Postbaccalaureate Research Assistant – Immunology / Spatial transcriptomics for tissue immunology

Postbaccalaureate Research Assistant – Immunology / Spatial transcriptomics for tissue immunology

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 Immunology is to advance the fundamental understanding of human immunology through the study of immune health and diseases where excessive or impaired immune responses drive pathological processes. The Institute will employ a multi-disciplinary team approach in collaboration with academic centers of human immunology to generate novel mechanistic insights into the immune synapse in health and in diseases such as autoimmunity or oncology. The Institute will simultaneously provide a foundational data set and tools for future immunological research as well as a novel collaboration portal for the broader scientific community.

At the Allen Institute for Immunology, we are investigating the cellular organization that underlies immune function, both at steady state and during active responses. Towards this aim, we are applying spatial transcriptomics methods to characterize cell states and gene expression in a range of healthy human tissues.

We are seeking a Postbaccalaureate Research Assistant to join ongoing efforts in the Computational Biology group to analyze and interpret spatial transcriptomics datasets, with the opportunity to engage in both deep biological interrogation and computational tool development, including:

• Expand upon existing computational frameworks within the group to detect cell types and gene expression gradients with respect to key anatomical structures in human tissue spatial transcriptomics data
• Run statistical tests to determine if these metrics vary across samples according to age and tissue type
• Work on computational method development goals, such as aligning gene expression data (spatial transcriptomics) with protein staining data (immunofluorescence) for integrated analysis

Through this work, the candidate will learn to perform and interpret data quality control, characterize immune cells at the single-cell level, study the spatial associations of cells and genes, and be challenged to develop a systems-level understanding of key immune processes as they unfold across different tissues. This role will provide opportunities to contribute to publications and to internal computational pipeline development that would involve writing end to end reproducible workflows for spatial data analysis. Overall, these projects will help the candidate build computational skills while engaging in the rapidly growing field of spatial transcriptomics.

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.

Applications must be received by January 7, 2025, to be considered.

Educational Objectives

This is a fully computational project focused on spatial transcriptomics analysis applied to complex immunology questions. Prior coding experience in Python and R and familiarity with single-cell omics analysis is desired.

Key learning objectives include:

• Develop a general understanding of existing single cell omics analysis techniques and their application to biological questions
• Gain proficiency in spatial transcriptomics analysis with an awareness of key challenges (for example, cell segmentation, cell type labeling, spatial domain identification)
• Learn how to leverage spatial transcriptomics data to address immunology questions focused on cell interaction and spatial organization
• Learn to read both computational methods and immunology literature critically and incorporate findings into analysis
• Learn to write clean, reproducible and documented code in a collaborative setting using GitHub version control and code reviews
• Communicate progress and findings to relevant teams within the Allen Institute

Required Education and Experience

• Bachelor’s degree
• Demonstrated commitment to science
• Ability to code in Python (preferred) and/or R, demonstrated by project or course work
• Exposure to single-cell omics analysis

Work Environment

• May enter laboratory environment - possible exposure to chemical, biological, or other hazardous substances.

Physical Demands

• Fine motor movements in fingers/hands to operate computers and other office equipment

Position Type/Expected Hours of Work

• Occasional evening and weekend hours required
• 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

• Completed a bachelor’s degree (or will have completed by the start of the program) and does not have an advanced degree in the role’s relevant STEM field
• Must be able to start in June or July 2025 and commit to the full one-year program, which will end on Friday, May 29, 2026
• Must be eligible to work in the U.S. for the program duration
• Must be 18 years of age or older

Additional Comments

• Postbacs are expected to participate as fully-engaged team members, attending and participating in team meetings, presenting on their work, etc.
• Aside from program activities, postbacs are expected to work full-time as regular team members unless otherwise approved by their manager
• **Please note, this opportunity offers relocation and housing assistance**
• **Please note, this opportunity requires U.S work authorization and does not sponsor work visas**

Annualized Salary

• $59,280 (non-negotiable)

Benefits

• Postbacs (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 Institutes 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.