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19 Jun
Bioinformatics Scientist/Programmer - Genomics-CCGL (BIOINFORMATICS PROGR 4)

Vacancy expired!

At UCSF Health, our mission of innovative patient care, advanced technology and pioneering research is redefining what's possible for the patients we serve – a promise we share with the professionals who make up our team.

Ranked by U.S. News & World Report as seventh in the country – UCSF Health is committed to providing the most rewarding work experience while delivering the best care available anywhere. In an environment that allows for continuous learning and opportunities for professional growth, UCSF Health offers the ideal atmosphere in which to best use your skills and talents.

Department Description

The Genomics - CCGL Department at UCSF aims to achieve the highest standards in patient care, research and education. The Department provides clinical genomics testing services in a wide variety of subspecialties with highly trained subspecialists who are recognized nationally and internationally for their expertise.

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

Job Summary

The Bioinformatics Scientist/Programmer for the Clinical Cancer Genomics Laboratory (CCGL) will be part of a 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.

Our internally developed cloud-based genomic analysis pipeline detects single nucleotide variants, small and medium indels, structural rearrangements, copy number variants, and microsatellite instability, and 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, will design and develop new components for our pipeline to support new and enhanced clinical testing. New features slated for development include gene fusion detection via RNAseq 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 new target capture panels and test validation as well as quarterly data analysis to improve QC and support clinical annotation. Will interface with molecular pathologists, laboratory and administrative staff, medical researchers, technical teams for related clinical systems and data repositories, and research consortia.

Required Qualifications

  • Five years experience with Illumina sequencing data, genetic variant calling, variant analysis, annotation and filtering

  • Bachelor's Degree in biological science, computational / programming, or related area and / or equivalent experience / training

  • In-depth knowledge of bioinformatics methods and data structures

  • In-depth knowledge of bioinformatics programming design, modification and implementation

  • In-depth knowledge of 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

  • Proficiency with Python, R, Unix/Linux OS and shell scripting, and associated libraries

  • Strong knowledge of statistics and experience working with large genomics datasets

  • The flexibility to orient and work at all UCSF Health locations

Preferred Qualifications

  • PhD in Bioinformatics or related field

  • 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

  • Advanced ability to interface with management on a regular basis

  • Familiarity with cancer variant databases and clinical ontologies

  • Working knowledge of Java


  • N/A

Living Pride Standards

Service Excellence

  • Demonstrates service excellence by following the Everyday PRIDE Guide with the UCSF Medical Center standards and expectations for communication and behavior. These standards and expectations convey specific behavior associated with the Medical Center's values: Professionalism, Respect, Integrity, Diversity and Excellence, and provide guidance on how we communicate with patients, visitors, faculty, staff, and students, virtually everyone, every day and with every encounter. These standards include, but are not limited to: personal appearance, acknowledging and greeting all patients and families, introductions using AIDET, managing up, service recovery, managing delays and expectations, phone standards, electronic communication, team work, cultural sensitivity and competency.

  • Uses effective communication skills with patients and staff; demonstrates proper telephone techniques and etiquette; acts as an escort to any patient or family member needing directions; shows sensitivity to differences of culture; demonstrates a positive and supportive manner in which patients / families/ colleagues perceive interactions as positive and supportive. Exhibits team work skills to positively acknowledge and recognize other colleagues, and uses personal experiences to model and teach Living PRIDE standards.

  • Exhibits tact and professionalism in difficult situations according to PRIDE Values and Practices

  • Demonstrates an understanding of and adheres to privacy, confidentiality, and security policies and procedures related to Protected Health Information (PHI) or other sensitive and personal information.

  • Demonstrates an understanding of and adheres to safety and infection control policies and procedures.

  • Assumes accountability for improving quality metrics associated with department/unit and meeting organizational/departmental targets.

Work Environment

  • Keeps working areas neat, orderly and clutter-free, including the hallways. Adheres to cleaning processes and puts things back where they belong. Removes and reports broken equipment and furniture.

  • Picks up and disposes of any litter found throughout entire facility.

  • Posts flyers and posters in designated areas only; does not post on walls, doors or windows.

  • Knows where the Environment of Care Manual is kept in department; corrects or reports unsafe conditions to the appropriate departments.

  • Protects the physical environment and equipment from damage and theft.

The flexibility to orient and work at all UCSF Health locations is required.

Equal Employment Opportunity

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. Further information about the University of California, San Francisco, is available at UCSF seeks candidates whose skills, and personal and professional experience, have prepared them to contribute to our commitment to diversity and excellence, and the communities we serve.

Vacancy expired!

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