Scientist I - Spatial Transcriptomics Analysis - Imaging
Location: Seattle, Washington
Required Education: Doctorate/Professional
Employer will assist with relocation costs.
The mission of the AllenInstitute 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 AllenInstitute 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
The Allen Institute for Brain Science is pursuing in-depth mapping of molecular cell types in the brain and the Imaging Department is recruiting a Scientist to analyze spatial transcriptomics data. The Imaging Department is a group of ~20 scientists and research associates using widefield, confocal, 2-photon, and light-sheet microscopes to support many projects. As a central focus of the department, spatial transcriptomics methods are now generating data at high rates and this Scientist will help translate this data into novel biological insight about the organization of cell types in the brain.
As part of this interdisciplinary team, you will develop analysis software to integrate gene expression at the single-cell level, molecular cell type identity and anatomical organization across multiple structures in the brain. To accomplish this, you will benchmark existing spatial analysis methods, create novel approaches of synthesizing spatial gene expression data from multiple experiments and develop methods for spatial parcellation of brain tissue based on cell types and gene expression. Initial work will focus on the mouse thalamus and subsequent projects will expand to include other areas of the brain and other species.
We anticipate two areas of experience will be useful for fulfilling this role: experience analyzing spatial transcriptomics data (MERFISH, in-situ sequencing, seqFISH, etc.), or experience with quantitative spatial analysis from computational biology, spatial statistics, image processing or related fields combined with a willingness to explore a new type of biological data.
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.
Research and benchmark existing spatial analysis methods for integrating spatial transcriptomics data in anatomical context
Develop new spatial analysis methods for registering and merging data across experiments and anatomical structures to reveal novel parcellations and the spatial organization of gene expression
Provide actionable feedback and interaction in a scientific team environment, including regular discussions on data collection, QC and pipeline engineering
Effectively communicate findings across the institute as well as to the greater scientific community in peer-reviewed journals, scientific conferences, and web documentation
Develop scientific software tools with clear documentation and good source code management
Note: Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions. This description reflects management’s assignment of essential functions; it does not proscribe or restrict the tasks that may be assigned.
**Please note, this opportunity offersrelocation 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.
Required Education and Experience
Ph.D. in computational biology, neuroscience, physics, applied mathematics, or related field, or equivalent combination of degree and experience
Experience in spatial statistics, scRNASeq analysis, computational anatomy or related fields
Preferred Education and Experience
Experience with analysis of spatial transcriptomics data in the brain
Understanding of transcriptomically-defined neuronal cell types from scRNASeq data
Experience with modern image processing, especially machine learning for large microscopy datasets
3-5 years experience in scientific computing in Python and Linux/UNIX environment
Contributions to open-source software projects, including source code management and documentation
Strong written and verbal communication skills
Fine motor movements in fingers/hands to operate computers and other office equipment; repetitive motion with lab 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 in a hybrid work environment.
Additional Eligibility Qualifications
In keeping with our focus on employee safety, all employees must be up to date with vaccinations against COVID-19 as a condition of employment unless a medical or religious accommodation is approved. All employees will be required to keep their vaccination status up to date according to CDC guidance.
Founded in 2003 by Paul G. Allen, The Allen Institute is fiercely committed to solving some of the biggest mysteries of bioscience, researching the unknown of human biology, in the brain, the human cell, and the immune system. At the same time, we are pushing the frontiers of bioscience to continue to explore the edges of scientific discovery.