Senior Research Associate – Throughput Screening

Senior Research Associate – 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 Senior Research Associate to join our synthetic enhancer flywheel. The Associate will work in the laboratory to clone and screen Massively Parallel Reporter Assay (MPRA) libraries in a variety of biological models from cell lines to multicellular in‑vivo models to mouse in‑vivo. They will optimize library delivery, process RNA and DNA through generation of Illumina sequencing data for model training, and then evaluate model success by testing designed sequences using ddPCR, flow cytometry, and other molecular biology assays as a readout.

They will be on the cutting edge of high‑throughput screening, optimizing workflows in new multicellular models as the active learning needs for the AI model evolve.

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.

• Develop advanced high‑throughput screen capabilities in multicellular models, preferably with single‑cell readout (e.g., mouse in‑vivo, gastruloids, embryoid bodies, teratomas)
• Design validation experiments to benchmark performance of synthetic enhancer design AI models
• Maintain and propagate human cell lines, optimize and perform plasmid DNA transfections and viral transductions
• Perform advanced genomics protocols (e.g., custom amplicon sequencing, RNA‑seq, single‑cell RNA‑seq, ATAC‑seq)
• Independently execute molecular biology protocols, including molecular cloning, flow cytometry, quantitative PCR, ddPCR
• Troubleshoot 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
• 6 years of relevant experience

• Master’s degree in Cell Biology, Genetics, Synthetic Biology, Bioengineering, Genomics, Molecular Biology, Bioinformatics, or related field
• 8+ years of relevant experience
• Experience in a Tech Bio setting where wet‑lab experiments primarily serve to build AI models
• Experience optimizing pooled high‑throughput screening workflows
• 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…