Senior Strain Engineer

Job Description

Senior Strain Engineer

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Status: Contract

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The Role

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This role is for a strain engineer ready to lead a metabolic engineering program end to end — not just execute one. You'll set the technical strategy, build and iterate on production strains, and use fermentation data to guide the next round of engineering, all in service of manufacturing target molecules in strategic microbial hosts.

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This is a fit for someone who wants real ownership: comfortable making technical calls in an environment where not everything is predefined, and ready to take responsibility for a strain program's outcomes. Candidates may come from academic, industrial, or startup backgrounds, but should be looking for a role where their judgment drives direction and their work has a clear line to scale-up and deployment.

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Function:

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• Lead the strain and metabolic engineering effort to overproduce target molecules in strategic microbial hosts — setting strategy, choosing engineering approaches, and delivering strains that perform under process-relevant conditions.
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• Design metabolic engineering strategies, including pathway selection and reconstruction, flux redistribution, precursor and cofactor supply, redox and energy balancing, transporter engineering, and elimination of byproduct/degradation routes.
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• Design and build genetic constructs end to end — DNA design, DNA assembly, and sequence verification.
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• Optimize plasmid-based and genomically integrated expression constructs: plasmid type and copy number, integration locus, promoter/terminator design, codon optimization, and multi-gene pathway tuning.
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• Build out the genetic toolbox in non-conventional hosts where one doesn't yet exist — selection markers, characterized promoters/terminators, integration sites, and editing/recombineering methods.
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• Help build and run screening pipelines across plate, shake-flask, and bioreactor formats, with the measurements needed to rank strains and predict scale performance.
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• Analyze metabolic pathways and fermentation data alongside omics datasets (genomics, transcriptomics, proteomics/metabolomics as relevant) to identify bottlenecks and inform the next engineering round.
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• Partner closely with fermentation engineering on strain characterization, process fit, and scale-up, and with downstream processing/analytical teams on broth quality and product spec.
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• Maintain scientific documentation — SOPs, strain records, sequence/lineage tracking, technical reports, and technology transfer packages.
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• Mentor associates and scientists, setting the bar for experimental rigor and reproducibility.
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• Model strong laboratory safety, biosafety, and chemical hygiene practices.
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Required:

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• Ph.D. in Metabolic Engineering, Synthetic Biology, Microbiology, Molecular Biology, Biochemical Engineering, or a related field with 3+ years of industrial microbial strain engineering experience — or a B.S./M.S. in a related field with 5+ years of that experience.
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• Demonstrated genetic and metabolic engineering of microbes — for example, non-conventional yeasts (Yarrowia lipolytica, Kluyveromyces species, Hansenula polymorpha) — for bulk or specialty chemical production.
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• Experience optimizing plasmid-based and genomically integrated expression constructs: plasmid type, integration locus, promoter design, codon optimization, and terminator design.
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• Experience testing microbial strain performance across plate, shake-flask, and bioreactor formats with a range of measurements.
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• Experience analyzing and designing metabolic pathways, and interpreting fermentation data to guide strain design.
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• Experience with bioinformatics analysis, including genomics and transcriptomics (genome assembly/annotation, variant calling, RNA-seq differential expression).
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• Hands-on experience with DNA design, DNA assembly, and DNA sequencing.
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• Hands-on experience designing and using CRISPR-based genome editing.
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• Ability to troubleshoot complex biological problems and translate findings into actionable design decisions.
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• Strong documentation, communication, and cross-functional collaboration skills.
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Nice to Have:

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• Working knowledge of scripting for data analysis (Python, R) and statistical design of experiments.
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• Experience with metabolic flux analysis, genome-scale models, or 13C labeling studies.
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• Experience with high-throughput screening, laboratory automation, or adaptive laboratory evolution.
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