Bioinformatics Specialist – Software Engineer

    Bioinformatics Specialist - Software Engineer at University of Washington
    • International
    • Seattle, WA, US
    • $7,302 to $10,834 USD / Year

    Website University of Washington

    Job Title: Bioinformatics Specialist – Software Engineer
    Req #: 230763
    Department: GENOME SCIENCES
    Job Location: Seattle Campus
    Posting Date: 02/02/2024
    Closing Info: Open Until Filled
    Salary: $7,302 to $10,834 per month
    Other Compensation:
    Shift: First Shift
    Benefits: 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.

    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.

    The Eichler Lab is located in the Department of Genome Sciences at the University of Washington. The University of Washington is proud to be one of the nation’s premier educational and research institutions. Our people are our most important asset in our pursuit of excellence in education, research, and community service. Thus, our staff enjoys outstanding benefits and professional growth opportunities as well as an environment noted for diversity, community involvement, intellectual excitement, artistic pursuits and natural beauty.

    The Department of Genome Sciences, part of the University of Washington School of Medicine, focuses on answering critical scientific questions by developing and applying genetic, genomic and computational approaches. In particular, we are making major contributions in the application of genomics to understand the fundamentals of biology and to improve human health and wellbeing. Genome Sciences boasts a collaborative, integrated environment supported by a diversity of academic disciplines. We also work with a multitude of others both on the UW campus as well as worldwide. The department has been highly successful, expanding since its beginning in 2001 to 63 training, teaching, and research faculty with annual grant awards of $63M in FY23.

    The Department of Genome Sciences is committed to creating an environment that is welcoming and inclusive. Our goal is to foster a place of learning and working where all members can thrive and where diversity is recognized and celebrated. At Genome Sciences, we aim to create supportive spaces for those who are marginalized in higher education or society. To achieve this, we recognize that it is our ongoing responsibility to understand, acknowledge, and challenge systems of privilege and disadvantage in higher education such as those based on race, color, creed, caste, religion, national origin, citizenship, sex, age, marital status, sexual orientation, gender identity or expression, disability, veteran status, or socioeconomic status.


    The Bioinformatics Specialist will collaborate with the Principal Investigator, postdoctoral fellows, staff, 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. The successful candidate 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 higher-quality genomes.

    Position Complexities:
    This lab is involved in several different projects simultaneously, which requires skills in integrating data and systems. Familiarity with existing bioinformatics-specific software tools, especially data mining of whole-genome shotgun sequence data analysis, is required. Experience in genomics research is necessary for performance of this job. The ideal candidate will independently 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.

    Position Dimensions and Impact to the University of Washington:
    This position will work in a prominent laboratory whose work impacts other researchers worldwide. High functioning will be reflected in even greater funding opportunities and enhancement of the reputation of the University as a biomedical research powerhouse.


    • Develop and maintain algorithms and computational tools to detect duplications, copy number variants, and single-nucleotide polymorphisms using data generated from genome sequencing projects. (40%)
    • Create tools to create, manage, and analyze next-generation sequencing datasets using massively parallel computing infrastructure (2500+ CPUs). (20%)
    • Develop programs and/or scripts, including graphical visualization software, to facilitate large-scale data mining of the genome, genetic, and expression databases. (15%)
    • Collaborate with postdoctoral and doctoral researchers and work independently on research projects as assigned by the Investigator. 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:

    • 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.
    • Deploy and manage shared software and reference resources.
      Guide the work of junior-level programmer analysts as well as computational students as needed


    • Bachelors of Science degree in computer science, bioinformatics or related field or equivalent in education and experience.
    • At least three years of experience developing computational methods and tools used in bioinformatics research.
    • In-depth understanding of data structures, algorithm design, and software implementation.
    • Extensive experience in two or more programming languages (Python, R, Java, C/C++, Perl, etc.).
    • Skilled with Linux/Unix and comfortable working in a command line environment
    • 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.


    • Masters of Science degree in computer science/bioinformatics or related field or equivalent in education and experience.
    • At least one year of bioinformatics or related research experience in data analysis of next-generation sequencing or whole-genome shotgun data.
    • Experience with PacBio, Oxford Nanopore, 10X, or Strand-seq technologies.
    • Proficient with integrating data and systems and existing bioinformatics tools (e.g., BWA, GATK, BLAST, CLUSTALW, MEGA), particularly data mining of whole-genome shotgun sequence data analysis.
    • Experience with Python and its scientific libraries (NumPy, SciPy, Pandas, Snakemake).
    • An understanding of common bioinformatics file formats (FASTQ, SAM/BAM, VCF, BED).


    This position is expected to respond immediately to questions from investigators and teammates and provide expert technical support for developing or trouble-shooting workflows. On occasion, it will be necessary to respond immediately to urgent questions from the P.I. and other managers if problems arise that impact the workflow or deadlines occasionally requiring extra hours worked.

    Application Process: The application process 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.
    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 an affirmative action and equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, gender expression, national origin, age, protected veteran or disabled status, or genetic information.

    To request disability accommodation in the application process, contact the Disability Services Office at 206-543-6450 or

    Applicants considered for this position will be required to disclose if they are the subject of any substantiated findings or current investigations related to sexual misconduct at their current employment and past employment. Disclosure is required under Washington state law.

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