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#107762 Senior Genomics Bioinformatics Programmer

Extended Deadline: Mon 5/17/2021

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

Special Selection Applicants: Apply by 02/24/21. Eligible Special Selection clients should contact their Disability Counselor for assistance.


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. We constantly seek to recruit highly motivated, technologically-advanced, and deeply interested individuals who are ready to become a part of our dynamic research and educational environment.

The Senior Bioinformatics Specialist is responsible for the implementation and overall supervision of bioinformatics analysis pipelines in a CMM laboratory that uses massively parallel sequencing technologies to investigate regulation of gene expression. In this capacity, the Senior Bioinformatics Specialist 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 Bioinformatics Specialist 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 Senior Bioinformatics Specialist 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 of related experience, education/training; 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. Demonstrated experience with programming languages: 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.

  • Advanced understanding of relational databases, web interfaces and operating systems. Proven ability to download high-throughput data sets, trouble shoot 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.

  • In-depth 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.

  • 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.

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

  • 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 programming languages: Perl, C#, C++, and 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.

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: http://www-hr.ucsd.edu/saa/nondiscr.html

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

UC San Diego School of Medicine
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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.