Bioinformatics Programmer
University of California, San Francisco · United States ·
- Experience
- 3+ years
University of California, San Francisco · United States ·
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:
Preferred Qualifications:
Education, Licenses/Certifications: