Senior Computational Microbiologist

About the role

CellX Biosolutions AG, an ETH spin-off developing microbial solutions to degrade persistent environmental pollutants such as PFAS and pesticides, is looking for a Senior Computational Microbiologist to build its in-house computational and molecular microbiology capability from the ground up. The role establishes a mechanistic and metabolic understanding of how bacterial strains and communities degrade PFAS and other chemicals, turns this into a computational pipeline that predicts strain performance and guides the design of synthetic microbial communities, and bridges computation and experiment. It is a senior, high-impact, 100% onsite position starting 01.01.2027.

Key responsibilities

• Supervise and mentor the Laboratory Technician, coordinating wet-lab, cultivation and sequencing workflows (Illumina, Oxford Nanopore, PacBio) and setting quality standards for sample preparation, sequencing and data handover.
• Design, build and maintain an in-house bioinformatics pipeline covering genome assembly, annotation and comparative genomics from short-read and long-read data, integrating AI/ML methods and keeping it reproducible and scalable.
• Establish a metabolic-level understanding of PFAS degradation, identify the genes, enzymes and pathways involved, and build genome-scale metabolic models to predict degradation capability.
• Design and run experiments, including genetic tools and functional assays, to validate predicted genes and pathways, and develop genetic tools for non-model environmental bacteria.
• Build models that learn from strain-level genomic and functional data to prioritize strains, and a framework for assembling synthetic microbial communities by use case.
• Work with R&D to align bioinformatics outputs with experimental and pilot-project needs, monitor strains in pilot and field deployments, contribute technical documentation for regulatory and biosafety approval, and share analyses in internal reports and client deliverables.

Required profile

• PhD in Bioinformatics, Computational Biology, Microbial Genomics or a related field.
• Senior-level experience (typically 5+ years) in microbiology research combining computational and experimental work.
• Strong programming skills (Python and/or R) and experience with workflow managers such as Nextflow or Snakemake.
• Hands-on experience applying AI/ML methods to biological or genomic data.
• Solid understanding of microbial physiology and metabolism, including enzymatic transformation and degradation pathways.
• Experience supervising, mentoring or leading junior team members.
• Excellent English (C1 or higher).

Preferred qualifications

• Direct experience in the PFAS field or with biodegradation of other recalcitrant pollutants.
• Experience designing or modelling synthetic microbial communities.
• Familiarity with long-read sequencing data (Oxford Nanopore, PacBio).
• Experience with regulatory documentation or field trials of applied microorganisms.
• Prior experience in a startup or applied biotech environment.

The company offers a competitive salary and a stock option package. Applications are submitted through the company's online form with a cover letter, CV, academic diplomas and contact details for two references.