Scientist I - Human Spatial Transcriptomics / Imaging

Scientist I – Human Spatial Transcriptomics/Imaging

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.

Our team is embarking on a novel and ambitious effort to characterize mammalian brain cell types using multiple single cell data modalities, including scRNAseq and Spatial Transcriptomics. These modalities will be integrated to create comprehensive and unprecedented maps of human and nonhuman primate brains. This scientist position would work with extensive spatial transcriptomics datasets to create and analyze maps of transcriptomically-defined cell types in human brain specimens in health and Alzheimer’s disease and will evaluate, benchmark and implement novel software packages for the analysis of these data. This role will work collaboratively with other computational biologists to develop new analysis approaches and software packages to complete this work. The tools needed to generate knowledge from these datasets will be invented and tested by the Allen Institute team and this scientist position will require expertise and experience in scRNAseq analysis, machine learning applications to transcriptomics analysis (i.e., Classification algorithms and Variational Autoencoders ), proficiency with bash/Linux, HPC experience and the ability to work with and analyze large datasets. This scientist would work closely with Imaging department scientists and research associates as well as an interdepartmental team dedicated to investigating the effects of Alzheimer’s disease on the cellular structure of the human brain.

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

• Evaluate and analyze Spatial Transcriptomics/MERFISH datasets derived from human brain tissue to identify molecularly-defined cell types and their relationships
• Perform dimensionality reduction and label transfer methods to integrate scRNAseq and spatial datasets, characterize spatial relationships of cells and compare across individuals and disease progression
• Provide an assessment of statistical significance for comparative studies of cell and tissue changes across disease states, brain regions and species
• Regularly communicate findings to collaborators, the Imaging Department and the Institute regarding key insights, findings and questions derived from data analysis
• Interact with scientists from diverse backgrounds and perspectives to design analytical approaches and refine computational strategies

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.

Required Education and Experience

• PhD degree in computational biology, bioinformatics, neuroscience, applied mathematics, or related field, or equivalent combination of degree and experience
• Experience in computational analysis and statistical assessment of biological datasets, spatial statistics, scRNASeq analysis, Spatial Transcriptomics, computational anatomy or related fields
• Expertise in scientific computing and analysis using Python and/or R, and Bash/LINUX, HPC utilization.

Preferred Education and Experience

• Familiarity with image processing
• Knowledge of human neuroanatomy and neurodegenerative disease processes

Work Environment

• May enter laboratory environment, including potential exposure to lasers, biohazards

Physical Demands

• 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 both remotely and onsite in a hybrid work environment. We are a Washington State employer, and the primary work location for all Allen Institute employees is 615 Westlake Ave N.; any remote work must be performed in Washington State.

Additional Eligibility Qualifications

• To be considered - complete your application including the following:
  • CV/resume with your current work, education, and research experience
  • 2 Letters of Recommendation
  • Cover Letter that includes: a personal statement describing your interest in Allen Institute for Brain Science and specifically this role; including how this opportunity will be meaningful to you and your career.

Additional Comments

• **Please note, this opportunity offers relocation assistance**
• **Please note, this opportunity offers work visa sponsorship**

Annualized Salary Range

• $75,003 - $105,004 *

• Final salary depends on required education for the role, experience, and level of skills relevant to the role, along with work location, where applicable.

Benefits

• Employees (and their families) are eligible to enroll in benefits per eligibility rules outlined in the Allen Institute’s Benefits Guide. These benefits include medical, dental, vision, and basic life insurance. Employees are also eligible to enroll in the Allen Institute’s 401k plan. Paid time off is also available as outlined in the Allen Institute’s Benefits Guide. Details on the Allen Institute’s benefits offering are located at the following link to the Benefits Guide: https://alleninstitute.org/careers/benefits.

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.