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#107949 Bioinformatics Programmer

Extended Deadline: Mon 4/26/2021

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

UCSD Layoff from Career Appointment: Apply by 02/17/21 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor.

Special Selection Applicants: Apply by 02/25/21. Eligible Special Selection clients should contact their Disability Counselor for assistance.

This position will be hired at the Bioinformatics Programmer 2 or Bioinformatics Programmer 3 level depending on the experience of the selected candidate.


The mission of the Center for Epigenomics at UC San Diego is to develop a quantitative and molecular framework to study the function and regulation of the human genome, with the ultimate goal to understand the molecular basis of cancer and other human diseases. Epigenomics is at the forefront of Precision Medicine. The epigenome, a term referring to the state of DNA methylation and the covalent modifications of histone proteins in a cell, plays a central role in regulating the functional output of the genome during development.

Changes in the epigenome that result from exposure to stress, pathogenic conditions, and aging can determine the patterns of gene expression and predispose an individual to diseases. Epigenome research promises to significantly improve our understanding of the factors that drive human development and disease. The UCSD Center for Epigenomics works with researchers on the UCSD campus and beyond to foster the application of epigenomic concepts and technologies to clinical, translational, and basic research.

Under the direction of the Associate Director of Single Cell Genomics, if hired at the Bioinformatics Programmer 2 level will work on assignments of moderate scope and complexity OR if hired at the Bioinformatics Programmer 3 level will combine expertise in computational biology, epigenomics, and single-cell genomics to make independent, original contributions to research projects at the intersection of gene regulation during development and disease as well as human genetics. The Bioinformatics Programmer will implement, run, customize, optimize and benchmark data analyses pipelines as well as data visualization for single-cell assays such as single-cell RNA-seq and single-cell ATAC-seq for a wide variety of sample types spanning multiple developmental and disease states. The incumbent will perform integrative data analyses, and prepare results for oral presentation, scientific publications, and grant applications.


  • Bioinformatics Programmer 2: Six (6) years of related experience, education/training, OR a Bachelor’s degree in biological science, computational/programming, or a related area plus two (2) years of related experience/training OR Bioinformatics Programmer 3: Seven (7) years of related experience, education/training, OR a Bachelor’s degree in biological science, computational/programming, or a related area plus three (3) years of related experience/training.

  • Working knowledge in genomics, epigenetics, biostatistics. Experience in analyzing next generation sequencing data. Experience with single-cell genomics data like single-cell RNA-seq, or single-cell ATAC-seq.

  • Demonstrated working knowledge of bioinformatics methods and data structures. Working knowledge in statistics and programming languages such as Python, Perl, and R.

  • Working knowledge of databases. Proficiency with relational databases and programming languages used in the development of web-based MIS systems is a plus (e.g. SQL Server, HTML).

  • Proven working project management skills. Excellent organizational, problem solving, and analytical skills, and attention to detail.

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

  • Self-motivated, able to learn quickly, meet deadlines and demonstrate problem solving skills.

  • Working knowledge of applications programming and web development.

  • Thorough working knowledge of application and data security concepts.


  • Master's degree or PhD degree in Bioinformatics, Computational Biology, or related field.


  • 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.