The mission of the AllenInstitute is to understand the principles that govern life and to advance health. Our creative and multi-dimensional teams focus on answering some of the biggest questions in bioscience. We accelerate foundational research, catalyze bold ideas, develop tools and models, and openly share our science to make a broad, transformational impact on the world.
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.
Investigating alternative splicing and clonal expansion in the normal immune system
Using data from the long-read RNA-seq, this project will investigate clonal expansion and somatic mutations in multiple dimensions. Using long-read sequence data from a bulk analysis of bone marrow (BM) and peripheral blood mononuclear cells (PBMCs) will allow us to identify germ line SNPs. Having established an individual map over germline encoded SNPs, we can search subpopulations of cells, or even single cells to identify additional mutations that has been acquired at some time during the life of the individual (somatic mutations). Having data from both BM and PBMCs should allow us to trace somatic mutations from early progenitors in the BM into the peripheral immune system. The data generated from normal cells can also be combined with existing data from multiple myeloma cells to explore the propagation of somatic mutations in the transformed cells. The long-read sequencing data should also identify BCR/TCR receptor sequences in both blood and BM allowing for an extensive analysis of clonal expansion of lymphoid cells in both the BM and in the periphery. It will be used to develop new analysis tools that can be explored in future projects and generation of AI based models for gene regulation. The project aims are highlighted below, with the expectation of contributing toward at least one of these.
• Aim 1: Study patterns of alternative splicing and alternative starting sites across healthy immune cell types using long read scRNA-seq data and potentially scATAC-seq data to identify alternative starting sites.
• Aim 2: Study allele-specific transcription and link it to polymorphisms in promoter and/or enhancer sites. In addition to imputations to long-read scRNA-seq data, we may also analyze scATAC-seq data to identify polymorphisms in promoter and/or enhancer sites.
• Aim 3: Identify BCR/TCR receptor sequences associated with expanded clones of lymphoid cells.
• Aim 4: Identify somatic mutations associated with expanded clones of immune cells. In addition to long read scRNA-seq data, we may also analyze scATAC-seq data to identify expanded clones of immune cells.
At the Allen Institute, we believe that science is for everyone – and should be open to everyone. We are dedicated to combating biases and reducing barriers to STEM careers more broadly.
We also believe that science is better when it includes different perspectives and voices. We strive to make the Allen Institute a place where everyone feels like they belong and are empowered to do their best work in a supportive environment.
We are an equal-opportunity employer and strongly encourage people from all backgrounds to apply for our open positions.
Educational Objectives
After completing an internship, we hope you will come away with the following experience:
• An understanding of human immune health and disease
• An understanding of the principles behind cutting edge single cell technologies
• Experience working with a cross-functional team structure including scientists, bioinformaticians and software developers
• Development of new data analysis and/or visualization tools within the context of a large, multimodal data analysis platform
Technical Objectives
We hope that an intern may be able to bring some of these skills to this position. However, we recognize that this is a learning experience, and will provide training and resources to expand on an intern's existing skillset.
• Write scripts in Python or R
• Use Jupyter Notebook environments to perform and explore data analysis methods
• Use Git and Github for version control
• Perform analysis with command-line scripting and tools
• Use Linux/Unix-like systems for data analysis
Required Education And Experience
• Currently enrolled in the Bioinformatics and Genomics Master’s Program at University of Oregon, or in an equivalent Master’s degree program
Work Environment
• Open office seating
• May enter laboratory environment, including potential exposure to lasers, biohazards
Physical Demands
• Working at a computer and using a mouse for extended periods of time
Position Type/Expected Hours of Work
• This is a full-time role for the duration of the internship (9 months, April 2026 to January 2027)
• This is a Monday through Friday, regular business hours position
• 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 Comments
• **Please note, this opportunity offers relocation assistance**
• **Please note, this opportunity requires U.S work authorization and does not sponsor work visas**
Compensation
• $35.58 per hour plus benefits and travel and/or housing stipend
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 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.
