• Bioinformatics Data Engineer I

    Location US-MA-Boston
    Job Posted Date 4 weeks ago(4 weeks ago)
    Job ID
    IT/Health IT/Informatics
    full time
  • Overview

    Located in Boston and the surrounding communities, Dana-Farber Cancer Institute brings together world renowned clinicians, innovative researchers and dedicated professionals, allies in the common mission of conquering cancer, HIV/AIDS and related diseases. Combining extremely talented people with the best technologies in a genuinely positive environment, we provide compassionate and comprehensive care to patients of all ages; we conduct research that advances treatment; we educate tomorrow's physician/researchers; we reach out to underserved members of our community; and we work with amazing partners, including other Harvard Medical School-affiliated hospitals.

    The generation, management, and interpretation of molecular data across the Dana-Farber Cancer Institute (DFCI) and its collaborators across Brigham and Women’s Hospital and Boston Children’s Hospital is critical for the advancement of precision oncology. This position will serve as the point person for the quality and availability of molecular testing data at DFCI.


    We are seeking a bioinformatics data engineer who is passionate about the potential for genomics data to inform clinical care of cancer patients and the groundbreaking discoveries that are a product of genomics and molecular data. The Bioinformatics Data Engineer will be focused on ensuring the highest of quality in our bioinformatics data that includes understanding and interrogating data for themselves as well as shepherding data to other systems for research and the enablement of precision medicine through the use of automation and data pipelines.


    • Serve as a subject matter expert for all genomics data, including having a thorough understanding of the exclusion/inclusion rules for data (e.g. what constitutes a failed sample, and why it would not be included in our applications), and having a solid grasp on the relationships between each table and how to query it
    • Manage ETL process between sources where bioinformatics data are generated and consumers of data including MatchMiner: a system for matching patients to clinical trials, cBioPortal: A system for visualizing genomics data, and OncDRS: a system for performing clinical research.
    • Work with vendor that maintains enterprise data warehouse to define rules for data extraction.
    • Develop automated QC measures to validate quality of data between each transition.
    • Manage rules engine around pathology data going to downstream systems.
    • Serving as conduit between problems and developers of systems.
    • Maintain updated ERDs for any environment that contains sequencing data
    • Maintain updated data dictionaries for any environment that contains sequencing data
    • Manage relationships with other groups that share interdependencies on Dana Farber molecular data.


    • Bachelors degree required, MS preferred or PhD in bioinformatics, computer science and/or the life sciences and 0-2 years relevant experience.
    • Experience with Perl, Python, or related scripting/data extraction language


    • Familiar with relational databases such as MySql, MsSql, or similar


    • Prior experience with genomics or Next Generation Sequencing data preferred


    • Experience with common cancer genetics databases a plus [COSMIC, TCGA, NCI, NCBI, etc.]


    • Detail oriented with ability and drive to gain deep understanding of technical systems


    • Ability to communicate issues in a succinct manner


    • Ability to prioritize and manage various tasks and projects reliably and in a timely manner


    • Experience in working with data transformation pipelines and understanding of nuances of such pipelines.


    • Requires minimal direction from leadership and possesses the ability to adapt to new challenges as they arise


    • Possess strong documentation skills

    Dana-Farber Cancer Institute is an equal opportunity employer and affirms the right of every qualified applicant to receive consideration for employment without regard to race, color, religion, sex, gender identity or expression, national origin, sexual orientation, genetic information, disability, age, ancestry, military service, protected veteran status, or other groups as protected by law.


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