Bioinformatics Programmer

University of California, San Francisco
Job Location
1450 3rd St
San Francisco, CA 94158
Job Description

The University of California, San Francisco is seeking a person to serve as Bioinformatics Programmer for the Clinical Cancer Genomics Laboratory. In this role, this individual will be part of a team responsible for design, construction, and maintenance of a genomic analysis pipeline for clinical cancer samples that communicates with sequencing core services, laboratory information management systems and clinical reporting software.

Under the general direction of the Associate Director of Informatics for the Clinical Cancer Genomics Laboratory, the Bioinformatics Programmer will design and develop new components for our internally developed cloud-based sequence analysis pipeline to support new and enhanced clinical testing. Features slated for development include gene fusion detection via RNAseq, detection of viral sequences, and detection of mutational signatures. 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 target capture panels and test validation as well as quarterly data analysis to improve QC and support clinical annotation.


• PhD in Bioinformatics or related field, or Master's degree and four years relevant experience
• Minimum five years of experience with Illumina sequencing data, genetic variant calling, variant analysis, annotation and filtering
• In-depth knowledge of bioinformatics methods and data structures
• In-depth knowledge of bioinformatics programming design, modification and implementation
• Python, R, Unix/Linux OS and shell scripting, and associated libraries
• Strong knowledge of statistics and experience working with large genomics datasets
• In-depth knowledge of genomics and modern 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

How to Apply
About Our Organization

The Department of Pathology at UCSF aims to achieve the highest standards in patient care, research and education. The Department provides diagnostic pathology services in a wide variety of subspecialties with highly trained subspecialists who are recognized nationally and internationally for their expertise. The Department’s research programs are diverse and interface with a wealth of basic and translational research programs that are a hallmark of UCSF.

The mission of the Clinical Cancer Genomics Laboratory (CCGL) at UCSF is to develop and validate genomic testing to support cancer clinical care and research. The CCGL provides 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.

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