(Senior) Computational Genomics Scientist - Pathogen

(Senior) Computational Genomics Scientist - Pathogen

EIT - Ellison Institute of Technology

Oxford, United Kingdom

We are seeking a highly skilled and collaborative (Senior or Non Senior) Scientist with recognised expertise in developing computational methods and algorithms for genomic sequencing data analysis, particularly in the context of genome assembly. This is an exciting opportunity to develop novel computational approaches for microbial data that will become part of our diagnostic products and thus help shape the future of infectious disease diagnostics. Reporting to the Lead Scientist in Computational Genomics, you will work closely with computational scientists, bioinformaticians, software engineers, and our database and data platform teams to deliver scientifically rigorous, scalable, and clinically relevant innovation in the microbial genomics space.

Key Responsibilities

• Design, develop and evaluate novel computational approaches in areas such as genome assembly, binning, and functional characterisation of genomes from metagenomic sequencing;
• Collaborate with scientists across EIT to apply the latest developments in AI/ML to real-world challenges in the pathogen space;
• Work with bioinformaticians and software engineers to implement methods in scalable, reproducible, and modular workflows;
• Communicate technical concepts to broad audiences and collaborate with interdisciplinary colleagues across the organization;
• Perform rigorous benchmarking using public and internal datasets, and guide experimental validation efforts in collaboration with our wet-lab teams.

Requirements

Essential Knowledge, Skills and Experience:

• PhD or equivalent experience in bioinformatics, computational biology, computer science, or a related field;
• Senior: At least 3 years of postdoctoral or industry experience developing computational methods for next-generation sequencing data Non-Senior: Hands-on experience developing computational methods for next-generation sequencing data;
• Significant experience with methods for efficient storage, search and assembly of DNA sequences (e.g. hashing, Burrows-Wheeler transform, De Bruijn graphs, embeddings and tokenization) and pangenomes;
• Proficient in the use of command-line interfaces, low and high-level programming languages (e.g. Python, Rust) and modern software development techniques (version control, CI/CD);
• Track record of scientific output and engagement with the computational genomics community.

Desirable Knowledge, Skills and Experience:

• Experience working with microbial genomes and shotgun metagenomics data;
• Experience working with long-read sequencing data (ONT);
• Experience with bioinformatics workflow frameworks (e.g. Nextflow) and cloud compute environments (e.g. OCI, AWS, GCP);
• Familiarity with Bayesian methods, machine learning, or causal inference in the context of biological data;
• Contributions to open-source bioinformatics software;
• Previous experience mentoring or line-managing scientists (For Senior).

Key Attributes:

• Strategic thinker with the ability to translate scientific insights into practical solutions;
• Effective communicator and enthusiastic knowledge sharer across disciplines;
• Rigorous and detail-oriented with a commitment to reproducibility and benchmarking;
• Comfortable in a fast-paced, interdisciplinary environment and able to adapt to evolving priorities;
• Collaborative ethos with the ability to work across teams and domains.