Senior Engineer III, Molecules - Throughput Screening & Technology

Our mission is to make biology easier to engineer. Ginkgo is constructing, editing, and redesigning the living world in order to answer the globe's growing challenges in health, energy, food, materials, and more. Our bioengineers make use of an in‑house automated foundry for designing and building new organisms.

Location:

Boston, MA

Team:
Data points – Small Molecule Develop ability & Functional Genomics

Reporting to:
Vice President, Small Molecules

We are hiring a Senior Engineer III, Small Molecules for a key technical leadership role owning Data points' high‑throughput small‑molecule and functional genomics screening capabilities. This person is a player‑coach and the technical heart of the screening and automation workflows that enable ADME, Drug Seq, imaging/viability assays, and related workcell operations across Data points.

• End‑to‑end ownership of screening workflows
  • Own HTS and Drug Seq linked workflows (workcell and walk‑up), including design, execution, QC, and data handoff.
  • Translate program objectives into executable workplans with realistic timelines and risk tradeoffs.
• Assay & workflow development
  • Develop, optimize, and qualify phenotypic and viability assays (e.g., imaging + CTG, Drug Seq primary/secondary).
  • Systematically improve throughput, data quality, and cost via experimental design and automation improvements.
  • Support continued development of new workflows on Ginkgo’s internal automation solutions (RACs).
• Operational ownership & risk management
  • Lead day‑to‑day operations of relevant workcells and walk‑up methods.
  • Drive root‑cause analysis and corrective/preventive actions when runs fail or deviate from expectations.
• Leadership, mentoring, and training
  • Provide technical leadership and day‑to‑day guidance for operators and junior scientists.
  • Contribute to the Data points skill matrix by defining training levels, shadowing plans, and up‑leveling operators on key assays.

• Ph.D. in biology, bioengineering, chemistry, chemical engineering, or related field and 3+ years relevant industry experience; or M.S. with 5+ years; or B.S. with 7+ years in high‑throughput experimental biology.
• Deep hands‑on experience with high‑throughput screening in at least one of:
  • Small‑molecule phenotypic or viability screens, or
  • Functional genomics / perturbation screens (e.g., CRISPR, RNAi, barcoded libraries), or
  • NGS‑linked assays such as Drug Seq or similar.
• Strong experimental design and statistical thinking for multi‑plate datasets (controls, replication, plate effects, hit calling).
• Proven ability to lead without formal authority, coordinating across biologists, automation engineers, and computational scientists.
• Excellent written and verbal communication skills, including clear documentation and stakeholder updates.

• Direct experience with one or more of:
  • Drug Seq or similar NGS‑based transcriptomic screening workflows (RT workcells, library‑prep interfaces, QC).
  • Imaging + CTG (or analogous) paired readouts for viability/phenotypic screening.
  • Complex compound management and cherry‑picking schemas, including randomization and replication logic.
• Experience operating or designing workflows involving:
  • HTS workcells (384‑well or denser formats) and walk‑up methods.
  • NGS prep workflows (RT, library prep, QC, and data integration).
• Prior experience mentoring and managing 1–3 scientists/engineers.
• Comfort working with metadata, LIMS, and analysis pipelines; able to partner closely with data/ML teams.
• Experience supporting multiple programs simultaneously.

• Data points programs experience predictable, high‑quality screening output with clear QC and minimal unplanned failures.
• Critical screening and automation workflows are documented, resilient, and transferable, with multiple trained operators.
• New team members ramp quickly on your workflows due to strong documentation, training plans, and mentorship.
• Recognized as a core technical leader for Data points screening and automation, and a key partner to both execution and strategy across the portfolio.

The base salary range for this role is $160k–$180k. Actual pay within this range will depend on a candidate’s skills, expertise, and experience. We also offer company stock awards, a comprehensive benefits package including medical, dental & vision coverage, health spending accounts, voluntary benefits, leave of absence policies, 401(k) program with employer contribution, 8 paid holidays in addition to a full‑week winter shutdown and unlimited paid time off policy.

It is the policy of Ginkgo Bioworks to provide equal employment opportunities to all employees, employment applicants, and EOE disability/vet.