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Software Engineer: Lead Single Cell Genomic Data Analyst

University of Washington, Genome Sciences, Brotman Baty Institute
Job Location
University of Washington, Department of Genome Sciences, Brotman Baty Institute
Seattle, WA 98195
United States
Commensurate with experience

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Job Description

The Department of Genome Sciences currently has an outstanding opportunity for a SOFTWARE ENGINEER.

Position purpose:
The purpose of the BAT-lab Analysis Team is to train BBI member labs in currently available single cell informatics in order to glean biological insights from the data generated by the BAT-lab. In addition, the team will continue to develop novel algorithms to integrate and visualize data across projects, tissues, time courses, etc. The BBI anticipates the capacity to generate additional datasets including single-cell chromatin accessibility profiling and co-assays as appropriate for specific projects. As a Lead Single Cell Genomic Data Analyst for BAT-lab Analysis team the candidate would be responsible for:

Software Engineering and Data Analysis: 85%

  • Optimizing and maintaining the data processing pipeline (either in the cloud or on UW Genome Sciences servers) that will mesh with BAT-lab sample tracking.
  • Developing analytic and/or visualization tools for a cohesive single cell atlas.
  • Managing a junior analyst.
  • Holding office hours with individual single cell collaborators to guide data analyses.
  • Holding video or in-person training workshops to teach collaborators how to use single cell analysis software tools. (i.e. Developing workshops for the BBI Single Cell Symposia and smaller training sessions).
  • Use BAT-lab project management tools.
  • Be open to the eventual management of more employees.
  • Attend conferences to keep up with the field.

    Lab Meetings: 10%
  • Attend Trapnell and/or Shendure lab meetings and BAT-lab huddles.

    Publications: 5%
  • Even though the BATLab Platform is a service, any BBI collaborative project with excessive hand-holding for data analysis will include the software engineer as an author. The software engineer’s contributions will be recognized not only in Seattle by the BBI community but nationally and internationally, as he/she will have ample opportunities to lead publications describing new data analysis or visualization tools as well as to attend/present at conferences. We anticipate this role has growth potential analogous to that of Institute Scientists at the Broad Institute many of whom are well recognized leaders in their field.
  • You would communicate results and progress directly to Dr. Lea Starita and Dr. Jay Shendure. You would participate in Shendure and Trapnell lab meetings to help maintain communications between the BAT-lab and their groups. The software engineer will also communicate with Dr. Cole Trapnell regarding new analyses and pipeline work. The software engineer will spend time at UW in the H-wing to work with the BAT-lab, Genome Sciences for lab meetings, and hold office hours at Seattle Children’s Research Institute and Fred Hutch.
  • As an early member of the BAT-lab, you will have the opportunity to shape that lab’s organization and culture, as well as that of the BBI more generally. The BAT-lab has a large budget and broad institutional support which will help us achieve maximum success. We expect that the single cell projects and your contributions will be recognized not only in Seattle by the BBI community but nationally and internationally.

Minimum requirements:

  • Ph.D. in genomics, computational biology, or related field.
  • At least four years relevant experience in software development for genomics.
  • Candidate should have outstanding academic and professional track record.
  • Candidate should be an analytical thinker with outstanding interpersonal and communication skills. Must be highly disciplined and organized.
  • Candidate should be enthusiastic about outreach to the local research community
  • Successful candidate will be highly self-motivated and eager to a hands-on approach to collaborative scientific discovery efforts.

    Preferred qualifications:
  • Expert R and/or Python programming skills – ideally both
  • Experience with pipeline development tools like Nextflow or Snakemake
  • Experience with cluster use (Sun Grid Engine or similar)
How to Apply

Follow this link, and click "Apply for this job" at the bottom of the job posting.

Application Process:
The application process for UW positions may include completion of a variety of online assessments to obtain additional information that will be used in the evaluation process.  These assessments may include Work Authorization, Cover Letter and/or others.  Any assessments that you need to complete will appear on your screen as soon as you select “Apply to this position”. Once you begin an assessment, it must be completed at that time; if you do not complete the assessment you will be prompted to do so the next time you access your “My Jobs” page.  If you select to take it later, it will appear on your "My Jobs" page to take when you are ready. Please note that your application will not be reviewed, and you will not be considered for this position until all required assessments have been completed.

About Our Organization

As a UW employee, you have a unique opportunity to change lives on our campuses, in our state and around the world. UW employees offer their boundless energy, creative problem solving skills and dedication to build stronger minds and a healthier world.

UW faculty and staff also enjoy outstanding benefits, professional growth opportunities and unique resources in an environment noted for diversity, intellectual excitement, artistic pursuits and natural beauty. All of which has allowed the UW to be nationally recognized as a “Great College to Work For” for four consecutive years.

The Brotman Baty Institute for Precision Medicine (BBI) is a recently launched, joint venture of the University of Washington, the Fred Hutchinson Cancer Research Center and Seattle Children’s Hospital, made possible by a $50 million gift from the Brotman and Baty Families. The BBI Advanced Technology Lab is a new entity within this institute tasked with making cutting-edge ‘-omics’ technologies broadly available to the Institute’s research community. Through the BBI Advanced Technology Lab, the institute will have the capacity to generate transcriptomic profiles from at least 10 million single cells across 30 investigator-initiated projects from all three institutions. We will soon start operating as a cost center, taking on projects first from BBI members followed by an expansion to the wider research community.

Committed to attracting and retaining a diverse staff, the University of Washington will honor your experiences, perspectives and unique identity. Together, our community strives to create and maintain working and learning environments that are inclusive, equitable and welcoming.

The University of Washington is a leader in environmental stewardship & sustainability, and committed to becoming climate neutral.

The University of Washington is an equal opportunity, affirmative action employer. To request disability accommodation in the application process, contact the Disability Services Office at 206-543-6450 / 206-543-6452 (tty) or

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