Scientist I – Integrative Analysis of SEA-AD and Community Multiomics Datasets – Human Cell Types

The mission of the Allen Institute is to understand the principles that govern life, and to advance health. Our creative and multi-dimensional teams focus on answering some of the biggest questions in bioscience. We accelerate foundational research, catalyze bold ideas, develop tools and models, and openly share our science to make a broad, transformational impact on the world.

The Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD) consortium strives to achieve a deep molecular and cellular understanding of the early pathogenesis of Alzheimer’s disease (AD). Leveraging advances in quantitative neuropathology and next-generation single cell molecular profiling technologies we are generating large-scale data sets from well-characterized donors that span the spectrum of AD pathology to comprehensively map human brain cell types across aging and disease. These data along with tools for their use are made freely and publicly available.

We seek to hire a Scientist to integrate, analyze, and interpret single nucleus multiomics datasets from the broader research community in conjunction with SEA-AD datasets. Community datasets will include those from other AD and AD/ADRD donor cohorts as well as animal models. This position will leverage existing computational tools and develop novel pipelines and approaches to analyze and interpret these data. This position is part of SEA-AD’s Integrative Analysis Center (IAC) and will collaborate with a dynamic team of quantitative and experimental scientists to build an integrated resource that defines how cell types are affected in AD and AD/ADRD across community datasets. The goal of the IAC is to synthesize knowledge from the field and share it widely and coherently.

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

• Collaborate with SEA-AD and SEA-AD IAC members and outside investigators to ensure community multiomic datasets are re-processed, their metadata is harmonized, and relevant secondary data types are obtained (e.g. whole genome sequencing, nuclear imaging, or blood based biomarkers)
• Adapt existing or develop novel computational tools to rigorously quantify changes in cell types in Alzheimer’s disease across community datasets
• Associate gene expression and chromatin accessibility changes with relevant and available donor metadata or secondary data types
• Compare cell type changes across disease progression between studies regions to identify common early changes that may inform biomarkers
• Interact with scientists from diverse backgrounds and perspectives to design analytical approaches and refine computational strategies
• Work with experimental scientists to design experiments to validate predictions of disease function
• Participate in a highly interactive and multidisciplinary environment
• Publish and present findings in peer-reviewed journals and scientific conferences

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 Neuroscience, Computational Neuroscience, Computer Science, Applied Math, or related field; or equivalent combination of degree and experience
• Fluency programming in Python in high performance computing
• Fluency with version control systems (e.g. Git/Github)
• Familiarity with analysis of RNA-sequencing or related data types

Preferred Education and Experience

• Experience with modeling disease or developmental trajectories, or related computational studies
• Additional experience in computational analysis and statistical assessment of biological datasets in other modalities such as spatial statistics, ATAC-seq analysis, computational anatomy, or related fields
• Previous work on studying Alzheimer’s disease or other neurodegenerative diseases
• Familiarity with additional programming languages (e.g., R)
• Experience with GPU-based deep learning
• Ability to work effectively in a highly collaborative environment
• Strong written and verbal communication skills
• Ability to work independently and collaboratively
• Strong publication track record

Physical Demands

• Occasional lifting up to 30 pounds
• Fine motor movements in fingers/hands to operate computers and other office equipment; repetitive motion with lab 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 attendance and participation in national and international conferences

Additional Comments

• Please attach a cover letter with your application
• **Please note, this opportunity offers relocation assistance**
• **Please note, this opportunity may offer visa sponsorship**

Annualized Salary Range

$92,250 - $114,100 *

* 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.

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.