109636 - Genomics Computational Specialist
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#109636 Genomics Computational SpecialistExtended Deadline: Wed 9/29/2021
For the safety and well-being of the entire university community, the University of California requires, with few exceptions, that all students, faculty and staff be vaccinated against the COVID-19 virus before they will be allowed on campus or in a facility or office. For more information visit: https://ucnet.universityofcalifornia.edu/news/2021/07/ucs-covid-19-vaccine-policy.html
This position will remain open until a successful candidate has been identified.
UCSD Layoff from Career Appointment: Apply by 06/10/21 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor.
Special Selection Applicants: Apply by 06/21/21. Eligible Special Selection clients should contact their Disability Counselor for assistance.
The UCSD Institute for Genome Medicine (IGM) is a center of excellence for organizing the multi-disciplinary resources necessary to effectively translate the discoveries of genetic and genomic research from "bench to bedside". The IGM aims to link clinical and genomic information to facilitate personalized health care. By combining UCSD’s expertise in Genetics, Disease Biology, and Clinical Practice with its strengths in Computer Science, Bioinformatics, and Systems Biology, the IGM is uniquely positioned to support all activities along the continuum of genomic medicine. The IGM Genomics Center provides a variety of high-throughput sequencing services to UCSD laboratories. The IGM Genomics Center aspires to perform routine acquisition of genomics data using cutting edge sequencing technologies at an affordable cost.
The incumbent will process raw Illumina sequencing data generated in the IGM Genomics Center and maintain the IGM customer database and data storage system. This will include working with the San Diego Super Computer Center for storage and processing needs. Responsibilities will also include providing ad-hoc technical support, benchmarking newly emerging computational tools for specific projects, and system maintenance. The work will be multi-faceted, largely tasked with participating in the analysis of a diverse collection of genetic data.
The incumbent will assist with implementing, running, customizing, and optimizing data analyses pipelines for next generation sequencing (NGS) data from epigenomic assays such as ChIP-seq, RNA-seq, ATAC-seq, Whole Genome Sequencing, as well as single-cell RNA-seq and single-cell ATAC-seq. Primary tasks revolve around development and maintenance of a variant analysis pipeline that processes sequencing data, integrates internal and external data, and prioritizes genetic variants based on an array of metrics. Additional work includes creating new visual summaries of data in R, and downloading and piloting new analysis tools. Integrating with a team of bioinformaticians, staff researchers and Principal Investigators to perform statistics-based analysis to achieve high-impact results.
Applies skills as an IT research professional. Uses computational, computer science, data science, and CI software research and development principles, with relevant domain science knowledge where applicable, along with professional programming concepts for medium-sized projects or portions of larger projects. Develops and optimizes a variety of computational, data science, and CI research tools and components. Performs research using Linux server and cluster system, data, hardware and software projects. Works on algorithm development, optimization, programming, performance analysis and/or benchmarking assignments of moderate scope where the tasks involve knowledge of either domain/computer science research requirements and/or CI design/implementation requirements.
Seven (7) years of related experience, education/training, OR a Bachelor’s degree in Computer /Computational/Data Science, or Domain Sciences with computer/computational/data specialization plus three (3) years of related experience/training.
Intermediate knowledge of HPC/data science/CI.
Advanced skills, and experience associated with one or more of the following: HPC hardware and software power and performance analysis and research, design, modification, Implementation and deployment of HPC or data science or CI applications and tools.
Proven ability to successfully work on multiple concurrent projects.
Demonstrated ability to regularly interface with management.
Effective communication and interpersonal skills. Ability to communicate technical information to technical and non-technical personnel at various levels in the organization and to external research and education audiences.
Proven skills and experience in independently resolving broad computing/data/CI problems using introductory and/or intermediate principles.
Thorough experience working in a complex computing/data/CI environment encompassing all or some of the following: HPC, data science infrastructure and tools/software, and diverse domain science application base.
Proven ability to understand research computing/data/CI needs, mapping use cases to requirements and how systems/software/infrastructure can support those needs and meet the requirements. Ability to develop and implement such solutions.
Broad experience in one or more of the following: optimizing, benchmarking, HPC performance and power modeling, analyzing hardware, software, and applications for HPC/data/CI.
Proven experience and ability to collaborate effectively with all levels of staff; technical, students, faculty and administrators
Demonstrated ability to contribute research and technical content to grant proposals.
- Master's degree.
- Employment is subject to a criminal background check.
Job offer is contingent on successful engagement in the UC COVID-19 Vaccination program (fully vaccinated with documented proof or approved exception/deferral).
UC San Diego Health is the only academic health system in the San Diego region, providing leading-edge care in patient care, biomedical research, education, and community service. Our facilities include two university hospitals, a National Cancer Institute-designated Comprehensive Cancer Center, Shiley Eye Institute, Sulpizio Cardiovascular Center, and several outpatient clinics. UC San Diego Medical Center in Hillcrest is a designated Level I Trauma Center and has the only Burn Center in the county. We invite you to join our dynamic team!
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UC San Diego Health is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age, protected veteran status, gender identity or sexual orientation. For the complete University of California nondiscrimination and affirmative action policy see: http://www-hr.ucsd.edu/saa/nondiscr.html
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