Bioinformatics Programmer III

University of California San Francisco
San Francisco CA
Jul 17, 2018
Required Education
Masters Degree/MBA
Position Type
Full time

UCSF is seeking a person to serve as Bioinformatics Programmer for the Clinical Cancer Genomics Laboratory (CCGL).  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 CCGL, the Bioinformatics Programmer will design and develop data analysis pipelines to support analysis of massively parallel sequencing of cancer samples for patient care. 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.

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.

The University of California, San Francisco (UCSF) is a leading university dedicated to promoting health worldwide through advanced biomedical research, graduate-level education in the life sciences and health professions, and excellence in patient care. It is the only campus in the 10-campus UC system dedicated exclusively to the health sciences.

Required Qualifications
Bachelor's degree in biological science, computational / programming, or related area and / or equivalent experience / training
Thorough knowledge of bioinformatics methods and data structures
Thorough knowledge of bioinformatics programming design, modification and implementation Thorough knowledge of genomics and cancer biology
Experience with Illumina sequencing data, genetic variant calling, variant analysis, annotation, and filtering
 Python, R, Unix/Linux OS and shell scripting, and associated libraries
Knowledge of statistics and ability to work with large genomics datasets
Communication skills to work with both technical and non-technical personnel in multiple fields of expertise and at various levels in the organization
 Strong project management skills
 Ability to communicate technical information in a clear and concise manner
 Self-motivated, work independently or as part of a team, able to learn quickly, meet deadlines and demonstrate problem solving skills

Preferred Qualifications
 Master's degree in bioinformatics
 Understanding of relational databases, web interfaces, and operating systems
 Ability to interface with management on a regular basis
Thorough knowledge of web, application and data security concepts and methods
 Familiarity with cancer variant databases and clinical ontologies



The University of California San Francisco is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, age, protected veteran or disabled status, or genetic information



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