SENIOR BIOINFORMATICS SCIENTIST
Req #: | 178287 |
Department: | GENOME SCIENCES |
Job Location: | Seattle Campus |
Posting Date: | 03/26/2020 |
Closing Info: | Closes On 04/02/2020 |
Salary: | Salary and benefits are competitive. Salary is commensurate with qualifications and experience. |
Shift: | First Shift |
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. All of which has allowed the UW to be nationally recognized as a “Great College to Work For” for six consecutive years.
The Department of Genome Sciences (GS) is part of the University of Washington School of Medicine and is comprised of 26 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. 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 $56M for FY19. The department has 47 training, teaching, and research faculty.
We have an outstanding opportunity for a Senior Bioinformatics Scientist to lead genome-wide analyses investigating 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 other emerging technologies. This person will participate in national and international consortia focusing on assembly of human and nonhuman primate genomes, characterizing of structural variation, improving the human reference genome, and understanding the genetic architecture of autism. The position will play an important role in the design, development, and maintenance of research-related, custom software used in a high-throughput DNA sequencing laboratory. This position requires the ability to dissect and analyze complex research problems using a multitude of programming languages that interact with existing software architecture. Skills and knowledge needed for this position include extensive scripting and computer programming skills (Python, Java, Perl, and Linux OS).
The Eichler lab is involved in several different projects simultaneously, which requires skills integrating data and systems. Familiarity with existing bioinformatics software tools is required, especially mining whole-genome shotgun sequence data through alignment, assembly, 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.
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.
Duties & Responsibilities:
• Develop, maintain, and streamline algorithms and computational tools to discover and genotype structural variants, small indels, and single-nucleotide polymorphisms using data generated from genome sequencing projects. (35%)
• Manage a local UCSC Genome Browser, interact with IT to maintain and optimize massively parallel computing infrastructure (2,500+ CPUs), and utilize cloud services as needed. Troubleshoot and resolve system problems in a Linux cluster and help minimize disruptions. Manage project data in a 3+ petabyte (PB) system. (20%)
• Function as a computational lead for all lab members by training programmers, organizing computational projects, and working with trainees on research projects as assigned by the Investigator. (15%)
• Prepare reports and presentations for research projects, including collaborations as part of international consortia, group meetings and national conferences. (10%)
• Provide support for PacBio Cost Center. (10%)
• Compare variants to public data sources and contribute new resources to public resources, such as NCBI and EMBL databases. (5%)
• 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. (5%)
• Thrive in a fast-paced work environment that requires independent self-direction with an aptitude for team collaboration and open communication.
Within these responsibilities, more specific job duties include:
• Product development: Interfacing with faculty, outside project collaborators, and staff both in-person and online; learning software requirements; communicating updates regarding job builds, specs, and all job duties listed above. Producing professional software implementations readily usable within the lab, among collaborators, or the scientific community as part of published work. Guiding junior staff and/or student employees through programming and software engineering tasks.
• Budgeting: Managing the budget for hardware and software purchases, maintenance renewals, replacement parts, contracts for cloud computing, consultants, etc., as well as providing budget information for future grants or additional funding requests.
• Communications: Effectively communicate with trainees, staff, and consortia for planning, troubleshooting, and communicating results. Produce publication-quality tables and visualizations and deliver impactful presentations.
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. Mentor and advise junior-level programmer analysts and/or student employees. Organize computational staff, help prioritize projects and fixes, resolve conflicts, and ensure staff members have the resources they need to be successful.
Supervisory Responsibilities:
No formal direct reports at this time, but possible in the future.
Requirements include:
• Bachelor's Degree in genomics, computational biology, computer science, or related field.
• Minimum four years’ related experience to include working with next-generation sequencing data and relevant tools for bioinformatics analysis.
• Good understanding of human genetics.
• Candidates should have an outstanding academic and professional track record.
• Successful candidates will be highly self-motivated and enthusiastic about taking a hands-on approach to collaborative scientific discovery efforts.
• Able to utilize computational tools in common scripting languages (e.g., Linux, Python, R, and Perl). Experience producing professional software programs that are maintainable.
• Experience working in high-performance computing environments with heterogeneous architectures.
• Ability to manage projects and solve problems independently.
• Candidates should also have excellent written and verbal communication skills. Interfacing with project collaborators in-person and online is a key aspect of the position.
• Ability to think creatively, independently, and effectively test new ideas.
Equivalent education/experience will substitute for all minimum qualifications except when there are legal requirements, such as a license/certification/registration.
Desired:
• In-depth understanding of genomic architecture including duplications, tandem repeats, genes, and gene regulation.
• Experience programming for distributed and parallel computation environments.
• Ability to independently troubleshoot networking and Linux systems.
• Proficient in multiple operating systems including Linux, Windows, and MacOS.
• Experience with cloud computing (e.g., Amazon, Google).
• Experience as a team lead or senior staff guiding projects, resolving conflicts, or budgeting.
Conditions of Employment:
• 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 work flow or deadlines occasionally requiring extra hours be worked.
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.
Application Process:
The application process for UW positions may include completion of a variety of online assessments to obtain additional information that will be used in the evaluation process. These 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 a leader in environmental stewardship & sustainability, and committed to becoming climate neutral.
The University of Washington is an equal opportunity, affirmative action employer. To request disability accommodation in the application process, contact the Disability Services Office at 206-543-6450 / 206-543-6452 (tty) or dso@uw.edu.