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Scientist I – Single-Cell Bioinformatics - Informatics & Data Science

Allen Institute
Seattle, Washington State
Commensurate with experience
Closing date
Oct 9, 2022

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 these data. This position will collaborate with an enthusiastic and dynamic team of computational and experimental scientists to build a quantitative census of cell types in mouse brain, and understand how cell types change during development and aging as well as in disease.

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.

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.

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 single-cell ATAC-seq data to understand regulatory landscapes in the adult mouse brain or in the context of aging, development, and exposure to drugs of abuse.
  • Work with experimental scientists to optimize experimental protocols, and design experiments to validate computational predictions of neurobiological function.
  • Participate in a highly interactive and multidisciplinary environment.
  • Write and publish manuscripts, grant, and internal progress reports, and grant applications.
  • Present findings in peer-reviewed journals and scientific conferences.

Required Education and Qualifications

  • PhD degree in computational biology, bioinformatics, genome science, or other quantitative disciplines such as computer science, applied mathematics, engineering, or related field; or an equivalent combination of degree and experience
  • Rigorous training in data science and experience in working with very large datasets
  • 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 Qualifications

  • Prior experience with single-cell RNA-Seq or single-cell ATAC-seq datasets
  • Knowledgeable about neuroanatomy and brain architecture.
  • Knowledgeable about mouse genetics and gene regulatory mechanism
  • Knowledgeable about the neurobiology of drugs of abuse
  • 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 – working two to three days per week onsite. 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 fully vaccinated against COVID-19 as a condition of employment unless a medical or religious exemption is approved. All employees will be required to keep their vaccination status up to date according to CDC guidance and our policy.

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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