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Scientist I - Imaging - Brain Science

Department: Imaging

Scientist I – Imaging

The mission of the Allen Institute is to unlock the complexities of bioscience and advance our knowledge to improve human health. Using an open science, multi-scale, team-oriented approach, the Allen Institute focuses on accelerating foundational research, developing standards and models, and cultivating new ideas to make a broad, transformational impact on science.

The mission of the Allen Institute for Brain Science is to accelerate the understanding of how the human brain works in health and disease. Using a big science approach, we generate useful public resources, drive technological and analytical advances, and discover fundamental brain properties through integration of experiments, modeling and theory.

The Allen Institute for Brain Science Imaging Department uses spatial transcriptomics data to build maps of molecularly-defined cell types in the mammalian brain. This scientist position would work with spatial transcriptomics datasets to create and analyze maps of transcriptomically-defined cell types in human brain specimens in health and disease and will evaluate and implement novel software packages for the analysis of these data. The Imaging department is a highly diverse and collaborative group of scientists and research associates with molecular, cellular, microscopy and imaging expertise that seeks a computational biologist or bioinformatics expert to move our projects forward. This scientist would work closely with Imaging department scientists and research associates as well as an interdepartmental team dedicated to investigating the effects of Alzheimer’s disease on the cellular structure of the human brain.

The Allen Institute believes that team science significantly benefits from the participation of diverse voices, experiences and backgrounds. High-quality science can only be produced when it includes different perspectives. We are committed to increasing diversity across every team and encourage people from all backgrounds to apply for this role.

Essential Functions

  • Evaluate and analyze spatial datasets derived from human brain tissue to identify molecularly-defined cell types.
  • Perform dimensionality reduction and label transfer methods to visualize and characterize spatial relationships of cells and compare across individual datasets
  • Provide an assessment of statistical significance for comparative studies of cell and tissue changes across disease states, brain regions and species
  • Regularly communicate findings to collaborators, the Imaging Department, and the Institute regarding key insights, findings, and questions derived from data analysis
  • Interact with scientists from diverse backgrounds and perspectives to design analytical approaches and refine computational strategies

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

  • PhD degree in computational biology, bioinformatics, neuroscience, applied mathematics, or related field, or equivalent combination of degree and experience
  • Experience in computational analysis and statistical assessment of biological datasets, spatial statistics, scRNASeq analysis, computational anatomy, or related fields

Preferred Education and Experience

  • 3-5 years experience in scientific computing and analysis using  Python and/or R,  and Bash/LINUX
  • Experience with the generation, analysis, and statistical assessment of spatial transcriptomics data
  • Familiarity with image processing
  • Knowledge of human neuroanatomy and neurodegenerative disease processes

Work Environment

  • May enter laboratory environment, including potential exposure to lasers, biohazards

Physical Demands

  • 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.

Additional Eligibility Qualifications

  • In keeping with our focus on employee safety, all employees must be up to date with vaccinations against COVID-19 as a condition of employment unless a medical or religious accommodation is approved. All employees will be required to keep their vaccination status up to date according to CDC guidance.

Additional Comments

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


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.







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