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Human Cell Types Intern - Human Cortex

Department: 2520- Human Cell Types
Location: Seattle


Characterizing selective vulnerability of cell types in human cortex


Project Overview:

Many neurodevelopmental and neurodegenerative diseases selectively target specific cell classes. For example, Parkinson’s disease causes selective loss of dopaminergic neurons in the substantia nigra, while genes associated with autism spectrum disorder are primarily found in maturing excitatory neurons in human cortical development. However, recent work from the Allen Institute and many others has identified many different types of these brain cell populations, and the specificity at which different diseases target these more selective cell types is not well understood. The primary goal of this project will be to compare single nucleus RNA sequencing data and associated cell type definitions from human cortex collected at the Allen Institute with published studies of brain disease to address the question of selective vulnerability of very specific cell types. The first half of the project will focus on framing the problem: what cell types do we find in human cortex; how do we work with gene expression data; how have other groups studied selective vulnerability in disease? The second half of the project will involve applying the analysis tools researched in the first part of the project to address the primary goal, for example by comparing disease genes identified in genome wide associate studies (GWAS) with genes selectively enriched in cell types. This is expected to be an entirely computational project (e.g., no “wet lab” work), and some prior programming knowledge is strongly encouraged, with R being the preferred language. Depending on the outcome of the analysis, this project could potentially be written up for a peer-reviewed journal.


Educational Objectives:

  • Learn how large gene expression studies can be used to define and characterize cell types
  • Acquire basic knowledge on multiple brain diseases, including affected genes and cell types
  • Learn how published analysis tools can be applied to a new problem
  • Learn strategies for collaborative science, including best practices for code sharing, scientific writing, and presentation of findings


  • U.S. Citizen or U.S. Permanent Resident currently enrolled in an accredited U.S. college or university.
  • Enrolled in undergraduate studies or in a Master’s program. You must be enrolled and returning to school Fall quarter.
  • Must be able to start on either June 3rd or June 17th, 2019 and commit to the full 10-12 week internship time period. Interns will be expected to work 35-40 hours a week.
  • Must be 18 years of age or older.


Interns will receive $15.00 per hour which is equivalent to $6,000 less taxes.


Housing is not provided as a part of the internship program. If selected we will provide a list of housing resources for you.


Interns will be provided with an ORCA business passport free of charge for the duration of their internship.

How to Apply

  1. Complete an application through this portal. The application deadline is January 30, 2019.
  2. Submit a resume as well as the following documents using the + supplemental documents button:
    • A personal statement describing your interest in Allen Institute for Brain Science
    • College transcript with Cumulative GPA and Courses taken (can be unofficial)

3. Send one letter of recommendation to

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