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The University of Washington (UW) School of Medicine (SOM) Departments of Laboratory Medicine and Pathology become a single Department of Laboratory Medicine and Pathology (DLMP) on July 1, 2020. The DLMP employs ~ 130 faculty, 800 staff, 60 residents and fellows, and 50 post docs and graduate students, with an annual budget of over $200 million: ~ $141 million in the SOM and ~$65 million in UW Medicine. A regional resource for clinical laboratory services required for cutting edge patient care, research and educational programs, we combine the sophisticated testing and informatics capabilities of fully accredited laboratories with the resources of an academic institution in its delivery of clinical and anatomical pathology services. Recognized for excellence in clinical training, world-class research initiatives, and a commitment to community service, we serve the five state WWAMI region: WA, WY, AK, MT, and ID.
We offer over 30 graduate medical education programs, including 18 subspecialty clinical fellowships (ACGME & Non-ACGME), a residency program in clinical and anatomical pathology, a clinical research fellowship, a post sophomore fellowship, and 13 medical student clerkships. Our graduate programs provide innovative educational opportunities to developing medical practitioners and bio clinical researchers. The Molecular Medicine and Mechanisms of Disease (M3D) PhD Program trains students to use advances in basic sciences to solve problems relevant to human disease; and, to use insights from human disease processes to solve fundamental biological problems. The UW Medical Scientist Training Program (MSTP) is a dual degree MD/PhD program between the SOM and UW Research. The program trains scientists to develop a broad knowledge in medicine and the ability to productively investigate detailed mechanisms associated with human diseases.
Our operations are based at the University of Washington School of Medicine, University of Washington Medical Center, Harborview Medical Center, and the Seattle Cancer Care Alliance. Faculty members also serve at Seattle Children's Hospital, the Veteran’s Administration Puget Sound Healthcare System, and the Fred Hutchinson Cancer Research Center. Our collaborative efforts have generated innovative, translational studies in the basic mechanisms of disease as they apply to diagnostic clinical and anatomical pathology. The 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.
The UW Department of Laboratory Medicine and Pathology has an outstanding opportunity for a full-time Software Engineer to support the analysis of clinical exome and genome sequencing assays.
Who we are:
Our department maintains all clinical testing and laboratory operations at the UW Medical Center, from sample collection to analysis and final reporting. We employ over 900 people and handle 30 million tests each year. In parallel, we research, develop and operationalize novel diagnostics, in particular novel next-generation sequencing (NGS) and genomics applications.
About the job:
This is an excellent opportunity to work in a challenging and rewarding environment that includes the development of bioinformatics tools to facilitate the implementation of genomic medicine. In this position, you will be responsible for evaluating, architecting and implementing bioinformatics pipelines and tools in order to support the growing needs of our exome sequencing and germline testing. The ideal candidate will have substantial expertise with analysis and manipulation of large next-generation sequencing data sets, common tools such as GATK, and background knowledge of human genetics and variation.
You’ll work closely with our laboratory directors and with our laboratory staff, bioinformatics, and infrastructure teams to gather requirements and interface with existing systems. Excellent project management and communication skills are highly desired.
40%: Software and bioinformatics engineering
•Identify, research and provide comparison of currently existing tools and algorithms designed for NGS data. •Design, build and update new and/or existing pipelines used for processing NGS data. •Efforts will support the department's germline (constitutional) and somatic sequencing assays.
40%: NGS data analysis and support
•Analyze NGS data in order to critically evaluate laboratory parameters of assays, establish validation documents, and ensure ongoing quality assurance. •Develop reports, dashboards, etc. to support data review and QC/QM activities. •Provide ad-hoc support for data analysis, data distribution, and data management as needed.
20%: Team/Laboratory Immersion
•Gain deep understanding of laboratory pre-analytic, analytic and post-analytic procedures and workflows •Integrate bioinformatic capabilities with new and existing computational infrastructure, including cloud-based analysis, data storage, and process orchestration systems, with intent of identifying streamlined solutions and workflows that support improved quality, efficiency and throughput.
Why UW Lab Medicine and Pathology?
•You'll impact patient care and outcomes through improvements to the quality, accuracy and speed of our laboratory tests. Our department prides itself in innovation and we are highly motivated to bring on new solutions that improve our clinical service. •You'll gain experience with real-world, highly complex and interesting data directly from our laboratory and clinical data streams. •You'll interface with a wide range of users and stakeholders, all of who are committed to the UW's "Patients are First" aim. •You'll have the opportunity to work with a motivated and energetic team.
•Bachelors of Science degree in computer science, engineering, Bioinformatics, Physics, Applied Math, or related discipline. •Minimum of 3 years' experience in diverse scientific computing environments, to include: LINUX, UNIX, Windows; implementing scientific algorithms; and implementing software testing methodologies •Knowledge of basic data processing steps needed for processing NGS data. •Experience with processing large datasets, summarizing results and providing interpretation for further development. •Experience with Linux, command line tools, modern software development infrastructure, version control software. •Excellent spoken and written communication and documentation skills.
Equivalent education/experience will substitute for all minimum qualifications except when there are legal requirements, such as a license/certification/registration.
•Knowledge of next-generation sequencing principles. •Experience with NGS analysis tools such as GATK, bwa, samtools, and other tools designed to identify germline variation. •Experience with workflow management and orchestration tools such as nextflow, snakemake, airflow, etc. •Experience with cloud computing services such as Amazon AWS, in particular AWS Batch, ECS, and S3. •Experience in development of or contribution to open source projects. •Wet-bench experience performing PCR and sequencing-based assays. •Experience with molecular diagnostics.
As a UW employee, you will enjoy generous benefits and work/life programs. For a complete description of our benefits for this position, please visit our website, click here.
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 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.
Founded in 1861, the University of Washington is one of the oldest public institutions in the west coast and one of the preeminent research universities in the world. The University of Washington is a multi-campus university comprised of three different campuses: Seattle, Tacoma, and Bothell. The Seattle campus is made up of sixteen schools and colleges that serve students ranging from an undergraduate level to a doctoral level. The university is home to world-class libraries, arts, music, drama, and sports, as well as the highest quality medical care in Washington State and a world-class academic medical center. The teaching and research of the University’s many professional schools provide undergraduate and graduate students the education necessary toward achieving an excellence that will serve the state, the region, and the nation. As part of a large and diverse community, the University of Washington serves more students than any other institution in the Northwest.