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

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)
• Operational ownership & risk management
• 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),
• 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
• Experience supporting multiple programs simultaneously

What Success Looks Like

• Datapoints 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
• 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

Pay

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.

Benefits

• 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.

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