Flagship Pioneering, Inc.

Senior Data Engineer

Sep 19, 2023

Cambridge, MA USA

About Empress

Flagship Pioneering has conceived of and created companies such as Moderna Therapeutics (NASDAQ: MRNA), Editas Medicine (NASDAQ: EDIT), Omega Therapeutics (NASDAQ: OMGA), Seres Therapeutics (NASDAQ: MCRB), and Indigo Agriculture. Since its launch in 2000, Flagship has applied its unique hypothesis-driven innovation process to originate and foster more than 100 scientific ventures. In 2021, Flagship Pioneering was ranked 12th globally on Fortune’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies.

Founded by Flagship Pioneering in 2020, Empress Therapeutics generates good medicines, fast, by starting with chemistry inside the human body. The Empress Chemilogics™ platform uses novel insights that connect the lines of code in DNA with drug-like chemistry made in the human body to create first- or best-in-class oral medicines for a broad range of diseases quickly, predictably, and cost-effectively.

About the Position

At Empress Therapeutics, we are seeking a highly motivated, innovative, and collaborative Senior Data Engineer to join our Computational Discovery team. As a key member of the team, the successful candidate will work in close partnership with Scientists and Engineers to build a next-generation, metadata- and automation-driven data experience that enables decision making, increase productivity and reduce time spent on data processing.

Key responsibilities:

  • Design architecture and enable complete implementation of a data lake(s) compliant with FAIR, data privacy and corporate data security standards.
  • Design, implement, and maintain ETL/ELT pipelines to process and integrate multi-omics datasets from disparate sources.
  • Enable data validation and monitoring procedures to ensure data quality and accuracy.
  • Enable automation of end-to-end data flows: Faster and reliable ingestion of high throughput data in genetics, genomics and multi-omics and optimize data delivery to the lab scientists.
  • Evaluate commercial and open-source tools to improve our bioinformatics research pipelines; implement pipelines into our research workflows. Maintain awareness of new technologies and industry best practices, and champion innovative solutions.
  • Stay up to date with developments in the open-source community around data engineering, data science, and maintain awareness of industry best practices.
  • Navigate and work independently and report results to scientific team and management.

  Key requirements:  

  • MS/BS in Computational Biology, Bioinformatics, Computer Science, or related discipline. MS with 2+ yrs of industry or academic research experience (or BS with 5+ yrs of similar experience).
  • Hands on experience in data lake design, implementation, and maintenance.
  • Experience using Infrastructure as Code (IaC) to automate data infrastructure provisioning and management (e.g. Terraform, AWS CDK toolkit, CloudFormation).
  • Hands-on experience with Docker containers and container orchestration.
  • Programming experience in scripting languages such as Python & R, using version control (GitHub/Gitlab), and continuous integration environments.
  • Experience with schema design and data modeling. Data warehouse & BI Tools (Spotfire preferable).
  • Strong communication and presentation skills, capable of conveying technical information in a clear and thorough manner. 
  • Ability to work independently in a multidisciplinary, fast-paced, entrepreneurial, and results-oriented environment.

Preferred requirements:

  • Background in life sciences, biotechnology, or biomedical engineering.
  • Experience working with Biotech and supporting genomic data pipelines, integrating data from data sources such as LIMS, ELN, and other 3rd party APIs.
  • Hands on experience with workflow management systems such as Snakemake, Airflow and Nextflow.
  • Knowledge of data science and AI/ML methodologies and experience building AI/ML-enabled solutions a plus

What We’ll Offer You

  • The opportunity to learn about all aspects of our drug discovery platform and variety of new skills including working with automation.   
  • Comprehensive, competitive healthcare and dental coverage through Blue Cross Blue Shield, vision coverage through VSP, family leave, paid time off, 401k retirement plan, disability and life insurance, and fully covered parking/commuter benefits.
  • A dynamic early-stage work environment and highly interdisciplinary, talented, and collaborative team.
  • Opportunities to invent and discover.

Flagship Pioneering and our ecosystem companies are committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status. At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

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