Scientist II, ML - Guided Protein Design Evaluation (AI)

Location: Emeryville, California, United States; hybrid with 2–3 days on-site. Applicants must have ongoing US work authorization that does not require employer sponsorship.

Salary: $147,000–$180,000 USD annually.

Company

hirify.global is an AI biology lab building foundation models for life’s molecules and applying them to medicine, agriculture, and protein design.

What you will do

• Partner with ML and Protein Design leads to scope design evaluation campaigns, including targets, assays, and required readouts.
• Define assay readiness levels, controls, and QC acceptance criteria for internal workflows and CROs.
• Review biochemical, biophysical, and NGS-based data for scientific quality before inclusion in the data warehouse and model training.
• Work with Bioinformatics to define metadata schemas and data ingestion processes that keep datasets consistent, queryable, and traceable.
• Evaluate CRO platforms, assay conditions, and controls for suitability in ML-guided optimization.
• Contribute to campaign charters, benchmarking, post-campaign readouts, and cross-functional technical forums.

Requirements

• PhD in Molecular Biology, Biochemistry, Protein Engineering, Biophysics, Immunology, or a related field, or an MS with equivalent industry experience.
• At least 5 years of hands-on protein engineering and functional characterization experience.
• Direct experience with therapeutic antibody discovery and engineering, including affinity maturation, developability optimization, humanization, or format engineering.
• Strong knowledge of NGS-based screening workflows, including deep mutational scanning, amplicon sequencing, high-throughput activity screens, or antibody display library sequencing.
• Experience defining assay quality standards such as signal-to-noise, reproducibility, and plate-level controls.
• Ability to collaborate across protein chemistry, antibody biology, bioinformatics, and ML-guided design.

Nice to have

• Experience closing Design–Build–Test–Learn loops in protein design, antibody engineering, or directed evolution.
• Experience with phage, yeast, or mammalian display platforms and single-cell B-cell screening.
• Experience overseeing externally run CRO assays and evaluating vendor platforms.
• Comfort with Python, pandas, SQL, LIMS, project-management systems, and experimental data schemas.
• Experience with kinases, nucleases, recombinases, gene editing enzymes, or work at the intersection of protein engineering and ML.

Culture & Benefits

• High-growth work focused on protein design and the intersection of AI and biology.
• Competitive compensation with equity participation.
• 401(k) with a strong employer match.
• Health, dental, and vision insurance.
• Generous PTO, work-life balance, and professional development opportunities.