Scientific Operations Lead: Oligonucleotide Synthesis & QC

Alloy Therapeutics, Inc.; Waltham (MA); On-site; USD 100,000 - 125,000; Full time

Benefits offered by this job

Equity compensation

401(k) match

Generous health benefits

Unlimited PTO

Education stipend

Job summary

Alloy Therapeutics, Inc. in Waltham, MA is seeking a Scientific Operations Manager / Associate Scientist to split time between managing the NAC workflow and hands-on chemistry in the lab.

You will oversee demand planning, scheduling, and instrument readiness while performing solid-phase oligonucleotide synthesis and QC tasks. You should bring an operations mindset, documentation rigor, and experience with bench work; prior oligonucleotide experience is not required as training is provided.

Qualifications

• Bachelor’s degree in chemistry, biochemistry, chemical engineering, pharmaceutical sciences, or related discipline.
• Minimum of 5 years of experience in research-scale synthesis, laboratory operations, or chemistry production environment.
• Bench experience in chemical or biochemical synthesis, purification, and analytical characterization.
• Experience with scheduling, demand planning, or production operations in a small-team or startup biotech/pharma setting.
• Experience with electronic lab notebooks and compound/batch registry or LIMS systems (Benchling strongly preferred).
• Familiarity with deviation management, root cause analysis, and CAPA processes.

Responsibilities

• Own end-to-end demand planning for the NAC team—intake and triage of sequence requests, capacity forecasting, batch scheduling, and queue prioritization with real-time status dashboards.
• Set and defend turnaround time commitments by sequence class and other factors to protect schedules.
• Design and facilitate a Tier Board system to drive daily accountability and KPIs.
• Serve as primary administrator for Benchling and other systems; configure registration schemas for traceability from request to COA.
• Manage inventory against production schedule and coordinate procurement.
• Own uptime and preventive maintenance for synthesis and analytical instruments; plan for downtime.

Skills

Laboratory operations

Demand planning

Project management

Lean principles

SOPs and quality systems

Benchling familiarity

Cross-functional collaboration

Scheduling

Education

Bachelor's degree in chemistry, biochemistry, chemical engineering, pharmaceutical sciences, or related discipline

Tools

Benchling

LIMS

HPLC

LC-MS

Analytical instruments

Job description

Alloy Therapeutics, Inc. in Waltham, MA is seeking a Scientific Operations Manager / Associate Scientist to split time between managing the NAC workflow and hands-on chemistry in the lab.

You will oversee demand planning, scheduling, and instrument readiness while performing solid-phase oligonucleotide synthesis and QC tasks. You should bring an operations mindset, documentation rigor, and experience with bench work; prior oligonucleotide experience is not required as training is provided.