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

Ginkgo Bioworks -
Boston, MA

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Job Details

$160,000 - $180,000 a year

Benefits

Paid holidays
Health insurance
Unlimited paid time off
Dental insurance
401(k)
Vision insurance

Qualifications

Research design
Laboratory experiment design
Technical documentation
Design of experiments
Statistical analysis for research
Assay development
Research project technical leadership
Managing engineering teams
Managing teams of scientists
Project stakeholder communication

Full Job Description

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’ 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)
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, 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.

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, 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.

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.

Privacy Notice

I understand that I am applying for employment with Ginkgo Bioworks and am being asked to provide information in connection with my application. I further understand that Ginkgo gathers this information through a third-party service provider and that Ginkgo may also use other service providers to assist in the application process. Ginkgo may share my information with such third-party service providers in connection with my application and for the start of employment. Ginkgo will treat my information in accordance with Ginkgo's Privacy Policy. By submitting this job application, I am acknowledging that I have reviewed and agree to Ginkgo's Privacy Policy as well as the privacy policies of the third-party service providers used by Ginkgo's associated with the application process.

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