Senior Scientist, AMR Genomics - Pathogen

Ellison Institute of Technology; Oxford; On-site; GBP 65,000 - 90,000; Full time

Benefits offered by this job

Travel Allowance

Bonus

Enhanced holiday pay

Pension

Life Assurance

Income Protection

Private Medical Insurance

Hospital Cash Plan

Therapy Services

Perk Box

Electric Car Scheme

Job summary

The Ellison Institute of Technology is seeking a Senior Scientist in Oxford with expertise in AMR genomics to join the Pathogen Program. This primarily desk-based role provides expert input across AMR tasks and collaborates with cross-functional teams to advance pathogen diagnostics.

You will develop rules for predicting antimicrobial phenotype from genotype, curate AMR gene catalogs, and support ML-driven AMR predictions, while liaising with stakeholders and contributing to data generation.

Qualifications

• PhD in a relevant scientific discipline (e.g. microbiology, molecular microbiology, clinical biology, biochemistry).
• 2+ years of post-doctoral research experience.
• Significant research experience in antimicrobial resistance.
• Experience interpreting genomic data from bacteria.
• Strong data analysis skills with R or equivalent.
• Good communication and meticulous record-keeping.
• Strong IT skills with spreadsheets/word processing/presentations.

Responsibilities

• Provide expert knowledge into AMR research and operational activities.
• Develop expert rules to predict antimicrobial phenotype from genotype.
• Curate catalogues of antimicrobial resistance loci (e.g., AMRFinderPlus).
• Collaborate with teams developing ML models for AMR prediction.
• Review MIC and WGS data to identify anomalies and drive follow-up testing.
• Liaise with internal and external stakeholders and document results.

Skills

AMR genomics

Genomic data analysis

R (data analysis)

Communication

Education

PhD in microbiology

Tools

Confluence

Jira

Lucidchart

Job description

At the Ellison Institute of Technology (EIT), we’re on a mission to translate scientific discovery into real world impact. We bring together visionary scientists, technologists, policy makers, and entrepreneurs to tackle humanity’s greatest challenges in four transformative areas:

• Health, Medical Science & Generative Biology
• Food Security & Sustainable Agriculture
• Climate Change & Managing CO₂
• Artificial Intelligence & Robotics

This is ambitious work - work that demands curiosity, courage, and a relentless drive to make a difference. At EIT, you’ll join a community built on excellence, innovation, tenacity, trust, and collaboration, where bold ideas become real-world breakthroughs. Together, we push boundaries, embrace complexity, and create solutions to scale ideas from lab to society. Explore more at https://www.eit.org

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 >400,00 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:

We are looking for a Senior Scientist with expertise in AMR genomics to join the Pathogen Program. This is a predominantly desk-based role working collaboratively across teams within the Pathogen Program to provide expert input on a range of AMR related tasks and topics. You will curate expert rules for interpretation of AMR genotypic data, provide domain-specific analysis and support for genome sequence and AST data generated by the laboratory, provide expert advice for AST testing and investigate putative novel mechanisms of resistance.

This is an excellent opportunity for an enthusiastic individual with a passion for AMR and strong domain-specific knowledge to contribute to an ambitious program of work aiming to revolutionise pathogen diagnostics.

Key Responsibilities:

• Provide expert knowledge and input into research and operational activities involving antimicrobials and AMR.
• Develop expert rules for prediction of antimicrobial phenotype from genotypic information.
• Curate catalogues of antimicrobial resistance loci, such as AMRFinderPlus output.
• Contribute to design and quality assurance of antimicrobial susceptibility testing.
• Review paired antimicrobial susceptibility and whole genome sequence data to identify possible anomalies or areas for further investigation.
• Review existing MIC data and identify priorities for further testing or re-testing.
• Interpret and curate data on plasmids and mobile genetic elements from genomic and metagenomic datasets.
• Collaborate with colleagues developing Machine Learning models for AMR prediction from genotype.
• Contribute to research to identify and investigate novel antimicrobial resistance mechanisms identified by Machine Learning models.
• Collaborate with laboratory scientists to produce and evaluate datasets for identification of AMR genes and prediction of antimicrobial susceptibility from metagenomic data.
• Liaise with key internal and external stakeholders involved in EIT’s AMR-related activities.
• Opportunity to conduct laboratory research to generate datasets for identification of AMR genes and prediction of antimicrobial susceptibility from metagenomic data.
• Opportunity to contribute to laboratory research investigating putative novel antimicrobial resistance loci.
• Keep up with the latest literature relevant to the field.
• Keep excellent records of work performed.
• Analyse and summarise data, and present data and results at internal or external meetings as required.

Essential Knowledge, Skills, and Experience:

• A PhD degree in a relevant scientific discipline (e.g. microbiology, molecular microbiology clinical biology biochemistry).
• over 2 years of post-doctoral research experience.
• Significant research experience in antimicrobial resistance.
• Significant experience working with and interpreting genomic data from bacteria.
• Strong data analysis skills and familiarity with data analysis packages such as R.
• Good communication skills.
• Excellent record-keeping and attention to detail.
• Strong IT skills and experience using spreadsheets, word processing and presentation software.

Desirable Knowledge, Skills, and Experience:

• Research experience in AMR genomics
• Research experience with plasmids or other mobile genetic elements
• Basic bioinformatic skills
• Microbiology and/or molecular biology laboratory skills
• Familiarity with metagenomic workflows and data
• Experience working with nanopore sequencing
• Previous experience of using Confluence, Jira, Lucidchart or other similar reporting and project management tools

Key Attributes:

• Enthusiastic and proactive individual with a “can-do” attitude.
• Ability to work effectively in a high-growth, fast-paced, dynamic environment.
• Ability to work independently and prioritise tasks.
• Collaborative team-player, able to work well within multi-disciplinary teams.
• Excellent oral and written communication skills, interpersonal skills, and the ability to work with a wide range of people from diverse backgrounds.
• Ability to effectively communicate across scientific domains.
• Good problem-solving skills.
• Highly organised, with excellent time management and prioritisation abilities.

Benefits

• We offer the following salary and benefits:
• Travel Allowance
• Bonus
• Enhanced holiday pay
• Pension
• Life Assurance
• Income Protection
• Private Medical Insurance
• Hospital Cash Plan
• Therapy Services
• Perk Box
• Electrical Car Scheme

Why work for EIT:

At the Ellison Institute, we believe a collaborative, inclusive team is key to our success. We are building a supportive environment where creative risks are encouraged, and everyone feels heard. Valuing emotional intelligence, empathy, respect, and resilience, we encourage people to be curious and to have a shared commitment to excellence. Join us and make an impact!

Terms of Appointment:

• You must have the right to work permanently in the UK with a willingness to travel as necessary.
• You will live in, or within easy commuting distance of, Oxford (or be willing to relocate).
• Hybrid working