[Next-Generation Sequencing Book]
  • [Photo] Claudia Q Mares • May 22, 2015

    RESPONSIBILITIES

    In collaboration with scientists, clinicians and bioinformatics staff within the Center of Personalized Medicine, the Sr. Software Engineer will create and implement software solutions. Provide direction, planning and application development to staff and leadership in support of the center's technical requirements, computational and analytical needs, related web sites and best practices. Suggests and implements solutions that comply with hospital guidelines and meets the requirements for security, supportability and portability while maintaining compliance with regulatory bodies. Implement state-of-the art computational methods, and develop innovative methods toward the development of rigorous diagnostic tests. Functions both independently and in a team environment to plan, design, develop, modify, and maintain new and existing professional grade analysis pipelines, databases and database applications. Responsible for all phases of software development life cycle and create deliverables by the end of each stage. Write SOPs and train users. Interact with clients, vendors and hospital IT support group efficiently. Provide IT support for group staff when necessary.

    REQUIREMENTS

    Preferred Experience:
    • M.S. in Computer Science or Bioinformatics with 2-5 years of related work experience, or Ph.D. in Computer Science or Bioinformatics with 1-3 year's experience or equivalent preferred
    • Advanced - expert level linux background and bash scripting experience
    • Advanced object oriented programming experience (C++, Java or R)
    • Advanced scripting language experience (Perl or Python)
    • Experience in database development (Oracle/SQL/MySQL/PostgreSQL/MongoDB)
    • Prior development experience in a research, industry or clinical environment with understanding of the software development cycle
    • Experience with pipeline development using multiple tools and across multiple environments
    • Understanding of key biological processes and genomics technologies is desired, specifically next generation sequencing (NGS)
    • Experience with bioinformatics tools such as GATK, BEDtools, VCFtools, SAMtools, Picard and tools within Bioconductor is desired.
    • Experience moving and analyzing large genomic datasets
    • Demonstrated ability to implement and understand complex algorithms
    • Demonstrated ability to manage multiple projects and overlapping deadlines
    • Excellent communication skills, both written and verbal is required.
    Additional Skills and Abilities:
    • Experience with data analysis, specifically whole genome sequencing (WGS), whole exome sequencing (WEX), transcriptome and copy number analysis is a plus.
    • Parallel programming experience (MPI/OpenMP/etc.) is desired.
    • LIMS experience is a plus.
    • Familiarity with REST and JSON is a plus.
    • Experience with MapReduce is a plus.

    HOW TO APPLY

    Please apply on line via http://www.chla.org or send your resume to cmares[at]chla.usc.edu

    POLICY

    EOE/Minorities/Women/Disabled/Veterans

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