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

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

The Company

Role Location: Waltham, MA

About The Role At Alloy Therapeutics

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‑scale 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.

Why This Role Is Unique

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.

Key Responsibilities

• Sequence Request Intake, Demand Planning, Scheduling & Queue Management
  • 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
• Tier Board System & Operational Excellence
  • 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
• Business Systems
  • 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
• Inventory Management
  • Manage reagent, raw material, and consumable inventory against the production schedule, coordinating procurement and lot‑level traceability as appropriate for research‑grade work
• Instrument & Equipment Readiness
  • 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
• Deviations, Root Cause Analysis & CAPA
  • Lead structured root cause investigations of synthesis and QC deviations, author and track CAPAs to closure, and report deviation trends to leadership

Laboratory Responsibilities

• 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

Qualifications

We recognize this is a broad role, and we don’t expect every candidate to check every box. If you bring the core bench and operations experience, we encourage you to apply.

Required Qualifications

• 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

Preferred Qualifications

• 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

Taking Care of Our People

We support the individuality of what people need to do outside of work to empower them to do their best at work. While you focus on making better medicine together, we focus on programs and benefits that support a diverse and growing team. Whether you’re single, in a growing family, or nearing retirement, Alloy offers a variety of comprehensive and competitive benefits starting from day one.

Compensation

• Competitive base and equity compensation commensurate with level of experience and independence
• 401(k) company match

Health & Family

• 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)

Unique Perks

• 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

Pay Transparency

At Alloy Therapeutics, we believe in fostering trust and open communication. For this role, the estimated range is $100,000 - $125,000, with the final offer based on factors like your experience, skills, and alignment with our needs. Additionally, this role is eligible for equity compensation, reflecting our commitment to shared success as we work together to make better medicines. We are proud to offer competitive compensation and benefits, aiming to support our team’s professional and personal well‑being. If you have any questions about pay or benefits, we’re here to help.

Alloy Therapeutics is an equal opportunity employer.

All qualified applicants will receive consideration for employment without regard to race, color, religion, national origin, sex, sexual orientation, gender identity, veteran status, disability, or other legally protected status. If you are unable to submit an application because of incompatible assistive technology or a disability, please contact us at [e-mail]. We will make every effort to respond to your request for disability assistance as soon as possible.