Senior Research Associate / Associate Scientist, Nonclinical

Flagship Pioneering, Inc.; Cambridge (MA); On-site; USD 81,000 - 127,000; Full time

Benefits offered by this job

Healthcare coverage

Annual incentive program

Retirement benefits

Broad range of benefits

Job summary

Alltrna in Cambridge, MA is seeking a hands-on Senior Research Associate/Associate Scientist for Nonclinical work. You will design and optimize cell-based assays to measure tRNA activity and support IND-enabling studies, handling DNA/RNA delivery and biomarker readouts.

The role requires a strong background in mammalian cell culture, molecular biology, and data analysis, with collaboration across the Nonclinical team to advance early programs toward clinical development.

Qualifications

• BS or MS in biology, biochemistry, pharmacology, or a related field.
• Minimum BS with 4+ years or MS with 2+ years of hands-on laboratory experience in academia, biotech, or pharma.
• Strong experience in mammalian cell culture and molecular assays.

Responsibilities

• Design, optimize, validate, and implement cell-based assays to support early-stage discovery and IND-enabling studies.
• Execute in vitro and in vivo sample processing to support nonclinical studies per SOPs.
• Conduct biomarker-related assays and analyze data for study decisions.
• Document experiments in ELN with data integrity and traceability.
• Collaborate across teams to share results and drive project timelines.

Skills

Cell culture

PCR/qPCR

Western blot

Flow cytometry

Molecular assays

Data interpretation

Team collaboration

Education

BS or MS in biology/biochemistry/pharmacology or related

Tools

CRISPR

Lentiviral/AAV transduction

qPCR machines

ELN

Job description

Senior Research Associate / Associate Scientist, Nonclinical

Cambridge, MA USA

Alltrna is looking for a hands-on scientist to join our Nonclinical team, where we test how well our engineered tRNAs work across a range of preclinical disease models. The ideal candidate is a strong cell and molecular biologist who is detail-oriented, intellectually curious, and energized by being part of a collaborative, fast-paced, small-company environment.

Working closely with the Nonclinical team, this individual will select, develop, and optimize the assays we use to measure tRNA activity and efficacy. These include cell-based assays in primary cells and hepatocyte models to the RNA and protein readouts that support in vivo studies. The candidate will design, execute and analyze data that support platform expansion and drive early-stage programs into clinical development. This role will have opportunities to propose new ideas, collaborate with groups across the company and participate in broader data reviews and decision-making.

We are hiring at the Senior Research Associate or Associate Scientist level, depending on experience. We are looking for someone who takes ownership of their experiments, works carefully and efficiently, and can troubleshoot technical challenges and adapt to changing priorities while maintaining scientific rigor.

Key Responsibilities:

• Design, optimize, qualify, validate, and implement cell-based assays that support early-stage discovery efforts, selection of new indications, and advancement of lead candidates into IND-enabling studies
• Execute in vitro assays and process in vitro and in vivo samples to support nonclinical studies, following approved protocols and SOPs
• Conduct biochemical assays to support the development of clinical and nonclinical biomarkers
• Document experiments accurately and promptly in the electronic laboratory notebook (ELN), ensuring data integrity, traceability, and complete records
• Perform mammalian cell culture, cell line characterization, and cell line development, including DNA/RNA delivery by transfection, transduction, electroporation, or LNP-based methods
• Perform molecular and cellular assays, including PCR/qPCR, Western blot/Jess, immunostaining, luciferase/bioluminescence assays, and flow cytometry
• Analyze, interpret, and clearly present experimental results to the Nonclinical and Research Leadership Teams
• Contribute to SOP development and manage reagents and inventory to support consistent, reproducible experiments
• Manage multiple studies in parallel, adapt to shifting priorities, and meet study timelines
• Collaborate with team members and cross-functional partners to share results and communicate progress or issues promptly

Key Qualifications:

• BS or MS in biology, biochemistry, pharmacology, or a related field
• Minimum BS with 4+ years or MS with 2+ years of hands-on laboratory experience in academia, biotechnology, or the pharmaceutical industry; more experience required at Associate scientist level.
• Strong experience in mammalian cell culture, including primary cells and cell lines; stem cell experience is a plus
• Experience with cell line characterization and development, including growth curves, kill curves, clonal expansion, and mycoplasma testing
• Hands-on experience with DNA/RNA delivery methods, such as transfection, lentiviral or AAV transduction, electroporation, or LNP-based delivery
• Experience with molecular and cellular techniques, including:
• PCR, qPCR/RT-qPCR, and molecular cloning
• Western blot/Jess
• Immunocytochemistry (ICC), immunohistochemistry (IHC), and immunofluorescence (IF)
• Luciferase/bioluminescence assays
• Flow cytometry
• Experience designing and optimizing cell-based assays for drug discovery
• Ability to analyze data using appropriate statistical methods and clearly communicate experimental results
• Strong attention to detail and ability to follow established procedures accurately
• Ability to manage multiple tasks, adapt to changing priorities, and work effectively in a fast-paced biotech environment
• Strong communication, organization, and teamwork skills

Preferred Qualifications

• Experience working with RNA therapeutics, including mRNA, siRNA, or antisense oligonucleotides
• Experience culturing primary human hepatocytes, induced pluripotent stem cells (iPSCs), or iPSC-derived hepatocyte-like cells
• Experience with high-content imaging, IncuCyte, or confocal microscopy
• Experience with genetic manipulation using CRISPR or other genome-editing approaches
• Experience developing disease-specific cellular assays
• Experience with ligand-binding assays and multiplex immunoassay platforms, such as MSD or Luminex, for cytokine, immunogenicity, or biomarker analysis

About Alltrna

Alltrna is the first clinical-stage biotech company advancing tRNA medicines to address shared disease-causing mutations across many indications. The company’s initial therapeutic programs are designed to restore full-length protein production in diseases caused by premature termination codons (PTCs), collectively referred to as Stop Codon Disease, which affects approximately 10% of people with a rare genetic disease. Alltrna's lead program, AP003, is a chemically modified, engineered tRNA oligonucleotide encapsulated in a clinically validated, liver-directed lipid nanoparticle. AP003 is being developed for the arginine-to-TGA (Arg-TGA) PTC in patients with liver Stop Codon Disease, including phenylketonuria, organic acidemias, and urea cycle disorders. Founded in 2018 by Flagship Pioneering, Alltrna has built an integrated platform to design, optimize, and deliver engineered tRNA therapeutics.

The salary range for this role is $81,000 - $126,500. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Alltrna currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Alltrna's good faith estimate as of the date of publication and may be modified in the future.