Software Engineer, Stam Lab

University of Washington - Genome Sciences
Job Location: 
Seattle, WA
Salary is commensurate with education and experience.
Job Description: 

The Department of Genome Sciences at the University of Washington has an outstanding opportunity for a Software Engineer with the Stam Lab. This is a mission critical position with significant impacts on high visibility research programs such as the ENCODE Project and the Roadmap Epigenomics Project. These NIH funded research programs are multi-center consortia and the Stam lab has been a key center both in data production and analysis, as well as in making this data available across consortia in an integrated fashion to the outside scientific user community. The position also supports high-throughput massively parallel sequence data production by the HTGC core facility for collaborators and customers, and prepares the data for timely submission to required national databases.

Core responsibilities for this position include the following:

Within a Linux command-line environment, manage bioinformatics pipelines
• Align sequences for multiple high-throughput sequencing assays (ChIP-seq, RNA-seq, DNase-seq)
• Process data and detect genetic polymorphisms
• Analyze data, compare data among samples, and make available to investigators
• Collect and maintain quality-control measurements.

Customer Support
• Build customer relationships
• Track customer projects, analyze plans and maintain timelines
• Collaborate with lab staff and scientists on projects
• Work with investigators and customers to determine and refine analysis requirements
The person in this position will work closely with research scientists and bioinformatics personnel in managing high throughput sequence data production and quality control analysis, and develop high throughput pipelines for facilitating these processes. He/she will interact with collaborators and HTGC customers on an as-needed basis to make the sequence data available to them in readily usable formats.


• Close interaction with bench scientists and other bioinformatics personnel
• Ability to manage tight deadlines for project completion



Bachelor of Science degree in Computer Science, Engineering, Informatics, or related field. AND 4+ years’ experience working in a scientific computing environment.
• Basic bioinformatics knowledge gained through direct work and/or academic experience
• Linux experience using: bash (operation and scripting), awk, find, grep, rsync, ssh
• Python, Perl scripting
• Working knowledge of R/Bioconductor
• Git source control management (or other source control experience)
• Excellent written and verbal communication, ability to communicate with scientists/customers
• Troubleshooting/reporting skills
• Detailed and consistent project/task management


• Basic understanding of statistics and hypothesis testing and multiple comparisons.
• Sun Grid Engine job submission and management
• Manipulation of spreadsheets
• Web development and maintenance using: Django, HTML, CSS, Javascript

About Our Organization: 

The University of Washington (UW) is proud to be one of the nation’s premier educational and research institutions. Our people are the most important asset in our pursuit of achieving excellence in education, research, and community service. Our staff not only enjoys outstanding benefits and professional growth opportunities, but also an environment noted for diversity, community involvement, intellectual excitement, artistic pursuits, and natural beauty.

The Department of Genome Sciences (GS) is part of the University of Washington School of Medicine (UW SoM) and is comprised of 27 labs addressing leading edge questions in biology and medicine by developing and applying genetic, genomic and computational approaches taking advantage of genomic information now available for a host of species. GS is making major contributions in the application of genome science to understand the fundamentals of biology and to improve human health and well-being.

Genome Sciences is a collaborative department supported by very different academic disciplines. We work with a multitude of Program Investigators (PIs) in departments both on the UW campus as well as worldwide. The department has gone through significant expansion since its beginning in 2001 with annual grant awards of $41.5M in FY12. The department has 47 training, teaching, and research faculty.

The High Throughput Genomics Center (HTGC) at the University of Washington is at the forefront of genomics and bioinformatics. The laboratory applies cutting edge technologies for massively parallel DNA sequencing to understand gene structure and regulation on a genome-wide scale, and supports hundreds of academic and industry investigators world-wide.

The HTGC seeks to expand our bioinformatics staff with a talented individual who will manage and coordinate analysis pipelines for high-throughput genomic data (DNA and RNA sequencing, chromatin, methylation, metagenomics, etc.). The job requires tracking and executing analysis requirements for multiple internal projects. The ability to maintain effective communication between co-workers and investigators/customers is a must.