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Bioinformatics Specialist I

Howard Hughes Medical Institute (HHMI) is an independent, ever-evolving philanthropy that supports basic biomedical scientists and educators with the potential for transformative impact. We make long-term investments in people, not just projects, because we believe in the power of individuals to make breakthroughs over time.

At HHMI, you are not just an employee – you are a part of a creative and talented team with colleagues in biomedical research, investment management, information technology, law, among many other areas of expertise. We encourage collaborative and results-driven working styles and offer an adaptable environment where employees can do their best work. Find more information about us at

We are currently seeking a highly skilled Bioinformatics Specialist I to work full-time in an Investigator lab at the University of Washington (UW) in Seattle, Washington. The Bioinformatics Specialist I 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. The successful 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.

  • 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 (if applicable)
  • 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.

  • Bachelor’s degree in bioinformatics, computer science, or similar discipline is required. Master’s degree is preferred.

  • At least 2-3 years of relevant research experience in bioinformatics and/or computational biology is required.
  • Experience in genomics research is required including at least 3 years of experience developing computational methods and tools used in bioinformatics research.
  • 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).

Knowledge, Skills, and Abilities
  • 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.
  • 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.