Job Description

Payroll Title:
Salary Range
Commensurate with Experience
Appointment Type:
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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.

#109084 Senior Genomics Bioinformatics Programmer

Extended Deadline: Fri 9/24/2021

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:

UCSD Layoff from Career Appointment: Apply by 04/27/2021 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor.

Special Selection Applicants: Apply by 05/07/2021. Eligible Special Selection clients should contact their Disability Counselor for assistance.

This position will remain open until filled.


The Senior Genomics Bioinformatics Programmer is responsible for the implementation and overall supervision of bioinformatics analyses pipelines necessary for interpretation of assays that are based on massively parallel sequencing technologies. In this capacity, the incumbent 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 Senior Genomics Bioinformatics Programmer 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. 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, 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.


  • Nine (9) years or more of related senior-level bioinformatics experience in a research setting OR a Bachelor’s degree in biological science, computational/programming, or related area plus five (5) years of related experience/training.

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

  • In-depth knowledge of bioinformatics programming design, modification and implementation. Experience in development of complex bioinformatic, knowledge-based application software. Ability to analyze scientific technical information.

  • Advanced 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.

  • Advanced 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.

  • Proven interpersonal skills in order to work with both technical and non-technical personnel at all levels in the organization, including senior project leadership. Proven ability to receive input and integrate ideas from colleagues to develop computational solutions that meet the needs of the laboratory.

  • Advanced ability to interface with management on a regular basis. Ability to communicate and deal effectively and productively with people at all levels of responsibility in various functional areas.

  • In-depth knowledge of web, application and data security concepts and methods.

  • Ability to communicate technical information in a clear and concise manner. 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 lead a team, meet deadlines and demonstrate problem-solving skills. Ability to work independently, as well as part of a team, establishing and maintaining good working relationships with P.I., supervisor, postdoctoral scholars, and other members of the research group.


  • 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 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!

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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