Bioinformatics Progr 3

University of California, San Francisco • San Francisco, CA

8d

About The Position

This role involves developing and utilizing computational tools and systems to analyze and interpret biological or other research data. The programmer will use and develop algorithms, computational techniques, and statistical methodologies, and assist in the design of new experiments. Responsibilities include implementing end-user needs in database searching and integration, maintaining computational infrastructure and local databases, and tracking the flow of samples and information for large-scale studies. The programmer will also develop analysis tools for use by lab personnel and for public dissemination. This is a seasoned, experienced bioinformatics programming professional role that requires a broad understanding of computational algorithms and systems, with the ability to identify and resolve a wide range of issues and software bugs. The individual will operate independently and demonstrate good judgment in selecting methods and techniques for obtaining solutions. Proficiency with modern AI coding frameworks (e.g., Claude, Codex, Cursor), traditional SQL and Python coding, modern machine learning toolkits for classification tasks using large-scale datasets (including transcriptomics and proteomics), and evaluating/optimizing protein modeling and folding approaches (e.g., Rosetta, AlphaFold3) is expected. A demonstrated track record of scholarly excellence is also required.

Requirements

• Bachelor's degree in biological science, computational / programming, or related area and / or equivalent experience / training.
• Minimum 3 years of related experience.
• Thorough knowledge of bioinformatics methods, nextgen sequencing processing, applications programming, web development and data structures.
• Thorough knowledge of Python bioinformatics programming design, modification and implementation.
• Thoroughly proficient with design, implementation, and management of SQL relational databases, web interfaces, and linux based operating systems.
• Thoroughly proficient with modern LLM application development tools.
• Thorough knowledge of protein folding algorithms, including AlphaFold3 and deploying packages on different hardware platforms, such as local systems and/or HPCs.
• Thorough knowledge of machine learning techniques for building predictive classifiers, including logistic regression methods, random forest, neural networks, on multi-modal data, including mass spectrometry spectra, single cell sequencing, B cell repertoire sequencing, phage immunoprecipitation, yeast display, and similar.
• Proficient knowledge of basic cell biology, genomics, and basic immunology.
• Self-motivated, work independently or as part of a team, able to learn quickly, meet deadlines, and demonstrate problem-solving skills.
• Thorough knowledge of genomic alignment algorithms, including Diamond, Minimap2, STAR.
• Conceptual familiarity with PhIPseq, yeast display, and antigen screening methods.

Nice To Haves

• Ability to interface with management on a regular basis.
• Doctoral degree in biological science, computational / programming, or related area and / or equivalent experience / training.
• Ideally in machine learning applied to biomedicine areas.

Responsibilities

• Applies complex bioinformatics concepts to implement existing software tools and systems, both command line and web based for large scale analysis of in-house generated genomic, proteomic, and immunology data.
• Develops new analysis tools, focusing on automated analysis, data aggregation, hypothesis generation. May include agentic systems.
• Develops, implements, and maintains web interfaces and SQL databases to share and display bioinformatics analysis and content with collaborators and other users.
• Performs complex data modeling, performance and integration testing, and builds user interfaces for a variety of internal and external constituents.
• Performs complex data analysis, including developing predictive machine learning classifiers, for in-house generated data.
• Assists with manuscript preparation, figure making, public data deposition.

What This Job Offers

• Job Type: Full-time
• Career Level: Senior