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We are currently seeking a skilled Bioinformatics Specialist/Senior Computer Specialist to work full-time in a prominent lab at the University of Washington (UW) in Seattle, Washington. The job will entail the development and implementation of computational pipelines to analyze genetic variation in human and non-human primate genomes with a specific emphasis on 3rd-generation long-read sequencing technologies. The Bioinformatics Specialist will work as part of a team relating this variation to disease with a particular emphasis on the discovery of mutations associated with autism spectrum disorder as well as the de novo sequence and assembly of human genomes.
The Bioinformatics Specialist will collaborate with the Investigator, postdoctoral fellows, and students to develop, implement, and execute computational methods and tools to assess the organization of recent segmental duplications and structural variation using next-generation Illumina and long-read technologies. This role will focus on the discovery of genetic variation relevant to neurocognitive disease, including autism, and will work as part of sequencing consortia to develop methods to sequence and assemble genomes at higher quality. Under limited supervision, the successful candidate will perform scientific investigative procedures applying professional judgment, interpreting experimental results, guiding lab members through bioinformatics methods and analyses, and preparing research reports for presentation or publication.
Develop and maintain algorithms and computational tools to detect duplications, copy number variants, and single-nucleotide polymorphisms using data generated from genome sequencing projects. Master python programming and become adept at using, installing, supporting, and trouble-shooting a variety of computational/variant tools routinely used in the lab such as bedtools, samtools, minimap2, bwa, freebayes, deepvariant, snakemake, long-read assemblers and numerous computational pipelines developed by the lab to characterize structural variation. (40%)
Evaluate, maintain, support, create, and adapt tools to create, manage, and analyze next-generation sequencing datasets using massively parallel computing infrastructure (2500+ CPUs) with guidance from senior developers. (20%)
Develop programs and/or scripts, including graphical visualization software, to facilitate large-scale data mining of the genome, genetic, and expression databases. Prepare associated technical documentation. (15%)
Collaborate with postdoctoral and doctoral researchers and work on research projects as assigned by the Investigator, with limited supervision. The latter will include the preparation of summaries and reports to be included in publications. (15%)
Integrate analysis data into existing genome browser. (10%)
Lead Responsibilities (if applicable)
Learn to supervise and manage massively parallel computing infrastructure including 2,500+ CPUs, 3+ PB of shared storage, and standalone web and database servers in collaboration with departmental IT staff.
Assist in deploying and managing shared software and reference resources.
Bachelor’s degree in bioinformatics, computer science, statistics, biology, biochemistry, genetics, or similar discipline is required.
At least 2 years of relevant computing experience in bioinformatics and/or computational biology is required.
A strong background in statistical methods with expertise in R programming.
Demonstrated research experience.
Desired Knowledge, Skills, and Abilities
Experience with PacBio, Oxford Nanopore, 10X, or Strand-seq technologies.
Extensive experience in two or more programming languages (Python, R, Java, C/C++, Perl, etc.); experience with Python and its scientific libraries (NumPy, SciPy, Pandas, Snakemake).
An understanding of common bioinformatics file formats (FASTQ, SAM/BAM, VCF, BED).
Proficient skill with integrating data and systems.
Proficient skill with existing bioinformatics software tools (e.g., BWA, GATK, BLAST, CLUSTALW, MEGA), particularly data mining of whole-genome shotgun sequence data analysis.
Skilled with Linux/Unix and comfortable working in a command line environment.
Experience in genomic research.
Ability to perform independent analyses and report findings to both national and international collaborative groups.
Technical proficiency and collaborative ability as well as independent thought.
Ability to develop innovative processes to achieve goals. Reviews work activities to determine where new information could improve processes or move projects forward.
Ability to work independently and as part of a multidisciplinary team.
Strong organizational skills with exceptional attention to detail.
Strong multitasking and project management skills.
Ability to be flexible and effectively adapt to changing priorities.
Physical Requirements: Remaining in a normal seated or standing position for extended periods of time; reaching and grasping by extending hand(s) or arm(s); dexterity to manipulate objects with fingers, for example using a keyboard; communication skills using the spoken word; ability to see and hear within normal parameters; ability to move about workspace. The position requires mobility, including the ability to move materials weighing up to a few pounds (such as a laptop computer or tablet).
Persons with disabilities may be able to perform the essential duties of this position with reasonable accommodation. Requests for reasonable accommodation will be evaluated on an individual basis.
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.
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