Data Engineer, Digital Pathology

Job description


We are looking for an expert in data engineering to join our digital pathology group as a (senior) Computational Researcher in Digital Pathology. Digital pathology is a new field with tremendous growth opportunities where we leverage advanced computational approaches to discover biological insights. You will join a team responsible for developing and deploying an advanced pathology analytics platform which includes image management and image analysis. This platform integrates big data frameworks and databases with advanced analytics, machine learning and sophisticated data visualization. You will work collaboratively in a diverse team of biologists, pathologists and computer scientists to integrate image-based data with clinical and molecular data to identify biomarkers of disease and drive drug discovery.

For this particular position, we are seeking a team member with a strong grasp of programming languages, databases, and computational tools, as well as the ability to collect, query, and store information from databases. Candidates should have demonstrated experience in data engineering using advanced computational methods including, but not limited to establishing and deploying database infrastructure (i.e. SQL) and corresponding schemas, use of programming languages to engineer image management and analysis solutions, implementation of machine learning solutions, and leveraging informatics for data evaluation (i.e. QC). Given the collaborative nature of our team we are looking for someone with a flexible and learning mindset, the ability to work in a fluid and dynamic environment, and a strong desire to pursue creative solutions to challenging problems.


  • Creating, deploying and managing databases containing structured and unstructured data from digital pathology.

  • Integrating databases with analytical systems using established APIs

  • Writing, documenting and deploying scripts using SQL, Python, R and KNIME

  • Collaborate with scientists and pathologists within the department to develop analysis strategies using large datasets of structured and unstructured data.

  • Develop and deploy code-free dashboards to enable democratic use of image analysis pipelines.

  • Implementation of data web portals with platforms such as Dash, Spotfire and KNIME


  • A degree in computer science (BS, MS, Ph.D.)

  • Extensive experience with engineering systems for managing and exploring very large data sets including structured and unstructured data (including large images)

  • Proficiency in data processing and management including the ability to query large data sets.

  • Fluency in programming languages (Python, R, Perl, Julia)

  • Proficient in workflow and data analysis platforms (KNIME, Dash, Partek)

  • Proficiency in SQL database management including use of postGIS, SQLite and SpatiaLite.

  • Excellent communication skills

  • skills to participate and thrive in a fast-paced, interactive and team-oriented culture

  • Prior experience in biomedicine, biology and pathology is appreciated.

Who We Are:

The Department of Pathology is embedded within Genentech’s Research and Early Development Organization and works to ensure that strategies for the treatment and cure of disease are based on accurate analyses of pathogenetic mechanisms. The Department Pathologists collaborate with and provide expert support to our core laboratories and research scientists in the discovery, characterization, and development of novel therapeutic products for a variety of human diseases. These include diseases caused by malignant transformation, or dysfunction of the nervous or immune systems. Our state-of-the-art labs are equipped with automated instrumentation, which evaluates and deploys existing tissue technologies for biomarker research, discovery, and assay development, as well as performing external due diligence of new assay, imaging, and analysis platforms.

Relocation benefits are available for this job posting.


    Job Sub Category

    Research Informatics


    Full time

    Job Type


    Posted Date

    Jan 13th 2022

    Job ID


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