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Scientist II - Analysis of cell-type specific interactions during learning

Department: Neural Circuits and Behavior

Scientist II – Analysis of cell type-specific interactions during learning


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 MindScope program seeks to understand the transformations, sometimes called computations, in coding and decoding that lead from photons to behavior and conscious experience by observing, perturbing, and modeling the physical transformations of signals in the cortical-thalamic visual system within a few perception-action cycles.

We are seeking a Scientist to be an essential member of a team investigating the functional role of genetically defined cell types in learning and behavior. The primary role of this Scientist will be to perform computational analysis of image-based transcriptomics datasets in order to map identified cell types to their functional properties measured in vivo. This Scientist will work closely with other Scientists, Engineers, and Technicians to guide experimental design, analyze and interpret large-scale multi-modal datasets, and to contribute to the development of standardized, open-source workflows for data processing and analysis (such as the AllenSDK and starfish).

The ideal candidate will have strong computational and programming skills, experience working with transcriptomic data and/or microscopy, and an interest in understanding cell type-specific circuit function in the context of learning and behavior. As part of a highly collaborative team environment, good communication and enthusiasm for working with, learning from, and teaching others is essential to this role.

The datasets and tools created as part of this project will be publicly released as an open resource for the community, in line with the Allen Institute’s core principles of big science, open science, and team science.

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

  • Work as part of a multi-disciplinary team to integrate transcriptomic and physiological datasets
  • Apply machine learning and other statistical methods to large-scale datasets and interpret results
  • Contribute to and lead experimental design by performing analyses to facilitate data-driven decisions
  • Manage relevant aspects of the project and effectively coordinate with other team members
  • Publish findings in peer-reviewed journals and present at scientific conferences

Required Education and Experience

  • PhD in Neuroscience, Computational Neuroscience, Bioinformatics, Bioengineering, Computer Science, or related field, or an equivalent combination of degree and experience
  • Minimum 3 years of relevant work experience
  • Demonstrated advanced computational and data analysis skills
  • Strong Python programming experience
  • Excellent organizational and interpersonal skills
  • Ability to manage time and complete tasks to meet deadlines
  • Enthusiasm for working collaboratively as part of a team

Preferred Education and Experience

  • PhD and 5 - 7 years of experience in computational neuroscience, bioinformatics, or a related field
  • Hands-on experience generating or analyzing transcriptomic data
  • Experience with microscopy, histology, image processing, or image registration
  • Experience applying machine learning methods to neuroscientific data
  • Experience contributing to shared or open-source codebases
  • Experience producing informative data visualizations

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 remotely due to COVID-19 and our focus on employee safety. We are a Washington State employer, and remote work must be performed in Washington State. We continue to evaluate the safest options for our employees. As restrictions are lifted in relation to COVID-19, this role will return to work onsite

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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