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Scientist I Single cell computational biology

Department: 2520 - Human Cell Types
Location: Seattle

Scientist I Single cell computational biology

Our mission at the Allen Institute is to advance our understanding of how the brain works in health and disease. Using a team science approach, we strive to discover how the brain implements fundamental computations through the integration of technological innovation, cutting-edge experiments, modeling, and theory.

The Allen Institute for Brain Science, located in Seattle, Washington, has an ambitious, multi-disciplinary effort to reverse engineer complex neural circuits by understanding their diverse cellular parts. Single nucleus RNA-seq has revolutionized this field by allowing a high-throughput analysis of cell types and classification based on their molecular profiles, which are highly predictive of specific aspects of cellular function and relation to disease.  Working with the NIH BRAIN Initiative, we are generating a map of cell types of the mouse and human brain and have characterized many of the properties of these cells.  We now seek to standardize the quantitative classification, organization, and nomenclature of these cell types in the way that the reference genome is the foundation for genomics, and to present information about each cell types in a manner of optimal use for the neuroscience community.

We seek to hire a scientist to focus on the identification and quantification of content for inclusion in a "cell type card".  Analogous to a GeneCard, a cell type card would include a to-be-determined set of information about a given cell type and would present it as a user-friendly collection in the Allen Cell Types Database (  The provided information will likely be a combination of (1) content already available or under construction for release on the website, (2) results published in manuscripts by the Allen Institute and other BRAIN Initiative Cell Census Network (BICCN) groups, and (3) supporting information to link this content with established (historical) cell types and data from other modalities.  This scientist will interface with technical and biological scientists from the Allen Institute about content to include in these cards and will work with the web product team to constrain these requests based on feasibility and available technical resources.  

Essential Functions

  • Interact with scientists to collect data, metadata, text, analysis code, and other content for inclusion in a cell type card.
  • Interface with the web product team to understand how each request aligns with the product road map.
  • Participate in designing data standards for the quantitative classification, organization, and nomenclature that will act as the scaffold for these cell type cards.
  • Compile a shareable codebase for collaborative science.
  • Participate in a highly interactive and multidisciplinary environment.
  • Publish and present findings in peer-reviewed journals and scientific conferences.

Required Education and Experience

  • PhD degree in neuroscience, bioinformatics, genetics, physics, applied mathematics, engineering, data science, software development, or related field.
  • Strong verbal and written communication skills.
  • Experience with cell type classification
  • Fluency programming in R and/or Python.
  • Strong organizational skills.

Preferred Education and Experience

  • Experience analyzing high-throughput transcriptomics or epigenetics data.
  • Fluency with GitHub (or other version control system).
  • Experience in website design or other visual arts.
  • Experience with machine learning techniques.
  • Proven independent thinking.
  • Strong publication track record.
  • Strong statistical background.
  • Ability to work in a collaborative environment.

Physical Demands

  • Fine motor movements in fingers/hands to operate computers and other office equipment; lab equipment

Position Type

  • This position is funded through a grant awarded by the NIH.
  • This role is currently working remotely due to COVID-19 and our focus on employee safety. We continue to evaluate the safest options for our employees. As restrictions are lifted in relation to COVID-19, this role may return to work onsite.

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

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