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

Scientist I – 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.

Brain Health is a new global collaborative research initiative designed to accelerate understanding of human brain diseases through large-scale human tissue analysis, open science, AI-enabled disease modeling, and translational platform technologies. Building on foundational advances in human brain cell atlases, quantitative neuropathology, single-cell and spatial biology, multimodal molecular profiling, and AI-enabled analysis, Brain Health is developing a scalable framework for understanding disease progression directly in the human brain and identifying new opportunities for therapeutic development.

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 . 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.

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

• 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:

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 accommodations for qualified individuals with disabilities.