Research Associate II, NGS

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 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. For more information, visit www.alltrna.com 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, K