploring an independent venture, the EMBL Fellows’ Career Service will provide you with a portfolio of activities and resources to help you.

To find out more please visit - EMBL-fellows-career-service. 

Why join us

Do something meaningful

At EMBL-EBI you can apply your talent and passion to accelerate science and tackle some of humankind's greatest challenges. EMBL-EBI, part of the European Molecular Biology Laboratory, is a worldwide leader in the storage, analysis and dissemination of large biological datasets. We provide the global research community with access to publicly available databases and tools which are crucial for the advancement of healthcare, food security, and biodiversity.

Join a culture of innovation

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.

Enjoy lots of benefits:

• Financial incentives: Monthly family and child allowances, generous stipend reviewed yearly, pension scheme, death benefit, long-term care, accident-at-work and unemployment insurances
• Flexible working arrangements Hybrid working, including 3 days per week spent on campus
• Private medical insurance for you and your immediate family (including all prescriptions and generous dental & optical cover)
• Generous time off: 30 days annual leave per year, in addition to eight bank holidays
• Relocation package 
• 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, 10 days of child sick leave, generous parental leave, holiday clubs on campus and monthly family and child allowances
• Benefits for non-UK residents: Visa exemption and financial support to relocate if you are based overseas. .
• For more details please see our employee benefits page. 

What else you need to know

• Contract duration: 3 year fellowship
• International applicants: We recruit internationally and successful candidates are offered visa exemptions. Read more on our page for international applicants.
• Diversity and inclusion: At EMBL-EBI, we strongly believe that inclusive and diverse teams benefit from higher levels of innovation and creative thought. We encourage applications from women, LGBTQ+ & individuals from all nationalities.
• Job location: Hinxton, near Cambridge, UK. You will be required to relocate if you are based overseas
• EMBL is a signatory of DORA. Find out how we apply DORA principles to our recruitment and performance assessment processes here
• How to apply: To apply please submit a cover letter and a CV through our online system.