Job Opportunity: Assistant Investigator - Allen Institute for Brain Science, Seattle, Washington

Kim Petrie
December 7, 2016

The Allen Institute for Brain Science, located in Seattle, Washington, is comprised of a multidisciplinary staff committed to understanding how the brain works and helping to unlock the mysteries of neurological diseases and disorders affecting millions worldwide. Serving the scientific community is at the center of our mission to accelerate progress toward understanding the brain and neurological systems.  The Institute is embarked on a 10-year mission to discovery underlying principles of cortical organization, circuitry and function.  A key part of that mission is to advance our understanding of detailed cortical circuitry by characterizing and classifying the cell type components that comprise the building blocks of these circuits in both mouse and human cortex.   

The candidate will act as a lead scientist in developing a classification effort toward understanding the organization of cell types in the neocortex, building on and guiding the use of a set of in-house high-throughput quantitative single cell phenotyping pipelines applied to the mouse and human cortex.  This is a multidisciplinary project requiring knowledge of the principal data types used for quantitative single cell analysis in modern neuroscience, including single cell transcriptomics, electrophysiology, dendritic and axonal morphology and cell type-specific synaptic connectivity. By applying techniques from computer science, machine learning, and ontology development, and through a strong interfacing with key experimentalists, this investigator will play a strong role in generating a computational framework for discretizing the cell types of the cortex to create a cellular ontology, deriving probabilistic multimodal representations and testable hypotheses about the biological relevance of these types, and identifying conserved and divergent features between mouse and human. 

This is a Principal Investigator position similar to an Assistant Professor in a University/Medical School setting.  The successful candidate will have demonstrated research productivity and is in early stages of defining and implementing an independent research program.  The candidate should have publications in relevant peer-reviewed scientific journals.   


  • Establish a group for the development of analysis and classification strategies for cell types and their ontologies in the cortex.
  • Develop technical methodologies for the quantitative characterization of cell types in the mouse and human cortex based on in-house data generation pipelines, and the correspondence between these data types.
  • Advise and mentor a group of scientists in developing these quantitative methods.
  • Compare cell type models with in-house and external primary data from transcriptome, electrophysiology, morphological and other modalities for accuracy.
  • Seek and evaluate new cutting-edge techniques in related areas.
  • Publish and present findings in peer-reviewed journals and scientific meetings.
  • Work with other in-house key stakeholders in the development of classification and ontology schemas.
  • Present a periodic summary of progress to the research community.


  • Ph.D. in a computational neuroscience or biology, physics, engineering, or related computational discipline.
  • 5-10 or more years of post-PhD working experience in computational neuroscience with interest in the cell type problem.
  • Experience and technical knowledge of neuroscience, modeling, and machine learning paradigms, with supporting publication record.
  • Exceptional knowledge of quantitative clustering algorithms and/or ontological/phylogenetic tree building.
  • Strong knowledge of systems, cellular and molecular neuroscience.
  • Strong written and verbal communication skills.
  • Ability to meet aggressive timelines and deliverables
  • Excellent management skills and ability to work in a group and interact closely with experimentalists.

Education and/or experience 

Doctoral degree (Ph.D.) or equivalent; 5-10 or more years of post-PhD research experience; or equivalent combination of education and experience.


This position requires the manual dexterity sufficient to operate phones, computers, and other office equipment.  This person must speak clearly using the English language to accurately convey information and be able to hear at normal speaking levels both in person and over the telephone.  

Generally good working conditions with little or no exposure to extremes in noises, temperature.  Little or no safety or health hazards.   Minimal lifting or climbing; work performed in an office setting.