Bioinformatics Specialist

Bioinformatics Specialist

Howard Hughes Medical Institute (HHMI)

Seattle, WA, United States

Job Description

About HHMI

Howard Hughes Medical Institute (HHMI) is a science philanthropy whose mission is to advance biomedical research and science education for the benefit of humanity. We empower exceptional scientists and students to pursue fundamental questions about living systems, and work to share scientific discoveries with researchers, students, and science-curious individuals around the world.


Founded in 1953 by aviator and industrialist Howard R. Hughes, HHMI is headquartered in Chevy Chase, Maryland, and employs more than 2,500 people across the U.S. Visit to learn more about working at HHMI.


The Howard Hughes Medical Institute has an exciting opportunity for a Bioinformatics Specialist to join the research team in a lab at the University of Washington in Seattle, Washington.


Position Purpose

The Bioinformatics Specialist will lead genome-wide analyses to investigate copy number and genomic structural variation within complex regions of the human genome, including regions of segmental duplications. This individual will work with the PI and postdoctoral fellows to develop computational pipelines using a suite of next-generation sequencing technologies, including Illumina, PacBio, Oxford Nanopore, and traditional capillary sequencing technology. This person may participate in national and international consortia focused on understanding the genetic architecture of autism, assembly of human and nonhuman primate genomes, characterization of structural variation, and improving the human reference genome.


Position Complexities

This lab is involved in several different projects simultaneously, which requires skills integrating data and systems. Familiarity with existing bioinformatics-specific software tools is required, especially mining whole-genome shotgun sequence data through alignment and variant detection. Experience with genomics research and an understanding of fundamental biological concepts are necessary to be successful in this position. The ideal candidate will independently perform scientific investigations requiring professional judgment, experimental results interpretation, guiding lab members through bioinformatics methods and analyses, and research report preparation for presentation or publication.


Dimensions and Impact to the University

This position is in a prominent laboratory whose work impacts researchers and clinicians worldwide. High functioning will be reflected in greater funding opportunities and will enhance the reputation of the University as a biomedical research powerhouse.


Responsibilities (Identify the percent of time spent on each major duty, listed in decreasing order of importance. The total job duties must equal 100% regardless of the position’s % FTE.)

  • Develop and streamline algorithms and computational tools to detect duplications, copy number variants, and single-nucleotide polymorphisms using data generated from genome sequencing projects. (30%)
  • Manage genome datasets, local UCSC Genome Browser, interact with IT to optimize massively parallel computing infrastructure (3,000 CPUs), and transfer data from and to cloud services. (20%)
  • Create new programs and/or scripts, including graphical visualization software to facilitate large-scale datamining of the genome, genetic and expression databases. (20%)
  • Prepare reports and presentations for research projects, including collaborations as part of international consortia. (10%)
  • Train programmers and work independently as well as with trainees on research projects as assigned by the Investigator (10%)
  • Provide support for PacBio Cost Center. (10%)


Supervisory Responsibilities

Supervise junior-level programmer analysts as well as computational students as needed.


Minimum Qualifications

  • 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.


Desired Qualifications

  • 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 existing bioinformatics tools (e.g., BWA, GATK, BLAST, CLUSTALW, MEGA).
  • Experience with Python and its scientific libraries (NumPy, SciPy, Pandas, Snakemake).
  • An understanding of common bioinformatics file formats (FASTQ, SAM/BAM, VCF, BED).


HHMI is an Equal Opportunity Employer

Required Skills

Required Experience

Please apply via recruiter’s website.

Quote Reference: Howard Hughes Medical Institute (HHMI)-hhmi-027780 - 866-908