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Bioinformatics Analyst II – High Throughput Single Cell Transcriptomics

Allen Institute for Immunology
Seattle, WA

The recently-launched Allen Institute for Immunology is seeking outstanding individuals with expertise in bioinformatics and biostatistics applied to high throughput single-cell RNA-sequencing.

The institute is launching a series of collaborations focused on understanding the behavior of the immune system in autoimmune diseases and cancer. We are therefore especially interested in individuals with a background in human immunology. For details of the Institute’s research plans and partners, see

The Allen Institute offers exceptional working conditions, and nurtures diversity and team-science in an intellectually rich and stimulating setting.

We will start reviewing applications and interviewing candidates immediately and will continue until all positions are filled.

Required Qualifications

  • Master’s degree or Bachelors degree plus 2 additional years of professional experience in bioinformatics, biostatistics, computational biology or related disciplines.
  • Minimum 2 years related post-graduation experience.
  • Fluency in R and/or Python, and shell scripting.
  • Working knowledge of version control systems such as Git.
  • Training in high-throughput single cell transcriptomic assays.
  • Training in molecular biology, high-throughput technologies, and immunology.
  • Strong track record of using contemporary bioinformatic tools, and hands on tool/pipeline development expertise.
  • Proven experience with high throughput data analysis.

Preferred Qualifications

  • Experience in integrative analysis of single cell and bulk data.
  • Experience in integrative analysis of multiple data modalities.
  • Experience in data visualization, dimensionality reduction and related methods.
  • Ability to develop, test, implement, and share new computational tools quickly, in an iterative manner, after feedback from experimental, data production, and analysis teams.
  • Experience studying human immunology.
  • Exceptional oral and written communication skills.
  • Ability to work independently as well as part of a team.
  • Demonstrated ability to track and meet goals and milestones across multiple projects.

Desirable General Abilities

  • Excellent written and verbal communication skills.
  • Demonstrated ability to document work accurately and precisely.
  • Strong organizational skills and careful attention to detail.
  • Able to work independently as well as in a collaborative high paced environment.
  • Experience working in a cross disciplinary, team-based environment.
  • Experience working with outside collaborators to achieve defined objectives.


  • Working at computer and using mouse for extended periods of time.
  • Travel Required: 3 – 6 trips per year.
  • May need to work outside of standard working hours at times.

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.

For more information, contact Jeannelle Roth at