Job Description

Payroll Title:
Salary Range
Commensurate with Experience
Appointment Type:
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Total Openings:
Work Schedule:
Days, 8 hrs/day, Mon - Fri

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

#113559 Genomics Bioinformatics Programmer

Extended Deadline: Tue 2/1/2022

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

UCSD Layoff from Career Appointment: Apply by 01/05/2022 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor.

Special Selection Applicants: Apply by 01/18/2022. Eligible Special Selection clients should contact their Disability Counselor for assistance.


Genomics Bioinformatics Programmer is responsible for the bioinformatics analyses pipelines necessary for interpretation of assays that are based on massively parallel sequencing technologies. Genomics Bioinformatics Programmer will interact with teams of experimental and computational scientists and trainees who work together to design, execute and analyze complex experiments investigating transcriptional mechanisms that control immune cell development and function. Current assays include RNA-seq, single-cell RNA-seq, ChIP-Seq, ATAC-Seq, and three-dimensional chromatin conformation capture assays. The incumbent will maintain and update ‘best practice’ computational methods and provide training and oversight to members of the laboratory in the application of assay-specific bioinformatics tools. Genomics Bioinformatics Programmer will interface with technical support at the San Diego Super Computer Center to maintain laboratory-specific computational infrastructure necessary for data storage and analysis. As necessary, the incumbent will generate new software tools and/or provide direction to trainees to develop such tools for problems lacking appropriate analytical methods. Additionally, they will be involved in writing primary research publications and grant applications and will be encouraged to attend and contribute to scientific meetings on related topics.

Uses skills as a seasoned, experienced bioinformatics programming professional with a broad understanding of computational algorithms; identifies and resolves a wide range of issues / software bugs. Demonstrates good judgment in selecting methods and techniques for obtaining solutions. Operates independently.


  • Graduate degree in biological science, computational / programming, or related area and / or equivalent experience / training.

  • Three (3) years of relevant experience/education.

  • Thorough knowledge of bioinformatics methods, applications programming, web development and data structures. Demonstrated experience with programming languages (Python and R are required, strong candidates will also have experience with Perl, C#, C++, or Java). Demonstratedexperience using UNIX/Linux.

  • Thorough knowledge of bioinformatics programming design, modification and implementation. Experience in development of complex bioinformatics, knowledge-based application software.

  • Understanding of relational databases, web interfaces, and operating systems. Proven ability to download high-throughput data sets, troubleshoot sequencing data, conduct standard statistical analysis and data visualization.

  • Strong project management skills. Proven ability to organize, prioritize and manage multiple project activities effectively and deal with changing priorities.

  • Thorough knowledge of modern biology and applicable field of research. Working knowledge of biological systems including transcription, genetics, and epigenetics.

  • Communication skills to work with both technical and non-technical personnel in multiple fields of expertise and at various levels in the organization. Proven ability to receive input and integrate ideas from colleagues to develop computational solutions that meet the needs of the laboratory.

  • Ability to communicate technical information in a clear and concise manner. Strong ability to communicate and teach complex concepts to scientists from various fields. Excellent communication skills for oral presentations, written reports, and one-on-one training.

  • Ability to interface with management on a regular basis.

  • Self-motivated, work independently or as part of a team, able to learn quickly, meet deadlines and demonstrate problem solving skills.

  • Thorough knowledge of web, application and data security concepts and methods.


  • Ph.D degree or equivalent experience/ training in bioinformatics, computer science or related field with programming and server experience or related combination of education and experience.

  • Experience with bioinformatics and metagenomics software and resources for analyzing high-throughput sequencing datasets.


  • Employment is subject to a criminal background check.

  • Occasional evenings and weekends may be required.

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 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.

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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