Bioinformatics Software Engineer

Melio Healthcare Ltd.; Greater London; On-site; GBP 90,000 - 120,000; Full time

Benefits offered by this job

Competitive salary + bonus

Pension and health insurance

Life assurance and income protection

Career development opportunities

Job summary

IMU Biosciences is seeking a Bioinformatics Software Engineer to drive flow cytometry data engineering, annotation pipelines, and model registry operations for a clinical biomarker discovery platform. You will ensure reproducible, production-grade features and compliant MedDev ML workflows.

In this role you will manage automated cell-type annotation, enforce data integrity, and oversee model artifact registries while leading peer code reviews with ML engineers and biostatisticians.

Qualifications

• Master’s or Ph.D. in Bioinformatics, Statistics, Computational Biology, Computer Science, Bioengineering, or related quantitative field.
• 3+ years of professional experience handling flow cytometry high-throughput data in regulated, academic, or biotech settings.

Responsibilities

• Flow Cytometry Data Engineering & Annotation Pipelines: Execute automated cell annotation workflows on large-scale cytometry datasets; generate cell membership files, cell subset ratio tables, and automated outlier quality-control (QC) reports. Apply locked automated gating ensembles across cross-validation and evaluation partitions, tracking and recording per-patient gating exposure metrics. Establish and lock baseline models and numerical stability criteria for flow cytometry feature extraction pipelines.
• Model Registry & Governance: Manage the formal model lifecycle registry—versioning, freezing, and locking gating ensembles and candidate predictive models in adherence with industry best practices and MedDev ML regulatory frameworks. Refit shortlisted machine learning models on expanded cohorts and execute final model freezing prior to blinded clinical evaluations. Ensure full reproducibility by committing versioned code, pinning environment specifications (Conda/Docker), and logging all random seeds and model hyperparameters.
• Code Quality, Review & Data Integrity: Serve as a primary code reviewer across the computational pipeline, enforcing strict data leakage controls, data integrity checks, and modular coding standards. Participate in Independent Method Reviews (IMRs), traceability audits, and regulatory compliance verification under industry best practices and MedDev ML guidelines while interfacing closely with Machine Learning Engineers, Bio-statisticians, and Clinical Scientists.

Skills

Python

Git

CI/CD

Nextflow

Docker

ML artifact tracking

Flow cytometry

Cross-validation

Education

Master’s or Ph.D. in Bioinformatics or related field

Tools

NumPy

Pandas

SciPy

scikit-learn

PyTorch

Job description

About IMU Biosciences

IMU Biosciences has developed proprietary platform technologies that generate and translate vast system-level immune data into actionable insights and tools to drive the development of precision medicines across a variety of diseases. IMU leverages advanced immune profiling with proprietary AI and machine learning analytics to uncover novel clinical immune signatures. IMU continues to establish partnerships with leading pharma and biotech companies to advance disease diagnosis, optimise product selection, and improve patient stratification and monitoring - while also building its own pipeline of innovative products.

About The Role

We are seeking a Bioinformatics Software Engineer to drive the flow cytometry data engineering infrastructure, annotation pipelines, model registry operations, and code governance for an advanced clinical biomarker discovery platform operating under machine learning industry best practices and Medical Device Machine Learning (MedDev ML) standards.

In this role, you will be responsible for translating high-dimensional flow cytometry data into reproducible, production-grade features compliant with industry best practices and MedDev ML framework requirements. Your key deliverables will include frozen, reproducible feature pipelines and locked model registry artifacts. You will oversee automated cell-type annotation, manage model artifact registries, enforce data integrity, trace compliance, and handle leakage controls across machine learning partitions while leading peer code reviews.

Core Responsibilities

• Flow Cytometry Data Engineering & Annotation Pipelines: Execute automated cell annotation workflows on large-scale cytometry datasets; generate cell membership files, cell subset ratio tables, and automated outlier quality-control (QC) reports. Apply locked automated gating ensembles across cross-validation and evaluation partitions, tracking and recording per-patient gating exposure metrics. Establish and lock baseline models and numerical stability criteria for flow cytometry feature extraction pipelines.

• Model Registry & Governance: Manage the formal model lifecycle registry—versioning, freezing, and locking gating ensembles and candidate predictive models in adherence with industry best practices and MedDev ML regulatory frameworks. Refit shortlisted machine learning models on expanded cohorts and execute final model freezing prior to blinded clinical evaluations. Ensure full reproducibility by committing versioned code, pinning environment specifications (Conda/Docker), and logging all random seeds and model hyperparameters.

• Code Quality, Review & Data Integrity: Serve as a primary code reviewer across the computational pipeline, enforcing strict data leakage controls, data integrity checks, and modular coding standards. Participate in Independent Method Reviews (IMRs), traceability audits, and regulatory compliance verification under industry best practices and MedDev ML guidelines while interfacing closely with Machine Learning Engineers, Bio-statisticians, and Clinical Scientists.

Team and Ways of Working

Embedded in a multidisciplinary team of 4 (ML Engineers, Biostatisticians, and Clinical Scientists) reporting directly to the Lead Data Scientist.

Qualification Requirements

• Master’s or Ph.D. in Bioinformatics, Statistics, Computational Biology, Computer Science, Bioengineering, or a related quantitative field.
• 3+ years of professional experience handling flow cytometry high-throughput data in regulated, academic, or biotech settings.

Technical Must-Haves (Essential Skills)

• Programming Mastery: Fluent in Python (NumPy, Pandas, SciPy, scikit-learn, PyTorch).
• Software Engineering & Version Control: Proven experience with software engineering best practices: Git version control, CI/CD, workflow managers (Nextflow), environment pinning (Docker), and ML artifact tracking.
• Cytometry Knowledge: Familiarity with flow cytometry feature generation and batch-effect harmonisation.
• Familiarity with cross-validation leakage traps in high-dimensional flow cytometry predictive modeling.

Nice-to-Haves (Desirable Skills)

• Experience working with clinical trial datasets, industry best practices, and MedDev ML regulations.
• Experience in transplant immunology, oncology, or hematologic malignancies.

Key Competencies

Strong collaboration and communication skills, including documenting computational methods for regulatory audits and effectively communicating technical workflows to clinical scientists and cross-functional teams.

Why Join Us?

• Competitive salary and company bonus scheme
• Pension, health insurance, life assurance, and income protection
• Fast-paced, collaborative startup culture
• Strong opportunities for career development and progression