Research Associate II, NGS

Flagship Pioneering; Cambridge (MA); On-site; USD 74,000 - 95,000; Full time

Benefits offered by this job

Healthcare coverage

Annual incentive program

Retirement benefits

Other benefits

Job summary

Alltrna, a Flagship Pioneering portfolio company, is seeking a Research Associate II / Senior Research Associate to join the NGS Core in the Computational and Molecular Biology team in Cambridge, MA. You will own end-to-end RNA-based NGS experiments from extraction to sequencing, ensuring data quality and traceability.

You will work with cross-functional scientists, operate automation platforms (KingFisher, Mantis, Biomek), maintain SOPs, and document procedures in Benchling, contributing to

Qualifications

• BS/MS in biology, molecular biology, biochemistry, or a related discipline.
• 2+ years RA or 4+ years Senior RA experience.
• Hands-on with RNA/DNA extraction, PCR/qPCR, Gel, Illumina library prep.

Responsibilities

• Execute end-to-end NGS experiments from RNA extraction to sequencing.
• Operate automation equipment (KingFisher, Mantis, Biomek).
• Evaluate QC metrics, flag deviations, troubleshoot issues.
• Follow SOPs and update workflows as needed.
• Document procedures and data in Benchling for traceability.
• Contribute to data-driven workflow improvements and throughput gains.
• Assist with inventory and lab readiness; collaborate with cross-functional teams.

Skills

RNA extraction

DNA extraction

PCR

qPCR

Gel electrophoresis

Illumina NGS library prep

QC metrics

Molecular biology

Cross-functional collaboration

Data-driven improvements

Education

BS/MS in Biology or related field

Tools

KingFisher

Mantis

Biomek

Benchling

Job description

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 affect 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.

Research Associate II / Senior Research Associate, Next-Generation Sequencing

Position Summary:

Come join Alltrna and be an integral part of the Next-Generation Sequencing (NGS) Core within our Computational and Molecular Biology team. We are seeking a highly motivated and organized Research Associate to support the RNA-based NGS methods and experiments that empower Alltrna’s platform. The role will own end-to-end execution of NGS experiments, spanning sample extraction through sequencing, quality control, and documentation. Alltrna’s NGS pipeline is central to company initiatives, and this role will collaborate closely with a cross-functional team of scientists in molecular biology, computational biology, and lab automation. The successful candidate should be able to work effectively in a team-oriented group and is accustomed to consistently delivering high-quality data on a timeline. This position reports to the NGS Core Lead.

Key Responsibilities:

• Execute end-to-end NGS experiments, including RNA extraction from tissues and cells, tRNA-seq and small RNA-seq library preparation, sequencer operation, and quality control.
• Independently operate automation equipment, including KingFisher, Mantis, and Biomek liquid handlers.
• Evaluate run and sample QC metrics, proactively flag deviations and out-of-spec results, troubleshoot to root cause.
• Follow SOPs and contribute to maintaining and updating these as workflows evolve.
• Document all procedures, data, and observations in our electronic laboratory notebook system (Benchling) to maintain accuracy and traceability.
• Contribute to the design and execution of experiments to evaluate data-driven NGS workflow improvements, supporting gains in quality, throughput, and efficiency.
• Contribute to sample and reagent inventory management, ordering, batch certification, equipment readiness, and laboratory organization.
• Collaborate with sample intake, computational, and automation teams to ensure both sample and data quality.

Qualifications and Skills

• BS/MS in biology, molecular biology, biochemistry, or a related discipline, with 2+ years (RA II) or 4+ years (Senior RA) of relevant experience.
• Hands‑on experience with nucleic acids, including RNA/DNA extraction and quantification, PCR, qPCR, gel electrophoresis, and Illumina NGS library preparation.
• Working understanding of the molecular biology and QC metrics that underlie NGS workflows and Illumina sequencing.
• Ability to stay organized and complete a high volume of requests on time, while maintaining accuracy and quality.
• Demonstrated ability to think critically, troubleshoot, and problem‑solve.
• Track record of identifying and contributing to data‑driven workflow improvements.
• Strong written and verbal communication skills, with the demonstrated ability to work effectively in a cross‑functional team.

The preferred candidate will ideally also possess the following skills:

• Experience with small RNAs or RNA library construction.
• Experience with automated liquid handling platforms (Biomek preferred, KingFisher).

The salary range for this role is $74,000 - $94,500. 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.

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