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Scientist I/II – Spatial Transcriptomics Analysis

Department: 2300-Structured Science
Location: Seattle

Scientist I/II – Spatial transcriptomics analysis

The Allen Institute for Brain Science is seeking an exceptional candidate who will be part of a Seattle-based multidisciplinary team within the Cell Types Program. The successful candidate will be a member of the Imaging team and the multiplexed fluorescence in situ hybridization (mFISH) pipeline for large-scale spatial transcriptomics data generation from primary mouse and human brain tissue. The mFISH project intersects with many projects within the Institute with the goal of defining the type, number, distribution, and correspondence of cell types within the mouse and human brain. 

This role will focus on analysis of image and bioinformatics data from the mFISH pipeline.  These results will yield key spatial transcriptomics results as well as continual improvements of the mFISH pipeline operations.  The role will interact directly with other members of the mFISH pipeline team and with bioinformaticians, data analysists, and modelers throughout the Institute to provide expert advice and data interpretation.  She/he will provide expert advice related to spatial transcriptomics for other projects and future Allen Institute products. 

The candidate will have a Ph.D. in neuroscience, bioinformatics, biomedical engineering, mathematics, or a related field. She/he will possess demonstrated knowledge of spatial transcriptomics, image analysis, and bioinformatics.

Job Responsibilities

  • Analyze, interpret, and synthesize results from spatial transcriptomics data to yield novel scientific results and aid in the design of follow-up experiments
  • Interface and collaborate with Institute and external scientists, providing expert interpretation and advice on spatial transcriptomics data and results
  • Provide data-driven advice and implementations for process improvements for spatial transcriptomics pipeline operations
  • Write and publish manuscripts, and internal and external progress reports
  • Present work internally and externally at conferences

Required Qualifications

  • Ph.D. in physical sciences, mathematics, or engineering (neuroscience, bioinformatics, image analysis, or related field)
  • Demonstrated knowledge of spatial transcriptomics and image analysis

Preferred Qualifications

  •    Experience with multiplexed FISH or other image-based spatial transcriptomics methods
  •    Experience in neuroscience or neuroanatomy
  •    Experience with programming in Python and/or R languages and with Linux operating systems
  •    Exceptional oral and written communication skills
  •    Demonstrated abilities in conveying complex scientific results through data visualizations
  •    Ability to work independently as well as part of a team to meet aggressive timelines in a collaborative environment

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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