Scientific Operations Manager / Associate Scientist, Oligonucleotide Synthesis & Analytical Sciences

Alloy Therapeutics • Waltham, MA

6d • $100,000 - $125,000 • Onsite

About The Position

We are seeking a Scientific Operations Manager / Associate Scientist to split their time approximately 50/50 between (1) managing the operational backbone of our oligonucleotide design-make-test cycle (Nucleic Acid Chemistry or NAC) and (2) hands-on chemistry work in the laboratory, including synthesis, purification, and quality control. The ideal candidate brings a strong operations mindset—a deep appreciation for process discipline, documentation rigor, and quality systems—paired with genuine comfort at the bench. Prior oligonucleotide experience is not required; we will train the right person on our synthesis platform and analytical methods. What matters is that you have run reactions, operated instruments, and managed the operational machinery of a research-stage chemistry or manufacturing organization. You are equally comfortable troubleshooting a synthesis as you are building a demand plan, and you thrive on bringing structure and visibility to fast-moving research operations. This is a rare opportunity to shape the operational foundation of a growing genetic medicines company from the ground up. You will have a direct impact on how our team designs, makes, and tests novel oligonucleotide therapeutics—while staying connected to the science at the bench. We will invest in training you on our nucleic acid chemistry platform so that you develop deep expertise in an exciting and rapidly expanding therapeutic modality. We offer competitive compensation, equity participation, and the chance to build something meaningful alongside a deeply experienced team.

Requirements

• Bachelor's degree in chemistry, biochemistry, chemical engineering, pharmaceutical sciences, or a related discipline.
• Minimum of 5 years of experience in research-scale synthesis, laboratory operations, or chemistry production environment, with demonstrated hands-on laboratory work and operational or project management responsibilities.
• Bench experience in chemical or biochemical synthesis, purification, and analytical characterization—in any modality (Oligonucleotide preferred; small molecule and peptides or similar modalities may be considered)
• Transferable hands-on experience with techniques such as solid-phase synthesis, HPLC purification, and analytical characterization is highly relevant.
• Proven track record managing 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.
• Strong organizational skills with the ability to manage competing priorities across lab and operations responsibilities simultaneously
• Experience managing laboratory inventory, reagent and consumable procurement, and vendor relationships against a production schedule.
• Demonstrated ability to build and maintain operational reporting—KPIs, dashboards, or status updates—that give stakeholders and leadership real-time visibility.
• Experience facilitating recurring operational meetings and driving accountability and escalation across cross-functional teams without direct reporting authority.

Nice To Haves

• Experience implementing tier board or daily management systems in a laboratory or manufacturing environment.
• Hands-on experience with oligonucleotide synthesis and QC—including solid-phase synthesis, cleavage/deprotection, HPLC or SPE purification, and analytical release testing (HPLC, LC-MS, CE)—or with nucleic acid and related therapeutic modalities (a plus, but not required).
• Experience scaling synthesis from µmol research scale toward multigram scale of oligonucleotides.
• Managing oligonucleotide CDMOs and reviewing vendor certificates of analysis
• Familiarity with lean, Six Sigma, or other operational excellence frameworks applied to R&D or CMC settings.
• Exposure to GLP or GMP environments and an understanding of how research-grade work feeds into regulated development stages.
• Experience owning process documentation and quality systems—SOPs, standard work, batch records, or change control—in a research or manufacturing setting.
• Proficiency with data visualization or dashboard tools for operational reporting.
• Demonstrated ability to work effectively across functions (chemistry, biology, program management) in a collaborative, fast-paced environment.

Responsibilities

• Own end-to-end demand planning for the NAC team—intake and triage of sequence requests (oligonucleotide length, chemistry, modification pattern, scale and conjugation), capacity forecasting against synthesizer column and plate availability, batch scheduling, and queue prioritization with input from biology, program management, and leadership—and provide real-time status visibility on every sequence from request through release via dashboards and reporting.
• Set and defend turnaround time commitments by sequence class, modified sequences, difficult couplings, high-GC or structured regions, scarce amidites at intake rather than after a failed synthesis.
• Design and facilitate a tactical tier board system (Tier 1 through Tier 3) to drive daily accountability and structured escalation, tracking KPIs (on-time delivery and turnaround time by sequence class, synthesis first-pass success rate, average stepwise coupling efficiency, isolated yield, purity at release, resynthesis/rework rate, and OOS rate), action items, and resource constraints, and champion continuous improvement using lean principles.
• Serve as primary administrator and power user for Benchling and other operational systems, leading their implementation, configuration, and ongoing optimization to support NAC workflows from request intake through QC release. Configure oligonucleotide-specific registration and schemas—sequence with chemistry and modification pattern, synthesis run, purification and lot records, and structured analytical results—so every batch is traceable from request through synthesis, purification, QC data, and certificate of analysis.
• Manage reagent, raw material, and consumable inventory against the production schedule, coordinating procurement and lot-level traceability as appropriate for research-grade work.
• Own uptime for the synthesizers, HPLC/UPLC, LC-MS, and CE instrumentation the queue depends on—preventive maintenance and calibration schedules, system suitability tracking, column lifecycle, spare-parts stocking, and vendor service coordination—so instrument downtime is surfaced and planned for rather than absorbed as schedule slip.
• Lead structured root cause investigations of synthesis and QC deviations, author and track CAPAs to closure, and report deviation trends to leadership.
• Perform solid-phase oligonucleotide synthesis on automated synthesizers, including preparation of reagents, programming of sequences, and troubleshooting instrument issues.
• Conduct downstream processing steps such as cleavage, deprotection, purification (e.g., HPLC, SPE), and formulation.
• Execute analytical QC testing (e.g., HPLC, LC-MS, UV quantitation, capillary electrophoresis) and interpret results against acceptance criteria.
• Record all experimental work in Benchling electronic lab notebooks in accordance with team standards and good documentation practices.
• Contribute to method development, process optimization, and technology transfer activities as the team scales.
• Bring a CMC quality mindset to all laboratory activities: attention to process controls, in-process testing, raw material qualification, and batch record completeness.

Benefits

• Competitive base and equity compensation commensurate with level of experience and independence
• 401(k) company match
• Generous personal and family medical, dental and vision benefits with 100% of premiums and deductibles covered
• Company-paid disability (STD, LTD) and life insurance
• Paid parental leave
• Family planning support up to $45,000 (e.g., IVF/PGT, adoption, surrogacy, egg retrieval)
• Unlimited PTO (paid time off) and flexible schedules
• Annual stipend for continuing education with commitment to your career through individualized professional development plan
• Wellness and Extensive Employee Assistance Program (EAP) including resources for mental wellness

What This Job Offers

• Job Type: Full-time
• Career Level: Mid Level