Senior Computational Genomics Scientist - Pathogen

Overview

At EIT we are seeking an experienced and detail oriented Senior or Non Senior Scientist with recognised expertise in developing computational methods and algorithms for genomic sequencing data analysis. 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 the 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 methods in areas such as genome assembly, binning, and functional characterisation of genomes from metagenomic sequencing data.
• 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.
• Perform rigorous benchmarking using public and internal datasets, and guide experimental validation efforts in collaboration with our wet lab teams.
• Communicate technical concepts to broad audiences and collaborate with interdisciplinary colleagues across the organization.

Requirements

• Three core technical skillsets for this role: bioinformatics algorithm development, machine learning methods, and microbial genomics.
• Strong candidates will have significant experience in at least two of these three areas, and experience in all three is a plus.
• For Senior: At least three years of postdoctoral or industry experience developing computational methods for next generation sequencing data, with the ability to plan and execute research projects independently.
• For Non Senior: Hands on experience developing computational methods for next generation sequencing data.
• PhD or equivalent experience in bioinformatics, computational biology, computer science, mathematics, physics, or another quantitative field.
• Significant experience developing bioinformatics methods for efficient search and storage of DNA sequences, genome assembly, genome annotation, pangenomes, phylogenetics, and/or comparative genomics.
• Solid understanding of data structures, algorithms and statistical methods such as De Bruijn graphs, hashing, Burrows Wheeler transform, Bayesian methods, mixed models, dimensionality reduction, embeddings.
• Experience with innovative machine learning applications in the context of biological data, particularly sequencing data.
• Proficient in the use of command line interfaces, low and high level programming languages (e.g., Python, C, C++, 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 management (e.g., Nextflow) and cloud computing (e.g., OCI, AWS, GCP).
• Contributions to open source bioinformatics software.
• Previous experience mentoring or line managing scientists (for Senior).