Job Description

Payroll Title:
Hiring Pay Scale
$87,000 - $144,800 / Year
Appointment Type:
Appointment Percent:
Total Openings:
Work Schedule:
Days, 8 hrs/day, Monday-Friday

#110035 Bioinformatics Programmer and Integration Manager

Extended Deadline: Mon 10/9/2023

UC San Diego values equity, diversity, and inclusion. If you are interested in being part of our team, possess the needed licensure and certifications, and feel that you have most of the qualifications and/or transferable skills for a job opening, we strongly encourage you to apply.

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

Job posting will remain open until a suitable candidate has been identified.


The Bioinformatics Programmer and Integration manager within CMI will undertake advanced programming research projects focused on understanding the impact of nucleic acids or other biological molecules (metabolites, proteins, etc.) processing and regulation in diseases and developmental processes.

In close collaboration with many CMI members (Principal Investigator, lab members, and CMI industry collaborators), the candidate will work to make innovative and significant contributions pertaining to bioinformatics algorithms, integration tools between key microbiome-related software developed within UC San Diego, while and generating biologically significant results.

The candidate is expected to use skills such 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 while working in a very collaborative manner.

The candidate will also serve as a mentor to students and postdocs on industry-related collaborations.

The candidate will be required to possess extensive knowledge of many metagenomic, metabolomic and other microbial analysis and modeling tools such and Qiime, Qiita, GNPS, BIG, Metaspade. Experience working with a longitudinal study will be a plus.


  • Master's degree in biological science, bioinformatics/computer science/engineering, or related area and/or equivalent experience/training.PhD preferred

  • In-depth knowledge of bioinformatics methods, applications programming, web development and data structures. Included but not limited to Qiime, Qiita, GNPS, BIGG, and Metaspade.

  • Proven knowledge of bioinformatics programming design, modification and implementation.

  • Advanced understanding of relational databases, web interfaces and operating systems. Intermediate to advanced knowledge and experience with relational database design, administration, Pearl scripting, and Java programming language.

  • Advanced project management skills. Demonstrated ability to organize large volumes of data using creative tools, logs and databases created to use with multiple research projects.

  • Thorough knowledge of modern biology and applicable field of research.

  • Successful, positive interpersonal and oral and written communication skills using tact, diplomacy, discretion, and flexibility with diverse personalities and situations. Skill to interact effectively with faculty, academics, students, and staff including those of diverse ethnicity, culture, and foreign nationals.

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

  • Advanced theoretical knowledge and independent experimental ability to perform applied bioinformatics in a molecular biology research laboratory or an equivalent combination of education and experience.

  • Advanced conceptual/theoretical experience in bioinformatics analysis of metagenomic related data.

  • Proven ability to develop tools and scripts in scientific programming using Java, C, C++, Perl and Python.

  • Advanced knowledge of database development and maintenance and proven experience with biological databases used in biomedical studies.

  • Proficiency with computer hardware and software including different operating system environments (such as Mac, Windows and UNIX) and High Performance Computing (HPC) clusters, schedulers and tools. Proven ability to update skills and knowledge as needed.

  • Knowledge, skill and ability to perform statistical analysis including experience with statistical analyses tools such as R.

  • Outstanding writing and editing skills using knowledge of conventions of academic style, English grammar, punctuation, and spelling. Ability to re-write text that is ambiguous, unorganized or grammatically incorrect.

  • Prior experience working in an environment where research relates to human diseases and developmental processes.

  • Experience with, Postgres, Redis, Bash, comfort with use and development of REST APIs, familiarity with RedCap, and Torque.


  • Job offer is contingent on a clear background check.

Pay Transparency Act

Annual Full Pay Range: $87,000 - $202,600 (will be prorated if the appointment percentage is less than 100%)

Hourly Equivalent: $41.67 - $97.03

Factors in determining the appropriate compensation for a role include experience, skills, knowledge, abilities, education, licensure and certifications, and other business and organizational needs. The Hiring Pay Scale referenced in the job posting is the budgeted salary or hourly range that the University reasonably expects to pay for this position. The Annual Full Pay Range may be broader than what the University anticipates to pay for this position, based on internal equity, budget, and collective bargaining agreements (when applicable).

Job offer is contingent on successful engagement in the UC COVID-19 Vaccination program (fully vaccinated with documented proof or approved exception/deferral).

To foster the best possible working and learning environment, UC San Diego strives to cultivate a rich and diverse environment, inclusive and supportive of all students, faculty, staff and visitors. For more information, please visit UC San Diego Principles of Community.

The University of California 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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