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

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.