Associate Scientist, Protein Science

Job Description

Job Description

Role Location: Waltham, MA

The Company
We are Alloy Therapeutics —a biotechnology ecosystem company empowering the global scientific community to make better medicines together. Through a community of partners, we democratize access to pre-competitive tools, technologies, services, and company creation capabilities that are foundational for discovering and developing therapeutic biologics. The company facilitates affordable, non-exclusive access to the entire drug discovery community from academic scientists, small and medium biotech, to the largest biopharma. At Alloy, we believe our industry should compete on getting the best drugs to patients as quickly as possible, not exclusive access to the best platforms. As a reflection of our relentless commitment to the scientific community, we reinvest 100% of our revenue in innovation and access to innovation. MAY THE BEST DRUG WIN.

Alloy has evolved from a startup into a global biotechnology infrastructure company operating 11 divisions across 5 research sites in 4 countries on 3 continents. Our model - Integrated Independence - combines centralized capabilities with entrepreneurial operating divisions. Successful members thrive in our shared culture of accountability, deliberate trust, and open communication. As a team we aspire to work together to exceed expectations and collectively contribute across the global organization to always maintain our nimble, startup culture.

At Alloy, we have an ethos of “Mentorship-By-Apprenticeship” in all of our positions. We strive to have workers in the office when needed to interact organically and face-to-face. Of course, as a lab-based operation, our cells and animals grow 7 days a week, 365 days per year. We respect and value our colleagues for their hard work that requires them to be in the lab every day. We ask our people who have more flexible accommodations, like this position, to appreciate their colleagues who have less flexibility. We are all one team!

About the Role 
In this role, you will support Alloy Discovery Services programs by executing protein science workflows central to antibody discovery, including transient transfection, recombinant DNA cloning, and immunogen design. You will contribute to protein expression at both high throughput and large scale as well as purification activities supporting the broader Protein Science team. The ideal candidate will bring hands-on experience with mammalian cell transfection, recombinant DNA techniques, and a working familiarity with downstream protein purification. We are looking for someone with the scientific curiosity to continuously improve our workflows and the organizational rigor to manage multiple projects in a fast-paced environment. Success in this role requires urgency, attention to detail, and a collaborative mindset that supports teammates and drives project goals forward.

How You'll Drive Impact 

• Support : Contribute to all Alloy modalities by enabling immunogen preparation, molecular biology reagent generation, protein production, and the greater antibody discovery pipeline
• Improve : Continuously evaluate and optimize standard protocols for transfection, cloning, and protein science workflows to enhance efficiency, reproducibility, and scalability
• Collaborate : Partner closely with cross-functional, multidisciplinary teams across biologics discovery programs and Alloy sites
• Deliver : Apply rigorous scientific thinking to experimental design and execution while maintaining thorough documentation; communicate results clearly to stakeholders to enable informed decision-making and project advancement

Key Responsibilities 

• Perform small- to large-scale transient transfections in mammalian cell lines (e.g. CHO) to drive high yield biologics production
• Independently manage multiple cell culture lines maintaining proper tissue culture techniques
• Systematically evaluate and optimize transfection efficiency, cell viability, and expression protocols across scales to improve throughput, consistency, and overall yield
• Execute recombinant DNA workflows, including PCR, Gibson assembly, and plasmid scale-up
• Contribute to antibody construct engineering to support the production of multi-specific antibody candidates
• Support protein expression and purification of biologics using AKTA chromatography systems, including affinity, IEX, and SEC
• Conduct regular QC on biologics including aSEC, CE-SDS or SDS-PAGE, and LAL as needed
• Analyze, interpret, and track deliverables in an electronic laboratory notebook in compliance with industry standards
• Coordinate project handoffs across functional teams to ensure seamless workflow continuity
• Present experimental data and findings during team and departmental meetings 
• Ensure timely execution of project activities in alignment with priorities
• Maintain laboratory organization and ensure compliance with safety protocols

Required Qualifications 

• MS with 2+ years or BS with 4+ years of hands-on research experience in molecular biology or a related discipline
• Degree in appropriate scientific discipline (molecular biology, cell biology, biochemistry, immunology, or related field)
• Extensive experience with transient expression of antibodies using mammalian expression systems from HTP to multi-liter scale, CHO preferred
• Deep technical understanding of various transfection methodologies (e.g., PEI, lipofectamine, or electroporation) and experience optimizing transfection efficiency and cell viability.
• Proficiency in high-density suspension cell culture management, including scale-up strategies from deep-well plates and shaking flasks to bioreactors.
• Hands-on experience monitoring cell culture health and metabolic profiles using analyzers such as Vi-CELL or equivalent instrumentation.
• Proficiency in recombinant DNA techniques including PCR, cloning, restriction digestion, gel analysis, and plasmid purification at small and large scale
• Experience with designing monoclonal, bispecific, and multi-specific constructs
• Strong organizational skills with the ability to manage multiple projects and prioritize independently
• Ability to maintain electronic laboratory notebooks in compliance with industry standards; familiarity with LIMS is a plus. Good communication skills and willingness to learn and adapt as part of a dynamic, team-oriented environment

Preferred Qualifications 

• Experience in stable cell line generation and vector engineering
• Working knowledge of protein purification techniques, including affinity and size-exclusion chromatography
• Familiarity with bioanalytical techniques to assess protein titer, yield, and purity

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 $93,000 - $110,000, 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 View email address on us.fitly.work . We will make every effort to respond to your request for disability assistance as soon as possible.

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