Scientist I • Regulatory genomics and cell type-targeted tools for brain health This effort centers on a lab-in-the-loop AI platform that designs and validates synthetic enhancer sequences for precision cell-type targeting across the brain. We train sequence-to-function models on the Allen Institute's cross-species whole-brain multiomic atlases, generate synthetic enhancers optimized for strength and specificity, and validate candidates in vivo with single-cell resolution across thousands of brain cell types. Thousands of enhancer AAVs have been screened in mice for functional activity using a consistent pipeline and released through the Genetic Tools Atlas . Each round of screening adds new tools and feeds back into model training, tightening the loop between computational prediction and biological discovery. Models, validated sequences, and the underlying codebase will be openly released as a platform for designing synthetic regulatory elements in any tissue or cell type.
We are seeking a
Scientist I to contribute to cross-team efforts defining the regulatory biology of this platform to interpret why designed sequences succeed or fail in the intact brain and to turn each round of in-vivo validation into a tuned model. In this role you will transform cross-species single-cell multiomic atlases into training and evaluation sets, analyze whole-brain enhancer-AAV screens across thousands of cell types, and work alongside scientists and machine learning colleagues to set the design objectives and prospective success criteria for each lab-in-the-loop cycle. The ideal candidate is a regulatory genomics scientist who is fluent enough in modern sequence models to shape them, and who is motivated by the prospect of building genetic tools that reach disease-relevant cell types.
Essential Functions - 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.
Required Education and Experience - 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
Preferred Education and Experience - 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
Work Environment - Working at a desk and at a computer analyzing data
- Occasional time in laboratory and imaging spaces coordinating with experimental colleagues
Physical Demands - Fine motor movements in fingers/hands to operate computers and other office equipment
Position Type/Expected Hours of Work - 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.
Travel - Occasional travel to collaborator sites and consortium meetings
- Attendance and participation in national and international conferences
Additional Comments - *Please note, this opportunity offers relocation assistance
- *Please note, this opportunity may offer visa sponsorship
Annualized Salary Range $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.
Benefits Employees (and their families) are eligible to enroll in benefits per eligibility rules outlined 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.
