Postdoctoral Fellow in Metagenomic Protein Families and Structure-Based Classification at EMBL-EBI (Finn Group), Hinxton

Job Description

EMBL’s European Bioinformatics Institute (EMBL-EBI) is hiring a postdoctoral fellow in metagenomics in Rob Finn’s research group to sort the proteins in the MGnify metagenomics resource into families based on their predicted structures, and to study how those families are spread across taxa and environments. The project is a new joint initiative with Christine Orengo’s team at University College London.

At a glance

• Position: Postdoctoral Fellow (reference JR4408)
• Where: EMBL-EBI, Wellcome Genome Campus, Hinxton, near Cambridge, UK
• Pay: year-1 stipend of £3,535 per month after tax, before pension and insurance contributions
• Contract: 3 years, fixed term
• Supervisor: Rob Finn, Research Group lead
• Apply: 27 September 2026 (23:59 CET)

What the postdoctoral fellow in metagenomics will work on

• Co-develop strategies to classify MGnify’s protein database into structure-based families, including clustering, functional labelling and criteria for choosing which structures to produce
• Add taxonomic information to MGnify from sources within the resource, and extend its biome information with a tool being built in the wider team
• Look for links between biome, taxonomy and the distribution of protein families, and relate them to function
• Use the functional and structural classification to find anti-defence systems encoded by bacteriophages (which counter bacterial defences) and propose how they might act
• Combine method development, including AI-based approaches, with data analysis at very large scale

Why this project matters

According to the advertisement, MGnify holds about 6 billion unique protein sequences, and structure prediction now works at that scale: the AlphaFold database has models for more than 200 million UniProt proteins, and the ESM Atlas more than 600 million models for MGnify proteins. Grouping these by structure is a way to find protein families nobody has described yet and to learn where in nature they occur. The Finn group (two PhD students and two postdocs) works closely with the Microbiome Informatics team that runs MGnify, the AMR portal and Ensembl’s microbial data.

What EMBL is looking for

• A PhD in biological sciences, computational biology, bioinformatics, computer science or a related field, with proven research experience
• A strong background in microbiology and/or metagenomics
• An understanding of protein classification approaches and the tools behind them
• Research experience with large datasets, plus UNIX/Linux and HPC or cloud environments
• Strong Python skills, with well-documented and tested code
• Good communication in English (CEFR C2 or equivalent) and the ability to work both in a team and independently

Nice to have

• Knowledge of bacterial defence or phage anti-defence systems
• Pipelines in Nextflow, Snakemake or similar, and relational databases such as MySQL or PostgreSQL
• Software good practice (Git, testing, code review) and critical use of AI-assisted coding tools
• Interest in mentoring PhD students

Pay and location

The year-1 stipend is £3,535 per month after tax but before pension and insurance contributions, on a three-year fixed-term contract. EMBL lists benefits including family and child allowances, a pension scheme, private medical insurance, 30 days’ annual leave and hybrid working, with relocation support and visa exemptions for international recruits. Fellowships are on site for at least part of each week, and the EMBL Fellows’ Career Service offers career advice.

How to apply

Apply through the official EMBL page. The closing date is 27 September 2026 (23:59 CET). Submit a cover letter and CV through EMBL’s online system; EMBL aims to reply within two weeks of the closing date.

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