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

Ginkgo Bioworks
paid time off, paid holidays, 401(k)
United States, Massachusetts, Boston
27 Drydock Avenue (Show on map)
May 14, 2026
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. Senior Engineer III, Small Molecules - High Throughput Screening & Technology Location: Boston, MA Team: Datapoints - Small Molecule Developability & 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' highthroughput smallmolecule and functional genomics screening capabilities. This person is a player-coach and the technical heart of the screening and automation workflows that enable ADME, DrugSeq, imaging/viability assays, and related workcell operations across Datapoints. You will design and run complex, automationenabled 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 Endtoend ownership of screening workflows Own HTS and DrugSeqlinked workflows (workcell and walkup), 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, DrugSeq 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 daytoday operations of relevant workcells and walkup methods (e.g., HTS chemical DrugSeq workcell, RT workcell, library prep handoff). Drive rootcause analysis and corrective/preventive actions when runs fail or deviate from expectations. Leadership, mentoring, and training Provide technical leadership and daytoday guidance for operators and junior scientists on screening workflows. Contribute to the Datapoints skill matrix by defining training levels, shadowing plans, and upleveling operators on key assays (e.g., HTS workcell, DrugSeq 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 highthroughput experimental biology. Deep handson experience with highthroughput screening in at least one of: Smallmolecule phenotypic or viability screens, or Functional genomics / perturbation screens (e.g., CRISPR, RNAi, barcoded libraries), or NGSlinked assays such as DrugSeq or similar. Strong experimental design and statistical thinking for multiplate datasets (controls, replication, plate effects, hitcalling). 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: DrugSeq or similar NGSbased transcriptomic screening workflows (RT workcells, libraryprep 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 (384well or denser formats) and walkup 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, highquality 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. 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. 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. Ginkgo has implemented a return to office policy effective October 1, 2025 with required in-office days 3x per week on Tuesday, Wednesday, Thursday. Some teams may require to be onsite 4-5 days per week and this will be discussed as part of the interview process. This policy applies to all employees who live within 50 miles of Ginkgo's offices in Boston, MA, Emeryville, CA and West Sacramento, CA. It is the policy of Ginkgo Bioworks to provide equal employment opportunities to all employees, employment applicants, and EOE disability/vet. 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