Systems engineer – Bioinformatics

Systems engineer – Bioinformatics

We are seeking a Systems engineer – Bioinformatics in the Computational Oncology Group. As a member of our team, you will work closely with the scientists and associates in the Computational Oncology group at Sage Bionetworks to support various research projects in cancer. The work includes prototyping software tools and setting up cloud infrastructure to support the harmonization and sharing of biomedical data (e.g., genomic, clinical, and imaging data) and DREAM Challenges ( You will also interact with other scientists and engineers in the global biomedical research community to discuss and apply cutting edge technologies to support scientific data coordination. Ideal candidates will be enthusiastic about the developing applications, processes, and standards that enable open, collaborative, and reproducible biomedical research.

Specific Responsibilities Include

  • Design and develop system architecture for managing and computing with clinical and biomedical research data types, utilizing an in-house data-sharing platform and state-of-the-art cloud technologies.
  • Design computational infrastructure to support DREAM Challenges, including for job queuing, provisioning scalable compute, and tracking status.
  • Design and build bioinformatics pipelines, including for data processing and extract-transform-load (ETL) procedures; author workflows in standardized languages.
  • Collaborate with in-house software engineering team on development of new platform functionality; prototype new tools, write documentation, and train users.

Basic Qualifications

  • BA/BS in Computer Science, Bioinformatics, Computer Engineering or related field with 3+ years of relevant job experience.
  • Proficiency in Python and working knowledge of R
  • Proficient with collaborative development and version control systems (e.g. git).
  • Proficient in Unix OS and cloud (AWS, Google) environments.
  • Proficient in container technologies such as Docker.
  • Experience maintaining RDBMS and knowledge of SQL.
  • Experience with software development life cycles.
  • Experience developing data models.
  • Experience working with web services through RESTful APIs.

Preferred Qualifications

  • Experience developing tools and workflows using either Common Workflow Language (CWL) or Workflow Definition Language (WDL).
  • Experience with NoSQL and search engine technologies such as GraphQL, MongoDB, or Elasticsearch.
  • Experience building and deploying applications to production environments (including unit/integration testing, continuous integration, and packaging).
  • Experience working with biomedical data.

About Sage Bionetworks

Sage was founded in 2009 as a non-profit spinoff from Rosetta Inpharmatics (Merck) to pioneer open approaches to advancing biomedical research.  We further our understanding of human diseases by integrating diverse clinical, genomic, imaging, and real-time sensor data to better predict disease progression and response to interventions. We are based in Seattle, Washington, and collaborate broadly throughout the world. Sage offers a comprehensive benefits package.

Apply here.

Current Positions

Computational Oncology

The Computational Biology group focuses on developing integrative probabilistic models for prediction of disease phenotypes and validating of hypotheses generated by novel methodologies. Currently opportunities include: positions in Oncology focused on conducting original research in analyzing large-scale high dimensional genomics data to develop predictive models of cancer phenotypes. Positions in collaboration with the recently merged Sage/DREAM effort, focused on designing and implementing crowd-sourced collaborative challenges around cancer phenotype prediction problems. Positions in stem cell bioinformatics with a focus on development of the data and analysis bioinformatics portal for the Progenitor Cell Biology Consortium, as well as research projects on modeling molecular mechanisms underlying stem cell differentiation.

Digital Health

Sage Bionetworks’ digital health program is designed to improve disease characterization through the use of sensor-based technologies and bi-directional feedback to improve health monitoring and provide quantitative metrics to assess disease impact on health and on quality of life. We maximize the insights gained from these efforts by providing them through Synapse, a collaborative compute platform. Our mHealth team includes expertise in software engineering (both iOS and Android), clinical study design and development, data governance and data analysis. We are actively involved in projects across a range of disease areas and within the Precision Medicine Initiative.

Neurodegenerative Research

An overarching goal of the Neurodegenerative Research (NDR) group is to improve understanding of the molecular mechanisms of neurodegeneration via computational analyses of high-dimensional genomic data-sets. Our group leads analyses of such data in consortia focused on Alzheimer’s Disease (AD) and related neurodegenerative disorders, including AMP-AD and MODEL-AD. We also work across disciplines to develop technologies that make these analyses available to a wide audience of researchers. Most notably, we recently celebrated the launch of Agora, an interactive, web-based explorer that provides access to research and analyses of nascent AD drug targets produced in conjunction with the NIH-led Accelerating Medicines Partnership.

Systems Biology

The Systems Biology research group at Sage Bionetworks is working to understand the underlying mechanisms causal to common disease. We use large-scale genomic analysis to identify disease subclasses, generate diagnostic and prognostic biomarkers, and to identify pathophysiology causal to disease in collaboration with academic and industry partners. Our current portfolio is focused on neurobiology, spanning both neurodegenerative and neuropsychiatric disorders, and includes projects in other disease areas including immunology, metabolic disease and craniofacial deformation.

Technology Platforms & Services

We’re working on the tools and platforms required to gather, share and use biomedical data in novel ways. These are targeted both at the research community, as well as organizations and individuals who are involved in providing data and being involved in the research process. They range from the technology platforms Synapse and BRIDGE, through novel methods of addressing governance issues around the distribution of human data such as E-Consent, to the ability to run Challenges to solve data-driven questions through our partnership with DREAM.