Senior Microfluidic Engineer Jobs in Everett, MA

Ampersand Biomedicines is a Flagship Pioneering company on a mission to transform patients' lives with programmed medicines that work precisely where needed, and nowhere else. We're building a collaborative, mission-driven team that thrives in a fast-paced environment and shares a genuine desire to make a difference. We ACT our values by working with Agility to adapt and deliver impact, leading with Compassion to put people first, and practicing Transparency to build trust through openness, clarity, and integrity. At Ampersand, employees are encouraged to explore breakthrough science, take chances, support one another, and contribute ideas and perspectives openly.
The Role
Ampersand Biomedicines is seeking a Senior Scientist I to help build and apply cell-based, high-throughput capabilities for engineered antibody and protein variant library screening. This scientist will play a central role in developing library cell systems and biological assays that enable the discovery of enhanced, engineered antibody and protein variants, while contributing to the continued evolution of Ampersand's high-throughput screening platform.
This role sits at the interface of molecular biology, cell biology, assay development, and microfluidic screening. The successful candidate will collaborate closely with molecular biologists on vector design, cell-based assay development, and library generation strategies before partnering with microfluidics engineers to integrate novel assays into robust high-throughput screening workflows. The ideal candidate is a hands-on experimentalist who enjoys leading the development of new biological systems, solving challenging assay-development problems, and working across disciplines to build innovative platform technologies.
Key Responsibilities

• Collaborate with molecular biology scientists to define vector designs, expression formats, transfection strategies, cell selection approaches, and assay-readiness criteria.
• Establish workflows for transfecting, expanding, selecting, and qualifying library cell populations for downstream screening.
• Lead the development and optimization of biochemical and cell-based droplet-compatible assays for high-throughput screening of engineered protein libraries.
• Develop and implement pathway-responsive reporter-cell assays to enable functional screening of engineered molecules and expand the capabilities of the screening platform.
• Optimize assay performance by systematically evaluating biological and technical parameters to maximize robustness, sensitivity, reproducibility, and scalability.
• Partner with microfluidics engineers to integrate biological assays into high-throughput microfluidic screening workflows.
• Analyze and interpret experimental data to guide assay optimization, platform development, and scientific decision-making.
• Troubleshoot biological and technical challenges, optimize established workflows, and identify opportunities to improve platform performance.
• Document experimental workflows, communicate findings to cross-functional teams, and contribute to SOP development and continuous platform improvement.

Required Professional Experience & Qualifications

• PhD in Cell Biology, Immunology, Molecular Biology, Bioengineering, Biomedical Engineering, Biochemistry, Biophysics, or a related field; or MS with substantial relevant industry experience.
• Strong hands-on experience with mammalian cell culture, cell handling, transfection workflows, cell selection, and cell-based assay execution.
• Demonstrated experience leading the development and optimization of biological assays, preferably protein-based, cell-based or high-throughput screening assays.
• Working knowledge of antibody biology, recombinant protein engineering, or antibody discovery workflows.
• Ability to design experiments, troubleshoot complex biological systems, interpret quantitative data, and make clear recommendations based on results.
• Experience with fluorescence-based detection platforms such as flow cytometry, FACS, microscopy, plate readers, or related systems.
• Strong analytical and problem-solving skills with experience interpreting complex biological datasets.
• Excellent written and verbal communication skills, with the ability to work effectively across biology, molecular biology, engineering, and platform teams.
• Enthusiasm for working in a fast-paced, early-stage biotech environment, including regular collaboration with colleagues across US and European time zones.

Preferred Professional Experience & Qualifications

• Experience developing engineered mammalian cell pools, stable cell lines, reporter cell lines, or functional cell-based screening systems.
• Experience with antibody engineering, antibody discovery, directed evolution, display technologies, recombinant protein library screening, or pooled cell-library workflows.
• Experience developing functional or cell-based assays for monoclonal antibody discovery is desirable.
• Exposure to cell-free protein synthesis or related in-vitro expression systems.
• Exposure to droplet microfluidics, single-cell screening, microfluidic sorting, or other high-throughput screening platforms.
• Familiarity with next generation sequencing-enabled antibody screening workflows.

Ampersand Biomedicines is 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: Ampersand Biomedicines does not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to Ampersand and/or Flagship Pioneering or its employees is strictly prohibited unless contacted directly by Ampersand or 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 Ampersand and FSP, and Ampersand/FSP will not owe any referral or other fees with respect thereto.
The salary range for this role is $126,000 - $159,500. Compensation for the role will depend on a number of factors, including a candidate's qualifications, skills, competencies, and experience. Ampersand currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Ampersand's good faith estimate as of the date of publication and may be modified in the future.