Senior Strain Engineer

BioPhase Inc.; San Diego (CA); On-site; USD 140,000 - 190,000; Full time

Job summary

BioPhase Inc. in San Diego, CA seeks a strain engineer to lead an end-to-end metabolic engineering program. You will set strategy, build production strains, and use fermentation data to steer successive engineering rounds toward scalable outcomes.

You will mentor associates, maintain rigorous documentation, and collaborate with fermentation and analytics teams to ensure process-relevant performance.

Qualifications

• PhD or BS/MS with relevant years of industry experience as specified.
• Demonstrated genetic/metabolic engineering in microbes, including non-conventional yeasts.
• Experience with plasmid-based and genomically integrated expression constructs.
• Experience across plate, shake-flask, and bioreactor formats.
• Bioinformatics experience incl. genomics and transcriptomics.
• Hands-on DNA design, assembly, and sequencing.
• CRISPR genome editing experience.
• Strong documentation and cross-functional collaboration.

Responsibilities

• Lead strain and metabolic engineering to overproduce target molecules in microbial hosts.
• Design metabolic engineering strategies including pathway selection, flux and redox balancing.
• Design and build genetic constructs end to end (DNA design, assembly, verification).
• Optimize plasmid-based and genomically integrated expression constructs (promoters, loci, codon optimization).
• Develop genetic toolbox for non-conventional hosts and screening methods.
• Run screening pipelines across plate, shake-flask, and bioreactor formats.
• Analyze pathways and fermentation data to identify bottlenecks and guide iterations.
• Collaborate with fermentation, downstream processing, and analytics teams for scale-up.
• Maintain SOPs, strain records, and transfer packages.
• Mentor scientists and uphold rigorous experimental practices.
• Model biosafety and chemical hygiene standards.

Skills

Metabolic engineering

Synthetic biology

Microbiology

Fermentation data analysis

Problem solving

Documentation

Mentoring

Biosafety

Education

PhD in Metabolic Engineering or related field

BS/MS +5 years industrial strain engineering experience

Tools

CRISPR genome editing

DNA design & assembly

DNA sequencing

Genomics data analysis

Job description

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.

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.

Function:

• 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.
• 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.
• Design and build genetic constructs end to end — DNA design, DNA assembly, and sequence verification.
• 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.
• 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.
• Help build and run screening pipelines across plate, shake-flask, and bioreactor formats, with the measurements needed to rank strains and predict scale performance.
• Analyze metabolic pathways and fermentation data alongside omics datasets (genomics, transcriptomics, proteomics/metabolomics as relevant) to identify bottlenecks and inform the next engineering round.
• 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.
• Maintain scientific documentation — SOPs, strain records, sequence/lineage tracking, technical reports, and technology transfer packages.
• Mentor associates and scientists, setting the bar for experimental rigor and reproducibility.
• Model strong laboratory safety, biosafety, and chemical hygiene practices.

Required:

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

Nice to Have:

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