Senior Engineer III, Molecules – Throughput Screening & Technology

Senior Engineer III, Small Molecules – High 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: Datapoints – Small Molecule Develop ability & Functional Genomics
Reporting to: Vice President, Small Molecules

Role Overview

We are hiring a Senior Engineer III, Small Molecules for a key technical leadership role owning Datapoints’ 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 Datapoints.

You will design and run complex, automation‑enabled experiments, harden them into reliable platform workflows, and lead a small group of scientists/engineers (directly and indirectly) to deliver multiple programs in parallel. You will also balance scientific thought leadership (connecting the "why" to the "how/when") with an intense focus on operational excellence.

Key Responsibilities

• 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 trade‑offs.
• 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).
• Lead day‑to‑day operations of relevant workcells and walk‑up methods (e.g., HTS chemical Drug‑Seq workcell, RT workcell, library prep handoff).
• 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 on screening workflows.
• Contribute to the Datapoints skill matrix by defining training levels, shadowing plans, and up‑leveling operators on key assays (e.g., HTS workcell, Drug‑Seq RT, imaging).

Minimum Qualifications

• 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, 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.

Preferred Qualifications

• 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 cherrypicking 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.

What Success Looks Like

• Datapoints programs experience predictable,…