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Bioinformatics Analyst I - Immunology

Department: Bioinformatics

Bioinformatics Analyst I - 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.

The Allen Institute for Immunology is seeking a Bioinformatics Analyst to develop processing and analytical pipelines for spatial transcriptomics and imaging data. The ideal candidate is a self-motivated team player who can work closely with experimentalists and bioinformaticians to analyze spatial technology data and other molecular omics data, implement and streamline in-house or open-source analysis pipelines, and provide solid bioinformatic support to institute research projects.

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

  • Perform hands-on analysis of clinical and molecular omics data, including but not limited to spatial transcriptomics data and imaging data
  • Develop and standardize processing and analytical pipelines for spatial transcriptomics data and imaging data
  • Implement and streamline in-house or open-source analysis pipelines including quality control and data mining for spatial transcriptomics data
  • Support wet-lab scientists on technology enhancement and development
  • Meet production deadlines for data analysis and be able to pivot between multiple projects
  • Be flexible to take on new challenges when needed
  • Contribute to a rigorously scientific, cohesive and efficient team environment

Note: Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions. This description reflects managementís assignment of essential functions; it does not proscribe or restrict the tasks that may be assigned.

Required Education and Experience

  • Bachelorís degree in Bioinformatics or closely related discipline

Preferred Education and Experience

  • 0 - 2 years of equivalent experience
  • Hands on experience analyzing high throughput RNA-seq data, NGS data or proteomics data
  • Track record of implementing analysis pipelines for omics data
  • Fluency in R, Python/Perl, Linux operation system, and shell scripting
  • Excellent written and verbal communication skills and organizational skills
  • Experience in bioinformatics research or technology development
  • Experience with single-cell sequencing data
  • Experience with spatial transcriptomics or imaging data
  • Experience with JAVA and GUI development
  • Experience in collaboration with web-lab scientists on technology development
  • Knowledge in high-throughput technologies and immunology
  • Working knowledge of cloud computing and version control systems such as Git

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

  • Occasional evening and weekend hours required
  • This role is currently working onsite and is expected to work onsite for the majority of working hours. The primary work location for this role is 615 Westlake Ave N., with flexibility to work remotely on a limited basis.


  • Occasional travel may be required
  • Attendance and participation in national and international conferences may be required

Additional Eligibility Qualifications

  • In keeping with our focus on employee safety, all employees must be fully vaccinated against COVID-19 as a condition of employment unless a medical or religious exemption is approved. All employees will be required to keep their vaccination status up to date according to CDC guidance and our policy.

Additional Comments

  • **Please note, this opportunity offers relocation 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.





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