Scientist I - ML/AI Regulatory Genomics and Cell Type-Targeted Tools for Brain Health

The Allen Institute accelerates science for a healthier world through large-scale research designed to answer some of the most complex questions in biology. Our multi-disciplinary teams generate foundational knowledge, tools, and data to understand how our brain, cells, and immune system work. We share our work openly so others can build on it, move faster, and ask bigger questions. We drive discovery forward and create new possibilities for improving human health.

• Curate training, validation, and benchmark sets from cross-species single-nucleus multiomic data
• Define cell-type targets and design objectives for synthetic enhancers from whole-brain single-cell atlas data
• Apply sequence-to-function models and guided optimization to prioritize candidate enhancers, and interpret them through motif content, syntax, and spacing
• Plan each design-and-test cycle with experimental colleagues, setting success criteria in advance and feeding screening results back into model training
• Publish and present findings, and openly release validated sequences, benchmarks, and documentation.

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.

• Ph.D. in genomics, computational biology, neuroscience, genetics, or a related field, or equivalent experience
• Experience with single-nucleus multiomic, spatial, methylation, or 3D genome data, and with enhancer screens such as MPRA, STARR-seq, or enhancer-AAV assays
• Research experience in gene regulation or regulatory genomics, including enhancers, chromatin accessibility, or transcription factor biology, with a supporting publication record
• Proficiency in Python or R for large, high-dimensional biological datasets, with working familiarity with sequence-based deep learning and AI-assisted research tools

• Experience interpreting validation data from enhancer-AAV screens
• Hands-on experience with sequence-to-function models (Enformer, Borzoi, ChromBPNet), guided sequence design, and model interpretation methods
• Domain knowledge of brain cell type taxonomies, molecular neuroscience, or AAV-based genetic tools, and cross-species genomic analysis
• Excellent written and verbal communication, with proven ability to manage several projects at once in a collaborative environment

• Working at a desk and at a computer analyzing data
• Occasional time in laboratory and imaging spaces coordinating with experimental colleagues

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

• This role is currently able to work both remotely and onsite in a hybrid work environment. We are a Washington State employer, and the primary work location for all Allen Institute employees is 615 Westlake Ave N.; any remote work must be performed in Washington State.

• Occasional travel to collaborator sites and consortium meetings
• Attendance and participation in national and international conferences

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

$87,450 – $108,250 *

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