Bioinformatics Specialist

Organization
University of Washington
Job Location
Seattle, WA 98105
Salary
Competetive
Job Description

POSITION PURPOSE
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, long-read single-molecule, real-time PacBio and traditional capillary sequencing technology. The successful candidate will focus on the discovery of genetic variation relevant to neurocognitive disease, autism and epilepsy and will work as part of sequencing consortia to develop methods to sequence and assemble genomes at higher quality. 

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 requiring application of professional judgment, interpret experimental results, guide lab members through bioinformatics methods and analyses, and prepare reports of research for presentation or publication.

DIMENSIONS AND IMPACT TO THE UNIVERSITY
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.

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 manage next-generation sequencing datasets using massively parallel computing infrastructure (2000+ CPUs). (20%)
• Integrate analysis data into existing MySQL-based genome browser. (20%)
• Develop programs and/or scripts, including graphical visualization software, that facilitate large-scale data mining of the genome, genetic and expression databases. (10%)
• 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. (10%)

LEAD RESPONSIBILITIES 
• Supervise and manage massively parallel computing infrastructure including 2,000+ CPUs, 2+ PB of shared storage, and standalone web and database servers in collaboration with departmental IT staff.
• As needed, mentor and advise junior-level programmer analysts and computational students.
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Requirements

MINIMUM QUALIFICATIONS
• Masters of Science degree in computer science/bioinformatics or related field or equivalent in education and experience as well as bachelors-level knowledge of biology (e.g., introductory genetics or evolution).
• In-depth understanding of data structure and algorithm design and implementation.
• Extensive experience in two or more programming languages (C/C++, Perl, Python, Java, etc.).
• Highly skilled with Linux/Unix and working in a command line environment.
• Ability to perform independent analyses and report findings to both national and international collaborative groups. 
• 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
• Strong programming skills and a demonstrated expertise in genome sequence analysis.
• Experience programming for distributed and parallel computation environments.
• In-depth knowledge of multiple areas and of the underlying principles and concepts.
• In-depth understanding of complex equipment or processes. Can resolve most problems without assistance or defines assistance required for resolution.
• 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 initiate and compose communications for various purposes in an appropriate style.
• Proficient in multiple operating systems.
• Proficient with existing bioinformatics tools (e.g., BWA, GATK, BLAST, CLUSTALW, or MEGA).
• Experience with cloud computing (e.g., Amazon, Google).

How to Apply

We require a recent code sample that demonstrates your programming ability and technique. Please include a link to your code sample in your cover letter.

Please apply on website: https://uwhires.admin.washington.edu/eng/candidates/default.cfm?szCategory=jobprofile&szOrderID=132858&szCandidateID=0&szSearchWords=Genome&szReturnToSearch=1 

About Our Organization

The University of Washington (UW) is proud to be one of the nation's premier educational and research institutions. Our people are the most important asset in our pursuit of achieving excellence in education, research, and community service. Our staff not only enjoys outstanding benefits and professional growth opportunities, but also an environment noted for diversity, community involvement, intellectual excitement, artistic pursuits, and natural beauty. 

The Department of Genome Sciences (GS) is part of the University of Washington School of Medicine (UW SoM) and is comprised of 27 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 well-being. Genome Sciences is a collaborative department supported by very different academic disciplines. We work with a multitude of Program Investigators (PIs) in departments both on the UW campus as well as worldwide. The department has gone through significant expansion since its beginning in 2001 with annual grant awards of $48.8M in FY15. The department has 47 training, teaching, and research faculty. 

The Department of Genome Sciences at the University of Washington has an outstanding opportunity for a Bioinformatics Specialist. He/she 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 nextgeneration Illumina, longreadsingle molecule realtime PacBio and traditional capillary sequencing technology. The successful candidate will focus on the discovery of genetic variation relevant to neurocognitive disease, autism and epilepsy and will work as part of sequencing consortia to develop methods to sequence and assemble genomes at higher quality. 

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