(Senior) Computational Genomics Scientist, Algorithms & AI/ML

Welcome to the Pathogen Program:

Within this ecosystem, the Pathogen Program exemplifies EIT’s dedication to ground-breaking science. It seeks to transform pathogen risk management, detection and response by leveraging Whole Genome Sequencing (WGS)-based metagenomic and pathogen-specific analytical tools. The goal is to power metagenomic devices using long-read sequencing technologies by building a comprehensive database of pathogen information to inform response.

The database will comprise >400,000 paired high-quality long read sequences with comprehensive antimicrobial susceptibility profiles. Enabled by Oracle Inc.’s cloud-computing scale and security, the Pathogen Program is advancing toward certified diagnostic tools for deployment in laboratories, hospitals, and public health organisations worldwide.

Your Role:

As a (Senior) Scientist, you will design, develop, and evaluate novel computational methods for translating metagenomic sequencing data into actionable results in a clinical or public health context.

You will develop algorithms and AI/ML methods that are accurate and robust enough to be integrated into our infectious disease diagnostic product. You will report to the Lead Scientist in Computational Genomics, and you will work closely with bioinformaticians, data scientists, microbiologists, and software engineers to deliver clinically relevant innovation in the microbial genomics space.

Key Responsibilities:

• Design, develop, and evaluate novel computational algorithms in areas such as taxonomic classification and antimicrobial resistance
• Develop ML/AI techniques to address real-world problems in the pathogen genomics space, in collaboration with scientists across EIT
• Validate and benchmark methods using public and internal datasets
• Work with bioinformaticians and software engineers to implement methods in scalable, reproducible, and modular workflows
• Communicate technical work clearly to interdisciplinary teams

Requirements

Requirements

This is a methods development role. Strong candidates will have deep expertise in either bioinformatics algorithm development or ML/AI in a genomics context. Depth in both areas is a plus.

Experience with microbial genomics and metagenomics is preferred but not required. We actively welcome applicants with genomics experience in other contexts who are interested in applying their methods development expertise in the pathogens space.

For Senior: Candidates will have a track record of independently executed research projects, typically with three or more years of experience in industry or as a postdoc.

Essential Knowledge, Skills and Experience:

• PhD or equivalent experience in a quantitative field, such as computational biology, computer science, mathematics, or physics
• Track record of developing computational algorithms or tools in the genomics space. Algorithms: Designed and released a tool in a relevant area, such as sequence search/storage, genome assembly/annotation, pangenome graphs, or phylogenetics. AI/ML: Ownership of model training and evaluation at scale, with a deep understanding of the underlying methods and architectures.
• Strong command of underlying fundamental data structures, algorithms, and statistical methods (e.g. De Bruijn graphs, embeddings, Bayesian methods)
• Solid programming skills (e.g. Python; C, C++, or Rust is a plus) and software development best practices (version control, CI/CD)

Desirable Knowledge, Skills and Experience:

• Experience in microbial genomics
• Experience with long-read sequencing data (ONT)
• Experience with cloud computing, workflow management, and ML ops
• For senior: Experience mentoring or line-managing scientists

Benefits

Our Benefits:

• Travel allowance
• Annual Bonus
• Enhanced holiday pay
• Pension
• Life Assurance
• Income Protection
• Private Medical Insurance
• Hospital Cash Plan
• Therapy Services
• Perk Box
• Electric Car Scheme

Working Together – What It Involves:

• You must have the right to work permanently in the UK with a willingness to travel as necessary. In certain cases, we can consider sponsorship, and this will be assessed on a case-by-case basis.
• You will live in, or within easy commuting distance of, Oxford (or be willing to relocate).
• We have a hybrid working model, 3 days in the office & 2 days from home