University of California , San Francisco

Bioinformatics Programmer

US

Sponsorship not specifiedDetected 91 days ago
PythonBashReactData StructuresAlgorithmsAWSLinuxMachine LearningData AnalysisLLMsRAGStatisticsProject ManagementBioinformaticsNGSResearchLeadershipProblem Solving

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Entry-level history60
PERM / green-card track50
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About the role

  • New features slated for development include tumor methylation- and whole transcriptome-based classifiers and AI tools to assist in clinical signout.
  • 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.
  • New features slated for development include long-read sequencing platforms to complement existing short-read whole genome sequencing.

Responsibilities

  • Applies advanced bioinformatics concepts to design, develop, modify, debug, and evaluate highly complex software programs, systems, and web tools.
  • Formulates logic for new systems, devises logic procedures, prepares flowcharting, performs coding and data analysis, and tests / debugs highly complex programs.
  • Recommends and implements changes in development, maintenance and system standards for analysis algorithms, tools, and infrastructure.
  • Performs highly complex data modeling, performance and integration testing and builds user interfaces for a variety of internal and external constituents.
  • Liaises with clinical researchers and provides documentation of internal processes to support research and publication.
  • 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.
  • 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.
  • 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.

Requirements

  • In-depth knowledge of bioinformatics methods and data structures
  • In-depth knowledge of genetics, genomics, and cancer biology
  • Ability to communicate technical information in a clear and concise manner
  • Minimum 5 years of experience with Illumina sequencing data, genetic variant calling, variant analysis, annotation and filtering
  • Proficiency with Python, R, Unix/Linux OS and shell scripting, and associated libraries
  • Strong knowledge of statistics and experience working with large genomics datasets
  • Minimum 3 years of experience with clinical pipelines, procedures, implementation, and documentation
  • Strong experience with APIs
  • 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.

Nice to have

  • Advanced understanding of relational databases, web interfaces and operating systems.
  • Advanced project management skills
  • Advanced ability to interface with management on a regular basis
  • In-depth knowledge of web, application and data security concepts and methods
  • Working knowledge of Amazon Web Services, including AWS Batch
  • Ability to critically evaluate emerging AI technologies and identify opportunities for implementation in clinical genomics workflows
  • Bachelor's degree in biological science, computational / programming, or related area and / or equivalent experience/training.
  • Master's Degree and 4 yrs relevant experience in bioinformatics.

Company info

  • 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.
  • 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
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