Job Description

Payroll Title:
Salary Range
Commensurate with Experience
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Work Schedule:
Days, 8 hrs/day, Monday-Friday

As a federally-funded institution, UC San Diego Health maintains a marijuana and drug free campus. New employees are subject to drug screening.

#119126 Bioinformatics Programmer II - Hybrid/Remote

Extended Review Date: Tue 10/25/2022

UC San Diego values equity, diversity, and inclusion. If you are interested in being part of our team, possess the needed licensure and certifications, and feel that you have most of the qualifications and/or transferable skills for a job opening, we strongly encourage you to apply.

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 and influenza before they will be allowed on campus or in a facility or office. For more information visit: Flu Vaccine Mandate / COVID Vaccine Policy

This position will remain open until a successful candidate has been identified.

UCSD Layoff from Career Appointment: Apply by 10/03/2022 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor.

Special Selection Applicants: Apply by 10/13/2022. Eligible Special Selection clients should contact their Disability Counselor for assistance.

This position will work a hybrid schedule which includes a combination of working both onsite on Campus and remote.


UCSD Department of Psychiatry is one of the most innovative and productive academic departments in the country, offering challenging career opportunities in the diverse areas of advanced educational programs, cutting-edge research, and state-of-the-art clinical services. The department is committed to offering a dynamic learning environment and growing opportunities to its talented and dedicated employees.

Under general supervision, the incumbent will be working as a Bioinformatics Programmer 2 performing research in psychiatric genetics in humans and across species (rats, mice, zebrafish etc.) within the Department of Psychiatry. The primary focus area of this position is within a National Institute of Health project aimed at developing tools for cross-species translation. The applicant will also be involved in large-scale genetic studies aimed at elucidating the genetic basis of psychiatric disorders. The incumbent will perform genetic analyses of complex traits, build systems for data organization, design computational pipelines for genetic analyses, and develop tools for genomics research.

This includes pipelines based on the established computations workflow, using Bash scripting and software such as PLINK, GCTA, LDSC, PRS-CS/PRSice/LDPred, PrediXcan, GEMMA, SAIGE and network analyses; performing routine quality control for data inputs and analysis outputs, assisting with data organization and backup. The incumbent will also participate in discussion and planning meetings, study existing research and suggest approaches for building developing tools for cross-species genomic integration and conducting large scale genetic analyses of complex traits and write sections on data analysis for the manuscripts, progress reports and proposals. Additional responsibility will include developing new pipelines, which require selecting software and testing different computational approaches. The successful applicant will have exceptional written and verbal communication, will carefully document their work and annotate their code. Excellent organization skills are required in order to work as part of a team.


  • Six (6) years of related experience, education/training, OR a Bachelor’s degree in related area plus two (2) years of related experience/training.

  • Working knowledge of bioinformatics methods and data structures.

  • Working knowledge of applications programming and web development.

  • Working knowledge of databases.

  • Working project management skills.

  • Working knowledge of modern biology.

  • Effective interpersonal skills in order to work with both technical and non-technical personnel at various levels in the organization.

  • Working knowledge of application and data security concepts.

  • Demonstrated experience in handling big data sets.

  • Experience in programming languages, including R, Python, and Bash script.

  • Demonstrated knowledge of Linux-based workflow development, including Bash scripting, High Performance Computing, cloud technologies such as Amazon EC2.

  • Experience performing genetic analyses using software such as TWAS/PrediXcan, PRS-CS/PRSice/LDPred, LDSC, PLINK, GCTA.

  • Experience performing routine quality control for genetic data using statistical analysis with software such as Plink.

  • Experience to study existing research and suggest approaches for building developing tools for cross-species genomic integration and conducting large scale genetic analyses of complex traits.

  • Proven ability to effectively manage time and see assigned parts of projects through to completion on deadline. Demonstrated experience in using software revision control systems (e.g. GIT). Proven ability to carefully document the work and annotate the code.

  • Strong communication skills. Ability to communicate technical information in a clear and concise manner.

  • Proven ability to write sections on data analysis for the manuscripts, progress reports and proposals.

  • Demonstrated knowledge of genetic analysis software such as GEMMA, GTCA, SAIGE.

  • Demonstrated knowledge of transcriptomic-related software such as PrediXcan.

  • Ability to use PostgreSQL queries to maintain, update and retrieve data from the custom database.


  • Employment is subject to a criminal background check.
  • Must be able to work weekends and overtime as needed.

Job offer is contingent on successful engagement in the UC COVID-19 Vaccination program (fully vaccinated with documented proof or approved exception/deferral).

If applicable, life-support certifications (BLS, NRP, ACLS, etc.) must include hands-on practice and in-person skills assessment; online-only certification is not acceptable.

UC San Diego Health Sciences is comprised of our School of Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, The Herbert Wertheim School of Public Health and Human Longevity Science, and our Student Health and Well-Being Department. We have long been at the forefront of translational - or "bench-to-bedside" - research, transforming patient care through discovery and innovation leading to new drugs and technologies. Translational research is carried out every day in the hundreds of clinical trials of promising new therapies offered through UC San Diego Health, and in the drive of our researchers and clinician-scientists who are committed to having a significant impact on patient care. We invite you to join our team!

Applications/Resumes are accepted for current job openings only. For full consideration on any job, applications must be received prior to the initial closing date. If a job has an extended deadline, applications/resumes will be considered during the extension period; however, a job may be filled before the extended date is reached.

To foster the best possible working and learning environment, UC San Diego strives to cultivate a rich and diverse environment, inclusive and supportive of all students, faculty, staff and visitors. For more information, please visit UC San Diego Principles of Community.

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:

UC San Diego is a smoke and tobacco free environment. Please visit for more information.

Application Instructions

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