Protein Engineering Jobs in Boston, MA (NOW HIRING)

Company Summary:

Serif Biomedicines is a privately held, early-stage biotechnology company pioneering Modified DNA as a new class of medicines. Modified DNA brings together the best features of mRNA and gene therapy, while mitigating their limitations, by enabling medicines that are durable, redosable, programmable, and scalable.  Serif was founded by Flagship Pioneering, an innovation enterprise that conceives, creates, resources, and grows first-in-category life sciences companies.

Flagship Pioneering has created over 100 groundbreaking companies over the past twenty years, all of which are pioneering novel and proprietary biological, industrial, and engineering approaches to solve major needs in human health and sustainability. These companies include Moderna (MRNA), Generate Biomedicines (GENB), Seres Therapeutics (MCRB), Tessera Therapeutics,  and Lila Sciences.

The role

We are looking for a Senior Scientist, Molecular Biology with experience in protein engineering, complex DNA library design, and pooled screening to help build next-generation DNA constructs for programmable medicines. This role is a good fit for someone who has worked on CAR/binder design and is comfortable designing and testing large libraries to support discovery and optimization of engineered proteins.

You will help build and scale platforms for plasmid DNA design, construction, and optimization, with a focus on practical, high-throughput workflows and data-driven decision making. We are looking for someone who brings strong technical skills, thinks critically about experimental design, and is comfortable working in a fast-paced, collaborative environment.

This role reports to the Director of Molecular Biology and includes management of one direct report. You will work closely with other scientists and group leads across the R&D team.

Key responsibilities

• Using protein prediction models and ab initio modeling to develop proteins of novel function in silico and drive their selection and validation on wet bench
• Deep expertise characterizing protein structure and function including affinity, stability, etc.
• Design and build complex DNA libraries, including barcoding strategies, to enable pooled screening and variant tracking.
• Automation experience for arrayed screening and other biochemical assays
• Help build and scale high-throughput workflows for DNA and RNA production, screening, and data analysis.
• Track record of demonstration execution of large-scale library screens to support protein engineering and CAR optimization or binder identification and characterization
• Protein production and characterization in both bacteria and mammalian cells
• Contribute to plasmid and construct design for engineered proteins and cell-based systems.
• Own construct QC, sequence analysis, and tracking of variants, including NGS-based workflows.
• Work with external vendors as needed, balancing internal builds and outsourcing to meet timelines.
• Partner closely with other teams, including CMC, to provide designs, materials, and timelines.
• Mentor junior scientists and support strong practices in experimental design and data quality.
• Maintain clear and reproducible records (ELN, sequence tracking, sample management).
• Communicate results clearly to cross-functional teams and leadership.

Who you are

We encourage all candidates with exemplary experience in related fields to apply.

Technical Expertise

• BS with 14+ years, MS with 12+ years, or PhD with 5+ years of relevant industry experience in molecular biology, bioengineering, or a related field.
• Deep expertise in protein engineering and CAR
• Proven track record designing and building complex DNA libraries, including barcoding strategies for pooled screening.
• Strong command of molecular cloning and plasmid design in high-throughput settings.
• Demonstrated ownership of large-scale library screens, from design through execution and data interpretation.
• Expert-level experience with NGS-based library analysis, variant tracking, and sequence QC.
• Ability to operate effectively in cross-functional teams and drive work forward in a fast-paced environment.
• Experience mentoring or managing junior scientists.

Leadership & Collaboration

• Proven ability to lead complex projects and influence cross-functional teams.
• Strong mentorship skills with commitment to developing others. Previous technical or professional management experience.
• Excellent communication skills, with the ability to translate complex ideas across disciplines.

Values and Behaviors:

Flagship is an experiment in institutional, entrepreneurial, and innovation practiced in the context of a small company with an insurgent mindset. We are seeking individuals with an entrepreneurial spirit, strong communication skills, and comfort in working in and contributing to a dynamic and cross-functional team environment.

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, we encourage you to apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background. The level of the role will be commensurate with the education and years of experience of the identified candidates.

Flagship Pioneering and our ecosystem companies are committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, "FSP") do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering's internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

The salary range for this role is $126,000 - $181,500. Compensation for the role will depend on a number of factors, including a candidate's qualifications, skills, competencies, and experience. Serif Biomedicines currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Serif Biomedicines's good faith estimate as of the date of publication and may be modified in the future.