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Data Analyst I - Molecular Genetics

Department: Molecular Genetics

Data Analyst I Ė Imaging analysis Ė 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.

The Genetic Tools team within the Molecular Genetics department at the Allen Institute for Brain Science generates high-precision genetic tools to effectively identify, monitor, and manipulate distinct cell types within the mouse brain. These viral and transgenic tools enable the analysis of the structure and function of neural circuits and represent foundational resources for the neuroscience community.

We seek an exceptional individual who will contribute to our newly established Institute pipeline by analyzing whole brain transgene expression and spatial transcriptomics data in mouse and nonhuman primate. This effort is funded by a newly awarded BRAIN UF1 grant from the NIH, which aims to generate an open-access AAV toolbox for Basal Ganglia cell types and circuits.  The candidate will be a B.S. or M.S. graduate in computational biology or a relevant technical discipline and will possess strong computational skills.

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 and interpret spatial transcriptomics (RNAscope or equivalent mFISH technology) cross-species data to evaluate the specificity of viral tools and completeness of labeling
  • Analyze and interpret whole brain transgene expression data (serial two-photon tomography and/or light sheet fluorescence microscopy) to validate viral tools
  • Support imaging analysis pipeline by performing quality control analyses and working closely with stakeholders and relevant cores involved in data acquisition
  • Create complex visualizations (e.g. 3D brain renderings, interactive web apps, dashboards, fly-through videos)
  • Manage the imaging experimental workflow
  • Generate figures for manuscripts, grants, and internal progress reports
  • Present work regularly to internal stakeholders and the external community

Note: Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions. This description reflects managementís assignment of essential functions; it does not proscribe or restrict the tasks that may be assigned.

Required Education and Experience

  • Bachelorís degree in computational biology, bioengineering, applied math, or equivalent
  • Proficiency in command line development tools in a Linux environment
  • Proficiency in scientific computing and visualization in Python and/or R
  • Experience in image analysis methods to extract quantitative information

Preferred Education and Experience

  • Masterís degree in a relevant technical discipline
  • 2 years of applicable experience
  • Experience analyzing biological datasets
  • Knowledgeable about neuroanatomy and brain architecture
  • Knowledgeable about mouse genetics and genome engineering methods
  • Knowledgeable about image registration to a common coordinate system
  • Working SQL knowledge and experience in relational databases
  • Proficiency in additional programming languages and tools (C++, Matlab, SQL, git)
  • History of contributing to open source and/or team-based project
  • Ability to work in a team environment to design, implement, and support novel software tools for scientific data analyses
  • Positive attitude, self-motivated, and ability to trouble-shoot
  • Exceptional oral and written communication and organizational skills

Physical Demands:

  • Fine motor movements in fingers/hands to operate computers and other office equipment
  • Occasional stooping, bending, crouching

Position Type/Expected Hours of Work

  • This role is currently working remotely with occasional onsite work 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 does not sponsor work visas **
  • **Please note, this opportunity offers relocation assistance**


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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