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Bioinformatics Analyst I Ė Brain Science

Department: Molecular Biology

Bioinformatics Analyst I Ė Brain Science

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 Brain Science is to accelerate the understanding of how the human brain works in health and disease. Using a big science approach, we generate useful public resources, drive technological and analytical advances, and discover fundamental brain properties through integration of experiments, modeling and theory.

This position is an entry level position within the Bioinformatics Core Team (BI Core) of the Molecular Biology department, which is an integral part of the Cell Types research program at the Allen Institute for Brain Science. Primary responsibilities of this position include processing and QC of sequencing data.

This individual will work closely with PhD-level scientists, both in the lab and on the computational data analysis teams in support of various projects. Each project requires specifically tailored analysis tools and data visualization.

This position requires a strong beginnerís background in computer science, experience with coding, some background in biology and/or chemistry, and a desire to work in a fast-paced team environment on large scientific 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 initial QC of sequencing data
  • Optimize data processing pipelines developed in R/Python and automate the manual steps in the pipeline
  • Design and develop software tools and methods to facilitate data analysis and visualization for various projects using RShiny
  • Support workflow of both lab scientists and secondary analysis teams
  • Understand basic genomic data formats such as fastq files, BAM/SAM, GTF etc.
  • Follow good coding practices (SDLC) and work with version control systems (git)
  • Assist other staff as necessary
  • Ability to work in a fast-paced environment
  • Willingness to cross-train and perform other duties as assigned

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 Life Sciences, computer science or related field
  • Experience in genomics data visualization tools
  • Some knowledge of statistics
  • Previous experience in processing and analyzing sequencing data
  • Understanding of single cell genomics data processing pipelines
  • Experience with Unix
  • Experience with R, Python and Shell scripting languages
  • Experience with relational database and structure query language (SQL)

Preferred Education and Experience

  • 0-2 years related experience with scientific computing (Python, R and shell script preferred)
  • Experience with High Performance Computing systems
  • Understanding of sequencing protocols and applications
  • Experience processing and analyzing single cell RNA-Seq data and/or ATAC-Seq data
  • Experience optimizing single cell analysis pipelines
  • Experience with relational databases (eg postgreSQL)
  • Experience with Docker
  • Experience with workflow management tools like Cromwell, Nextflow and Snakemake
  • Experience using cloud platforms (AWS, GoogleCloud) for genomic data analysis
  • Detail oriented / analytical mindset
  • Exceptional attention to good coding practices
  • Excellent interpersonal and communication skills
  • Demonstrated ability to work collaboratively within cross-functional teams

Work Environment

  • Working at a desk in an office or lab setting

Physical Demands

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

Position Type/Expected Hours of Work

  • 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

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

Additional Comments

  • **Please note, this opportunity does not sponsor work visas **

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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