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Scientist I - Human Cell Types

Department: Human Cell Types

Scientist I – Human Cell Types - Allen Institute for 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 integration of experiments, modeling, and theory.

As part of the NIH BRAIN Initiative Cell Atlas Network, the Allen Institute is helping to lead a major new international consortium effort to create a comprehensive cell atlas of the human and closely related non-human primate brain. This project aims to make the most detailed map of the human brain ever produced, linking cellular and molecular phenotypes to brain imaging and functional architecture. To tackle this ambitious goal we are seeking talented and highly motivated individuals to help create these atlases and help to make them transformative for neuroscience and biomedical research through open data sharing. The atlas will be based on a range of cutting-edge high-throughput single-cell molecular, spatial, and cell phenotyping assays to map the structural and functional organization of the primate brain. We strive to build a catalytic brain cell reference and resource that will dramatically accelerate our understanding of brain structure, function, and disease, and to create tools to help the community take advantage of these resources.

As one component to this effort, we are combining patch-clamp recordings, morphological reconstructions, and transcriptomic profiling of single human and non-human primate neurons (“patch-seq”). This effort leverages recent success applying patch-seq to relate transcriptomic definitions of cell types to phenotypic diversity in human middle temporal gyrus. (Berg et al., 2021; Kalmbach et al., 2021; Lee et al., 2021). With this recent success, we are now well positioned to apply patch-seq across multiple human brain regions and the entire non-human primate brain to make novel discoveries about functional diversity of primate cell types. We are seeking a Scientist I to independently lead an effort to develop and apply computational techniques to relate transcriptomic data to morpho-electric data for the purpose of annotating cell type atlases with biological discoveries about human/non-human primate cell types.

Essential Functions

  • Design and implement data analysis pipelines for linking data across modalities (transcriptomic, electrophysiological, and morphological) in close collaboration with experimentalists
  • Contribute to ongoing efforts in extracting physiological and morphological data from large-scale patch-clamp and patch-seq experiments
  • Develop scientific questions relevant to the project and contribute intellectually to experimental designs
  • Publish/present findings in peer-reviewed journals/scientific conferences
  • Prepare written and oral reports on a regular basis
  • Develop and lead cross-team/site analysis through regular meetings
  • Maintain clear and accurate communication with supervisor, team members and external collaborators about key deliverables, milestones and deadlines
  • Facilitate sharing of data through public repositories

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.

Required Education and Experience

  • PhD in Neuroscience, Computational Neuroscience, Computer Science, Applied Math, or related field;  or equivalent combination of degree and experience

Preferred Education and Experience

  • At least three years of equivalent experience
  • Fluency programming in Python
  • 2+ years of experience analyzing RNA-seq data, preferably at the single cell level
  • Strong verbal and written communication skills; proven independent thinking
  • Fluency programming in R
  • Familiarity with a neurobiological system
  • Strong track record of biological discovery

Physical Demands

  • Occasional lifting up to 30 pounds
  • Fine motor movements in fingers/hands to operate computers and other office equipment; repetitive motion with lab equipment

Position Type/Expected Hours of Work

  • Occasional evening and weekend hours required
  • 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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