> Markdown version of [/jobs/ext/4183224-scientist-i-ml-ai-regulatory-genomics-and-cell-type-targeted-tools-for-brain-health](https://www.wearedevelopers.com/jobs/ext/4183224-scientist-i-ml-ai-regulatory-genomics-and-cell-type-targeted-tools-for-brain-health). Every page supports `.md` or `Accept: text/markdown`. Links point to the HTML versions so they work for humans too. Agent guide: [/agents.md](https://www.wearedevelopers.com/agents.md). --- # Scientist I - ML/AI Regulatory Genomics and Cell Type-Targeted Tools for Brain Health - **Company:** ClearCompany - **Location:** United States (Remote available) - **Experience:** Starter - **Salary:** $87,450.0 - **Contract:** Permanent contract - **Skills:** Artificial Intelligence, Data Analysis, Computational Biology, Python (Programming Language), Deep Learning - **Published:** October 7, 2026 - **Apply:** https://alleninstitute.hrmdirect.com/employment/job-opening.php?req=3833385&req_loc=1499600&&cust_sort1=29268&&nohd#job ## About the Role * 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. ## Description * 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.