Senior Genomics Bioinformatics Programmer

UC San Diego Health
United States California Berkeley


UC San Diego Health
Senior Genomics Bioinformatics Programmer
Filing Deadline: Open Until Filled
Salary Range: Commensurate with Experience

The UCSD Department of Cellular and Molecular Medicine (CMM) is one of two basic science units in the School of Medicine where world-class researchers study fundamental cellular processes and pathways using a variety of techniques from classical genetics and fluorescence microscopy to high-throughput genomics, systems biology, and crystallography.

Our 36 faculty and over 200 postdoctoral scholars, graduate students, and research staff work on the cutting edge of biology, cutting across fields from basic biochemistry and genetics to genomics, systems biology and stem cell biology. The faculty also play a major role in medical and graduate student training, providing educational and programmatic offerings that span several disciplines and provide diversity to meet the interests of a broad spectrum of students and scholars.

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 Senior 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. The Senior 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, 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.


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:


• Bachelor's Degree in biological science, computational/programming, or related area and/or equivalent experience/training.
• A minimum of five (5+) or more years of relevant experience.
• Advance knowledge of bioinformatics methods, applications programming, web development and data structures. Experience with programming languages, including Python and R. 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.
• Demonstrated ability to analyze scientific technical information.
• In-depth knowledge of web, application and data security concepts and methods.
• Advanced understanding of relational databases, web interfaces and operating systems. Ability to download high-throughput data sets, troubleshoot sequencing data, conduct standard statistical analysis and data visualization.
• In-depth knowledge of modern biology and applicable field of research. Working knowledge of biological systems including transcription, genetics, and epigenetics.
• Strong project management skills. Ability to organize, prioritize and manage multiple project activities effectively and deal with changing priorities.
• 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.
• Advanced ability to interface with management on a regular basis. Proven ability to communicate and deal effectively and productively with people at all levels of responsibility in various functional areas.
• Demonstrated ability to lead a team, meet deadlines and demonstrate advanced 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.
• Demonstrated experience with Perl, C#, C++, or Java.
• 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.

Start date

To be determined

How to Apply