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The Department of Genome Sciences (GS) is part of the University of Washington School of Medicine and is comprised of 30 labs addressing leading edge questions in biology and medicine by developing and applying genetic, genomic and computational approaches taking advantage of genomic information now available for a host of species. GS is making major contributions in the application of genome science to understand the fundamentals of biology and to improve human health and wellbeing. Genome Sciences is a collaborative department supported by very different academic disciplines. The department has gone through significant expansion since its beginning in 2001 with annual grant awards of $57M for FY20.
We have an outstanding opportunity for a Bioinformatics Specialist, Software Engineer to 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. 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 genomes at higher quality.
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.
Impact to UW
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.
Duties & Responsibilities
• 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%)
• 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.
Equivalent education/experience will substitute for all minimum qualifications except when there are legal requirements, such as a license/certification/registration.
• 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).
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.
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