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Scientist I - Spatial Transcriptomics Analysis- Brain Science

Department: Imaging

Scientist I – Spatial Transcriptomics Analysis - Brain Science


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 the integration of experiments, modeling, and theory

We seek to hire an exceptional scientist to apply computational tools to analyze and interpret novel datasets to generate a next-generation molecular and cell type atlas of the mouse brain. This position is situated within the imaging department which consists of ~20 scientists and research associates using widefield, confocal, 2-photon, and light-sheet microscopes. You will collaborate with an enthusiastic, dynamic, and growing team (~10) of computational and experimental scientists within the imaging department to build an infrastructure for large-scale analysis of spatial transcriptomics data. This infrastructure will be crucial to future atlasing projects, which include developing mouse brain atlas and human and non-human primate brain atlases. Your work will consist of evaluating existing spatial analysis methods as well as developing novel algorithms that help us understand the spatial organization of cell types in the 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

  • Develop and apply scalable computational tools to rigorously define and characterize cell types based on extremely large datasets
  • Integrate single-cell RNA-seq and spatial transcriptomics data to understand cell-type composition in brain tissue in mice, non-human-primates, and humans
  • Research, evaluate, and apply novel computational tools for spatial analysis
  • Provide actionable feedback and interaction in a scientific team environment, including regular discussion on data collection, QC, and pipeline engineering
  • Effectively communicate findings across the institute as well as to the greater scientific community in peer-reviewed journals, scientific conferences, and web documentation
  • Develop scientific software tools with clear documentation and good source code management

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, genome science, or other quantitative disciplines such as computer science, applied mathematics, engineering, or related field; or an equivalent combination of degree and experience
  • Understanding of single-cell genomics (transcriptomics, epigenomics), and experience in genomics data analysis
  • Proficiency in R and/or python and Linux shell scripting

Preferred Education and Experience

  • Prior experience with single-cell RNA-Seq or spatial transcriptomics datasets
  • Experience in analysis of spatial data
  • Experience in image processing
  • Knowledgeable about neuroanatomy and brain architecture
  • Knowledgeable about mouse genetics and gene regulatory mechanism
  • Positive attitude, self-motivated, and ability to troubleshoot
  • Exceptional oral and written communication skills
  • Ability to work independently and within a collaborative, multi-disciplinary environment to meet aggressive timelines

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.

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.

Addition 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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