Bioinformatics Programmer

UCSF•San Francisco, CA

7d•$148,000 - $165,000

About The Position

The University of California, San Francisco is seeking a Bioinformatics Programmer to join the bioinformatics team supporting the Clinical Cancer Genomics Laboratory (CCGL). Involves developing and utilizing computational tools and systems to analyze and interpret biological or other research data. Utilizes and develops algorithms, computational techniques, and statistical methodologies. Helps in the design of new experiments. Implements end-user needs in database searching and integration. Maintains the computational infrastructure and tracks the flow of samples and information for large-scale studies. Provides web-based bioinformatics and access to public and proprietary databases. 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.

Requirements

Developing and utilizing computational tools and systems to analyze and interpret biological or other research data.
Utilizes and develops algorithms, computational techniques, and statistical methodologies.
Helps in the design of new experiments.
Implements end-user needs in database searching and integration.
Maintains the computational infrastructure and tracks the flow of samples and information for large-scale studies.
Provides web-based bioinformatics and access to public and proprietary databases.
Design, construction, and maintenance of a genomic analysis pipeline supporting the UCSF500 Cancer Gene Panel assay.
Develops new components and pipelines to support new and enhanced clinical testing.
Develops tumor methylation- and whole transcriptome-based classifiers and AI tools to assist in clinical signout.
Develops software to support automating aspects of sample analysis and error reporting and integration with other clinical systems.
Supports the development of new target capture panels and test validation.
Performs quarterly data analysis to improve QC and support clinical annotation.
Interfaces with molecular pathologists, laboratory and administrative staff, medical researchers, technical teams for related clinical systems and data repositories, and research consortia.

Responsibilities

Design, construction, and maintenance of a genomic analysis pipeline supporting the UCSF500 Cancer Gene Panel assay.
Design and develop new components and pipelines to support new and enhanced clinical testing.
Develop tumor methylation- and whole transcriptome-based classifiers and AI tools to assist in clinical signout.
Develop software to support automating aspects of sample analysis and error reporting and integration with other clinical systems.
Support the development of new target capture panels and test validation.
Perform quarterly data analysis to improve QC and support clinical annotation.
Interface with molecular pathologists, laboratory and administrative staff, medical researchers, technical teams for related clinical systems and data repositories, and research consortia.