Scientist III – Proteome Editor Design / AI BioDesign

About the role

The Allen Institute accelerates science for a healthier world through large‑scale research that answers complex questions in biology. Our multidisciplinary teams generate foundational knowledge, tools, and data to understand how the brain, cells, and immune system work, sharing results openly so others can build on them and ask bigger questions. AI BioDesign is an initiative to make biology engineerable by combining AI and high‑throughput experimentation. We are building interconnected design‑test‑loop “flywheels” that enable the design of synthetic enhancers, protein binders, and more. As a scientist leading the proteome editor flywheel, you will drive the effort to produce a model that can design de novo proteome editors that work out of the box, focusing on degraders as described in recent literature.

Responsibilities

• Lead the Proteome Editor team to build and run a rapid, repeatable design–test–learn pipeline focused on proteome editor screening
• Design and oversee library screening and degrader evaluation experiments to generate high‑quality, model‑ready datasets
• Partner with machine learning colleagues to define next targets, curate data, and implement active‑learning strategies that choose the next best experiments
• Optimize flywheel performance by improving turnaround time, throughput, cost, and per‑cycle model lift; identify and remove experimental bottlenecks
• Coordinate closely with other flywheel leads and AI BioDesign stakeholders to align priorities, timelines, and dependencies across the broader program
• Mentor and manage a high‑performing team, fostering a collaborative culture and clear communication grounded in strong emotional intelligence
• Present scientific results and complex concepts internally in talks and progress reports
• Present results to the external community at conferences and in publications
• Travel occasionally to national and international conferences as invited

Requirements

• PhD degree in biochemistry, molecular biology, or a related field; or equivalent combination of degree and experience
• Minimum 5 years of relevant post‑doctoral experience
• Experience with functional genomics, massively parallel reporter assays, multiplexed assays of variant effect, saturation mutagenesis, or plasmid library‑based screening
• Experience architecting cellular library screening workflows (e.g., MPRAs or other high‑throughput cell‑based discovery platforms)
• Proven ability to lead scientific projects and collaborate cross‑functionally, including partnering effectively with computational/ML teammates

Qualifications

• 5–8 years relevant post‑doctoral experience
• Experience designing or optimizing cell‑based synthetic effectors
• Experience building or operating data‑driven/active‑learning experimental loops and translating assay outputs into model‑ready datasets
• Experience with protein engineering/interaction prediction approaches and modern analysis pipelines (e.g., sequence‑to‑function modeling, structural modeling, or high‑throughput data QC/processing)
• Experience performing molecular biology methods including library cloning, Golden Gate assembly, Gibson assembly, CRISPR/Cas9‑editing, mammalian cell culture, stem cell culture, and NGS library prep

Benefits

Employees (and their families) are eligible to enroll in benefits per the Allen Institute’s Benefits Guide, including medical, dental, vision, and basic life insurance, as well as eligibility for the Allen Institute’s 401k plan. Paid time off is also available as outlined in the Benefits Guide (https://alleninstitute.org/careers/benefits). This opportunity offers relocation assistance and may offer work visa sponsorship.

Pay

Annualized Salary Range: $128,050 – $160,050. Final salary depends on required education, experience, level of skills relevant to the role, and work location where applicable.

Schedule

This role is currently working onsite and is expected to work onsite for the majority of the working hours. The primary work location for Allen Institute employees is 700 Dexter Ave N., Seattle, WA; any remote work must be performed in Washington State.