Bioinformatician

Mission

NIUM is seeking a skilled and proactive Bioinformatician to develop and manage robust data pipelines for metagenomic analysis of samples processed through our IMAT platform. This role will also contribute to the IngredientAI project, supporting the biological validation of new cartridge designs through standardised and scalable bioinformatics workflows. The ideal candidate combines strong scientific curiosity with hands-on coding ability, experience in high-performance and cloud computing environments, and a passion for microbiome data science.

Responsibilities

    • Contribute to troubleshooting and provide technical feedback to inform the design refinement of IMAT. 
    • Design, implement, and maintain reproducible bioinformatics pipelines for preprocessing, quality control, taxonomic and functional profiling of metagenomic datasets.
    • Analyze and interpret microbiome sequencing data generated from experiments, generating insights that support R&D and product development.
    • Work closely with wet lab and engineering teams to ensure experimental data flows smoothly into computational analysis.
    • Contribute to the data analysis component of cartridge validation trials in collaboration with IngredientAI consortium members.
    • Standardize comparative analysis of microbial community structure and function across different cartridge versions and experimental conditions.
    • Support reporting and visualization of results for both internal stakeholders and grant deliverables.
    • Leverage AWS cloud services and HPC clusters to manage large datasets and run computationally intensive pipelines.
    • Implement and maintain data versioning, metadata tracking, and code documentation in line with FAIR principles.
    • Ensure scalability, reproducibility, and automation of data workflows using tools such as Snakemake, Nextflow, or equivalent.

    Required qualifications

      • Master’s or PhD in Bioinformatics, Computational Biology, or related field.
      • Minimal experience in metagenomics (shotgun sequencing or 16S), with demonstrated use of tools like QIIME2, HUMAnN, MetaPhlAn, Kraken2, etc.
      • Experience in Python and/or R for statistical analysis and visualization.
      • Experience with workflow managers (Snakemake, Nextflow, CWL) and job scheduling in HPC environments.
      • Good understanding of AWS services (e.g., EC2, S3, Batch) for data processing and storage is a plus.

      Desired experience

        • Git-based version control and collaborative development practices.
        • Comfortable navigating multidisciplinary projects with flexibility and a proactive mindset. Familiarity with microbiome research in gut health, nutrition, or host-microbiome interaction contexts.
        • Prior contributions to open-source bioinformatics tools or repositories.
        • Fluency in English.
        • Experience working on EU-funded projects or collaborative research environments.
        • Comfort working across disciplines with biologists, engineers, and clinical partners.

        Location

        Porto/Braga, Portugal