About this role
Job title: Bioinformatics Programmer
About the Role Join UCSF's bioinformatics team supporting the Clinical Cancer Genomics Laboratory (CCGL) as a Bioinformatics Programmer. You will develop and apply computational tools, algorithms, and statistical methods to analyze cancer genomics data, design new experiments, and maintain scalable computational infrastructure and data flows. You will also provide accessible web-based bioinformatics resources and integrate with clinical systems.
What You'll Do
- Design, develop, and maintain genomic analysis pipelines for the UCSF500 Cancer Gene Panel and related RNAseq workflows.
- Build and enhance cloud-based pipelines; ensure integration with sequencing core services, LIMS, and clinical reporting software.
- Collaborate with molecular pathologists, laboratory staff, researchers, and data repositories to support clinical testing and research.
- Develop new features such as tumor methylation- and whole-transcriptome-based classifiers and AI tools for clinical signout.
- Automate aspects of sample analysis and error reporting and integrate with other clinical systems; support QC, test validation, and annotation.
- Contribute to target panel development and quarterly data analysis to improve QC and annotation.
- Maintain and extend documentation and provide end-user support for data access and analyses.
What We're Looking For
- In-depth knowledge of bioinformatics methods and data structures.
- In-depth knowledge of bioinformatics programming design, modification and implementation.
- In-depth knowledge of genetics, genomics, and cancer biology.
- Advanced interpersonal and communication skills to work with technical and non-technical stakeholders.
- Ability to communicate complex technical information clearly.
- Minimum 5 years of experience with Illumina sequencing data, genetic variant calling, variant analysis, annotation and filtering.
- Proficiency with Python, R, Unix/Linux OS and shell scripting, and related libraries.
- Strong knowledge of statistics and experience working with large genomics datasets.
- Minimum 3 years of experience with clinical pipelines, procedures, implementation, and documentation.
- Strong experience with APIs.
- Advanced skills in data migration and data conversion.
Nice to Have
- Advanced understanding of relational databases, web interfaces, and operating systems.
- Advanced project management and leadership abilities; ability to interface regularly with management and lead teams.
- Knowledge of web, application, and data security concepts and methods.
- Working knowledge of Amazon Web Services, including AWS Batch.
- Experience developing, evaluating, or deploying machine learning models for genomics, biomedical, or healthcare applications.
- Ability to critically evaluate emerging AI technologies and identify clinical genomics implementation opportunities.
- Familiarity with large language models, retrieval-augmented generation, prompt engineering, and generative AI in healthcare or life sciences.
- Education: Bachelor’s degree in biological sciences or computational areas; Master’s with 4+ years in bioinformatics; PhD preferred.