Bioinformatics Intern - CompBio Operations

Bioinformatics Intern - CompBio Operations

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.

The Allen Institute for Immunology is seeking a Bioinformatics Intern to help develop and maintain standardized computational workflows and analyze our pipeline data in support of our broad immunology research projects. The ideal candidate is a self-motivated team player, is a good organizer and communicator, pays close attention to details, and has experience analyzing next-generation sequencing data. The position will collaborate with wet-lab scientists, bioinformaticians, and software developers to ensure implementation and execution of robust and efficient data analysis processes that enable faster biological discovery and facilitate data accessibility. 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 omics data analysis.

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

The Bioinformatics intern will have the opportunity to engage in both deep biological interrogation and computational tool development which may include:

• Implementing new computational methods by writing end-to-end reproducible pipelines for omics data analysis to enable viewing the immune system through many different lenses (data types) and at multiple time points, creating a more complete picture of the immune system in different contexts
• Updating the single cell data processing pipeline by improving and standardizing cell type labeling methods to resolve cell identities as well as interrogate shared and tissue-specific expression modules and cell states
• Building innovative data dashboards to visually track QC metrics for spatial transcriptomic data over time to assist wet lab scientists in making our spatial biology platform more robust and efficient
• Contributing to standardized data processing and analysis for numerous projects across immunology
• Learning to read both computational methods and immunology literature critically and incorporate findings into analysis
• Learning to write clean, reproducible and documented code in a collaborative setting using GitHub version control and code reviews
• Communicating progress and findings to relevant teams within the Allen Institute for Immunology

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

• Currently enrolled in the MS program in Bioinformatics and Genomics at University of Oregon, or in an equivalent MS program
• Hands-on experience in analyzing high throughput sequencing data (RNA-seq, ATAC-seq, DNA-seq, etc.)
• Fluency in Python, R, linux operation system, and shell scripting

Preferred Education and Experience

• Familiarity with single-cell technologies and literature
• Demonstrated experience in writing code for omics data analysis
• Experience creating interactive data visualizations
• General experience in molecular biology, immunology and high-throughput wet lab technologies
• Working knowledge of cloud computing and version control systems such as Git
• Excellent written and verbal communication skills and organizational skills
• The successful candidate must be self-motivated, a quick learner, a team player, and attentive to details

Work Environment

• Open office seating
• 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; lab equipment
• 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 2025 to January 2026)
• 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**

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.

Salary : $36