Bioinformatics Programmer

The University of California, San Francisco is seeking a Bioinformatics Programmer to join the bioinformatics team supporting the Clinical Cancer Genomics Laboratory (CCGL), the Genomic Medicine Laboratory (GML), and the Institute for Human Genetics Sequencing Core (IHG Core).

Responsibilities for CCGL

In this role, this individual will be part of a bioinformatics team responsible for design, construction, and maintenance of a genomic analysis pipeline supporting the UCSF500 Cancer Gene Panel assay, a molecular test profiling DNA from tumor and normal tissue to identify mutations that may drive a patient’s cancer and aid in diagnosis and treatment, and a related RNAseq pipeline to identify gene fusions. Our internally developed cloud-based genomic analysis pipelines detect single nucleotide variants, small and medium indels, structural rearrangements, copy number variants, and microsatellite instability, and communicate with sequencing core services, laboratory information management systems and clinical reporting software.

Under the general direction of the Associate Director of Bioinformatics for the Clinical Cancer Genomics Laboratory, the Bioinformatics Programmer will design and develop new components and pipelines to support new and enhanced clinical testing. New features slated for development include tumor methylation- and whole transcriptome-based classifiers and AI tools to assist in clinical signout. Other new software developed will provide support for automating aspects of sample analysis and error reporting and integration with other clinical systems. Additional responsibilities will include supporting the development of new target capture panels and test validation as well as quarterly data analysis to improve QC and support clinical annotation. In this role, the Bioinformatics Programmer will interface with molecular pathologists, laboratory and administrative staff, medical researchers, technical teams for related clinical systems and data repositories, and research consortia.

Responsibilities for GML

The individual will be part of the bioinformatics team responsible for building and maintaining pipelines to support genomic analysis for the clinical tests performed by GML including: Rapid Whole Genome Sequencing, Exome Sequencing, Hereditary Cancer Panel, and exome subpanels. New features slated for development include long-read sequencing platforms to complement existing short-read whole genome sequencing. The individual will build infrastructure to route data to, from, and between numerous 3rd party platforms, kick off appropriate analyses, and manage data storage. New pipelines will also be built to support auto verification of negative cases, QC analyses, and retrospective studies. The individual will also perform ad hoc analyses and processing of clinical data to support lab initiatives and special cases that must be handled outside of the standard pipelines.

Responsibilities for IHG Core

The individual will work as part of the bioinformatics team responsible for building and maintaining an end-to-end automated pipeline to transport raw sequencing data from sequencing machines to UCSF Amazon Web Services Secure Enterprise Cloud, convert raw sequencing data to sequencing reads, route clinical data to downstream systems, perform individual analyses for custom research projects, return data to customers, and manage data storage.

Other responsibilities

The individual will be required to be on call nights and weekends for a minimum of 13 weeks of the year, to quickly react to any situations that may arise to ensure prompt data transfer and processing for CCGL, GML, and the IHG Core. Maintenance of pipelines, applications, and servers must often be performed outside of standard business hours to minimize disruptions to the labs.

%

of time

Essential Function (Yes/No)

Key Responsibilities

25

Yes

Applies advanced bioinformatics concepts to design, develop, modify, debug, and evaluate highly complex software programs, systems, and web tools.

30

Yes

Conducts advanced bioinformatics programming and testing of new algorithms that will interact with other related databases.

10

Yes

Formulates logic for new systems, devises logic procedures, prepares flowcharting, performs coding and data analysis, and tests / debugs highly complex programs.

10

Yes

Recommends and implements changes in development, maintenance and system standards for analysis algorithms, tools, and infrastructure.

10

Yes

Performs highly complex data modeling, performance and integration testing and builds user interfaces for a variety of internal and external constituents.

5

Yes

Interacts with senior level internal personnel.

10

Yes

Liaises with clinical researchers and provides documentation of internal processes to support research and publication.

100%

Required Qualifications

• 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 skills in order to work with both technical and non-technical personnel at all levels in the organization, including senior project leadership
• Ability to communicate technical information in a clear and concise manner
• 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 associated 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

Preferred Qualifications

• Advanced understanding of relational databases, web interfaces and operating systems.
• Advanced project management skills
• Advanced ability to interface with management on a regular basis
• Ability to lead a team, meet deadlines and demonstrate advanced problem solving skills
• In-depth knowledge of web, application and data security concepts and methods
• In-depth 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 opportunities for implementation in clinical genomics workflows
• Familiarity with large language models (LLMs), retrieval-augmented generation (RAG), prompt engineering, and generative AI applications in healthcare or life sciences

Education, Licenses/Certifications

• Bachelor's degree in biological science, computational / programming, or related area and / or equivalent experience/training - Required
• Master's Degree and 4 yrs relevant experience in bioinformatics - Required
• PhD in Bioinformatics or related field - Preferred