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Scientist II - Single Cell Genomics - Molecular Genetics

Department: Molecular Genetics

Scientist II – Molecular Genetics: Single Cell Genomics 


The mission of the Allen Institute is to uncover 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. 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 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 Molecular Genetics department at the Allen Institute for Brain Science seeks to hire an exceptional individual who will develop and apply computational techniques to integrate single-cell transcriptomic, epigenomic, and spatial transcriptomic data from adult and developing mouse brain to characterize its cell types. They will make key contributions to identification of cell types in various mouse brain regions and characterize changes in gene regulation associated with development or experimental perturbations.

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

  • Analyze large-scale single-cell genomics data to define cell types, their epigenomic signatures, and putative cell-type-specific enhancers
  • Design validation and follow-up experiments to place the genomics results in the neurobiological context
  • Write and publish manuscripts, grant progress reports, and grant applications
  • Present work internally and externally at scientific conferences
  • Maintain clear and accurate communication with supervisor, team members, and external collaborators

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 Neurobiology, Molecular Biology, or related field; or equivalent combination of degree and experience
  • Minimum of 3 years of relevant work or research experience
  • Strong background in scientific computing and analysis of large datasets
  • Understanding of single-cell genomics (transcriptomics, epigenomics) and experience in genomics data analysis
  • Proficiency in Python and/or R

Preferred Education and Experience

  • 5 – 7 years of relevant work or research experience
  • Strong organizational and communication skills 
  • Prior experience in analyzing single-cell RNA-Seq and/or ATAC-Seq datasets
  • Ability to develop, test, implement, and share new experimental and computational tools quickly, in an iterative manner, and after feedback from experimental, data production, and analysis teams
  • Ability to work independently and within a collaborative, multi-disciplinary environment to meet aggressive timelines
  • Proven independent thinking

Physical Demands

  • Occasional lifting up to 30 pounds
  • Frequently required to sit, stand, or walk
  • Fine motor movements in fingers/hands to operate computers and other office equipment; 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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