Ginkgo Bioworks

Senior Engineer III, Small Molecules – High Throughput Screening & Technology

Boston, Massachusetts · Senior

Sponsorship not specified$160k-$180kDetected 69 days ago

Machine LearningBioinformaticsCRISPRNGSExperimental DesignLeadershipCommunicationMentoring

About the role

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 also balance scientific thought leadership (connecting the "why" to the "how/when") with an intense focus on operational excellence.

Own HTS and Drug‑Seq‑linked workflows (workcell and walk‑up), including design, execution, QC, and data handoff.
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.
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.
Our bioengineers make use of an in-house automated foundry for designing and building new organisms.
Comfort working with metadata, LIMS, and analysis pipelines; able to partner closely with data/ML teams.
You are recognized as a core technical leader for Datapoints screening and automation, and as a key partner to both execution and strategy across the portfolio.

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:

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

End‑to‑end ownership of screening workflows
Translate program objectives into executable workplans with realistic timelines and risk trade‑offs.
Assay & workflow development
Operational ownership & risk management
Leadership, mentoring, and training
Provide technical leadership and day‑to‑day guidance for operators and junior scientists on screening workflows.

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.

This listing is sourced directly from Ginkgo Bioworks's careers page and normalized into a canonical job model.