Scientist I – ML/Modeling for Synthetic Biological Design

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 the Seattle Hub for Synthetic Biology (SeaHub), an initiative at the intersection of academic creativity and start-up style execution. Our mission is to reimagine living cells and genomes as devices for recording biology and diagnostic information over time, as well as for encoding real-time therapeutic decision-making.

We are seeking a highly motivated computational biologist to build integrated design pipelines that leverage the best domain-specific ML/AI models. Currently most biological design is still done in crude ways, e.g. by cutting and pasting ACGT nucleotides. Existing computational models for biological design and prediction — such as Enformer, Borzoi, CREsted, AlphaGenome, SpliceAI, AlphaFold, RosettaFold and Evo 2 — are enabling but challenging to deploy effectively for design purposes, especially in aggregate. In this role, you will implement and evaluate existing models, becoming an expert in their strengths, weaknesses, and applications. Situated at the intersection of biological application and computation, you will fill a critical role in enabling our team to leverage ML/AI to design improved DNA sequences that harbor specific biological functions. You will also support our larger team in developing new models.

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.

Essential functions

• Apply existing AI/ML models to design synthetic DNA sequences to perform a variety of molecular biological functions
• Evaluate the performance of state-of-the-art public models, through collaboration with experimental teams
• Develop design tools & pipelines that incorporate the most helpful AI/ML models, including decision trees or agentic workflows for design
• Identify which ML/AI models are most suitable for synthetic sequence design as it relates to molecular recording
• Integrate genomic, transcriptomic, epigenetic, and editing outcome datasets to inform predictive models of editing efficiency, fidelity, and sequence constraints
• Stay at the forefront of advances in AI-driven molecular biological design
• Present findings to internal teams and external collaborators
• Drive projects forward independently and with minimal supervision

Note: Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions. This description reflects management’s assignment of essential functions; it does not proscribe or restrict the tasks that may be assigned.

Required Experience and Education

• Ph.D. in Computational Biology or Genomics, or equivalent combination of degree and experience
• Strong background in machine learning and AI applied to biological problems
• Demonstrated expertise in genomics, synthetic biology, or related fields
• Proficiency in Python and major ML/AI frameworks

Preferred Education and Experience

• 3-5 years post-Ph.D. experience
• Experience with prime editing in mammalian systems
• Background in in vivo lineage tracing, synthetic barcoding, or molecular recorders
• Knowledge of DNA repair pathways and how they influence editing outcomes
• Strong publication record in computational genomics, ML/AI for biology, or genome editing
• Experience working in small start-up style environments

Physical Demands

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

Work Environment

• 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

Position Type/Expected Hours of Work

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

Travel

• The successful candidate may be invited to attend occasional national and international conferences

Additional Comments

• **Please note, this opportunity offers relocation assistance**
• **Please note, this opportunity may offer work visa sponsorship**

Annualized Salary Range

• $92,250 - $114,100 *

* Final salary depends on required education for the role, experience, and level of skills relevant to the role, along with work location, where applicable

Benefits

• Employees (and their families) are eligible to enroll in benefits per eligibility rules outline in the Allen Institute’s Benefits Guide. These benefits include medical, dental, vision, and basic life insurance. Employees are also eligible to enroll in the Allen Institute’s 401k plan. Paid time off is also available as outlined in the Allen Institutes Benefits Guide. Details on the Allen Institute’s benefits offering are located at the following link to the Benefits Guide: https://alleninstitute.org/careers/benefits.

It is the policy of the Allen Institute to provide equal employment opportunity (EEO) to all persons regardless of age, color, national origin, citizenship status, physical or mental disability, race, religion, creed, gender, sex, sexual orientation, gender identity and/or expression, genetic information, marital status, status with regard to public assistance, veteran status, or any other characteristic protected by federal, state or local law. In addition, the Allen Institute will provide reasonable accommodation for qualified individuals with disabilities.