Research Associate II

Research Associate II – High Throughput Screening

The mission of the Allen Institute is to unlock the complexities of bioscience and advance our knowledge to improve human health. Using an open science, multi‑scale, team‑oriented approach, the Allen Institute focuses on accelerating foundational research, developing standards and models, and cultivating new ideas to make a broad, transformational impact on science.

Join our artificial intelligence powered lab, an initiative at the intersection of academic creativity and start‑up style execution. Our mission is to apply machine learning to biological design. Join us as we build a series of interconnected design‑test‑loop “flywheels” that enable design of synthetic enhancers, protein binders, and more.

We are looking for a Research Associate to join our synthetic enhancer flywheel, responsible for expanding our ability to rapidly build datasets that will train the next generation of DNA design machine learning models. Under moderate supervision, the Research Associate will be working in the laboratory to clone and screen Massively Parallel Reporter Assay (MPRA) libraries in a variety of cell lines.

They will deliver libraries to cells, process RNA and DNA through generation of Illumina sequencing data for model training, and evaluate model success by testing designed sequences using ddPCR, flow cytometry, and other molecular biology assays as a readout.

At the Allen Institute, we believe that science is for everyone – and should be open to everyone. We are dedicated to combating biases and reducing barriers to STEM careers more broadly. We also believe that science is better when it includes different perspectives and voices. We strive to make the Allen Institute a place where everyone feels like they belong and are empowered to do their best work in a supportive environment.

We are an equal‑opportunity employer and strongly encourage people from all backgrounds to apply for our open positions.

• Maintain and propagate human cell lines, optimize and perform plasmid DNA transfections and viral transductions
• Perform complex genomics protocols (e.g., custom amplicon sequencing, RNA‑seq, single cell RNA‑seq, ATAC‑seq)
• Execute molecular biology protocols, including molecular cloning, flow cytometry, quantitative PCR, ddPCR
• Assist in troubleshooting technical barriers in the generation of high quality NGS libraries, from library delivery to cell lines through NGS library generation
• Review and analyze data, participating in quality control and troubleshooting of processes and results
• Contribute to the development of new protocols as needed
• Present results and summarize progress to help frame internal decision‑making
• Comply with SOPs, good laboratory practices, and regulatory requirements
• Adhere to a team schedule and individual time management
• Maintain accurate laboratory documentation using established methods
• Other duties as assigned

• Bachelor’s degree in Cell Biology, Genetics, Synthetic Biology, Bioengineering, Genomics, Molecular Biology, Bioinformatics, or related field
• 2 years of equivalent experience

• 2–5 years of equivalent experience
• Experience performing molecular biology methods including molecular cloning (such as restriction cloning, Gibson Assembly, Golden Gate assembly, plasmid prep)
• Experience cloning complex libraries is a plus
• RNA isolation, DNA isolation, and PCR
• Track‑record of being an effective team member
• Competence and ability to work in a molecular biology/cell culture laboratory
• Experience with nucleic acid sequencing, especially custom amplicon sequencing
• Experience performing cell biology methods including mammalian cell culture, murine embryonic stem cell culture, primary cell culture, nucleofection, and lipofection

• Fine motor movements in fingers/hands to operate computers and other office/lab equipment

• Frequently required to sit, stand, walk, stoop, kneel or reach
• Possible exposure and handling of laboratory animals
• Laboratory atmosphere – possible exposure to chemical, biological or other hazardous substances