Bioinformatics Programmer 3 (5227C) #85723

At the University of California, Berkeley, we are dedicated to fostering a community where everyone feels welcome and can thrive. Our culture of openness, freedom and belonging make it a special place for students, faculty and staff.

As a world-leading institution, Berkeley is known for its academic and research excellence, public mission, diverse student body, and commitment to equity and social justice. Since our founding in 1868, we have driven innovation, creating global intellectual, economic and social value.

We are looking for applicants who reflect California's diversity and want to be part of an inclusive, equity-focused community that views education as a matter of social justice. Please consider whether your values align with our Guiding Values and Principles, Principles of Community, and Strategic Plan.

At UC Berkeley, we believe that learning is a fundamental part of working, and provide space for supportive colleague communities via numerous employee resource groups (staff organizations). Our goal is for everyone on the Berkeley campus to feel supported and equipped to realize their full potential. We actively support this by providing all of our full-time staff employees with at least 80 hours (10 days) of paid time per year to engage in professional development activities. Find out more about how you can grow your career at UC Berkeley.

The Department of Integrative Biology (IB) is part of the College of Letters and Science. Its focus on biological integration and diversity encompasses the full spectrum of biological organization (e.g., from molecular to biosphere) for organisms ranging from viruses to plants and animals. The faculty represent a wide range of expertise, including paleontology, population genetics, physiology, anatomy, human biology and health sciences, and organismal, ecological, and evolutionary botany and zoology.

The First Review Date for this job is May 4, 2026

Software and Pipeline Development: Designs, develops, and maintains analysis pipelines for large-scale behavioral, genomic, and imaging datasets; writes modular, documented, and version-controlled code following software engineering best practices; contributes to open-source tools developed by the lab. Adapts existing pipelines to accommodate new data modalities (e.g., spatial transcriptomics, behavioral tracking outputs), including data ingestion, quality control, and structuring outputs for downstream analysis.

Code Review and Quality Assurance: Conducts systematic code reviews for lab members to ensure correctness, reproducibility, and adherence to best practices; establishes and maintains coding standards and documentation requirements across lab projects. Identifies inconsistencies in shared analysis workflows (e.g., preprocessing steps, undocumented parameter choices), audits end-to-end pipelines, and implements standardized SOPs to ensure reproducibility across projects. Works with lab members to remediate identified issues, including rerunning analyses where necessary.

Statistical Consulting: Provides statistical guidance to lab members on experimental design, analysis approaches, and interpretation; assists in selecting and implementing appropriate methods for complex biological datasets, including mixed models, dimensionality reduction, and behavioral quantification. Supports analysis of complex biological datasets, including mixed models, dimensionality reduction, and behavioral quantification.

Research Computing and Data Infrastructure: Manages lab data storage, organization, and access on high-performance computing clusters; oversees software environments, version control, and computational reproducibility practices; serves as the primary liaison with campus research computing resources. Diagnoses and resolves pipeline failures in HPC environments (e.g., dependency conflicts, environment issues) using environment management and workflow tools; documents solutions to prevent recurrence. Identifies and resolves performance and scalability issues in large-scale workflows (e.g., optimizing parallelization, data chunking, and storage efficiency for high-volume datasets).

• Thorough knowledge of bioinformatics methods, applications programming, web development, and data structures.
• Thorough knowledge of bioinformatics programming design, modification, and implementation.
• Understanding of relational databases, web interfaces, and operating systems.
• Strong project management skills.
• Thorough knowledge of modern biology and the applicable field of research.
• Communication skills to work with both technical and non-technical personnel in multiple fields of expertise and at various levels in the organization.
• Ability to communicate technical information in a clear and concise manner.
• Ability to interface with management on a regular basis.
• Self-motivated, work independently or as part of a team, able to learn quickly, meet deadlines, and demonstrate problem-solving skills.
• Thorough knowledge of web, application, and data security concepts and methods.
• Demonstrated proficiency in scientific programming (Python, R, or equivalent), version control (git), and HPC environments
• Bachelor's degree and/or a minimum of five years of equivalent research software engineering experience.

• Advanced degree or PhD in computational biology, bioinformatics, statistics, computer science, or a related field.

This is a full-time, career position.

This position is eligible for full UC benefits. For information on the comprehensive benefits package offered by the University, please visit the University of California's Compensation & Benefits website.

Under California law, the University of California, Berkeley is required to provide a reasonable estimate of the compensation range for this role and should not offer a salary outside of the range posted in this job announcement. This range takes into account the wide range of factors that are considered in making compensation decisions including but not limited to experience, skills, knowledge, abilities, education, licensure and certifications, analysis of internal equity, and other business and organizational needs. It is not typical for an individual to be offered a salary at or near the top of the range for a position. Salary offers are determined based on final candidate qualifications and experience.

The budgeted annual salary range that the University reasonably expects to pay for this position is $101,600.00 - $189,800.00.

This position is covered by the collective bargaining agreement between the UAW (United Auto Workers) and the University of California Regents for RP.

This is not a visa opportunity. This position does not include sponsorship of a new consular H-1B visa petition that would require payment of the $100,000 supplemental fee.

To apply, please submit your resume and cover letter.

As a condition of employment, the final candidate who accepts a conditional offer of employment will be required to disclose if they have been subject to any final administrative or judicial decisions within the last seven years determining that they committed any misconduct; received notice of any allegations or are currently the subject of any administrative or disciplinary proceedings involving misconduct; have left a position after receiving notice of allegations or while under investigation in an administrative or disciplinary proceeding involving misconduct; or have filed an appeal of a finding of misconduct with a previous employer.

"Misconduct" means any violation of the policies or laws governing conduct at the applicant's previous place of employment, including, but not limited to, violations of policies or laws prohibiting sexual harassment, sexual assault, or other forms of harassment, discrimination, dishonesty, or unethical conduct, as defined by the employer. For reference, below are UC's policies addressing some forms of misconduct:

UC Sexual Violence and Sexual Harassment Policy
UC Anti-Discrimination Policy
Abusive Conduct in the Workplace

The University of California is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, protected veteran status, or other protected status under state or federal law.