Senior Bioinformatics Data Engineer

Company Summary:

Prologue Medicines, Inc. is a privately held early-stage company that is leveraging advanced biological and computational tools to develop breakthroughs in our understanding of secreted protein function and regulation in human physiology. More specifically, Prologue is pairing high throughput -omics technology with AI/ML based protein structure prediction to define and discover novel therapeutic protein biology.

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.

Position Summary:

We are seeking a highly motivated and creative Senior Bioinformatics Data Engineer with expertise in the integration, management, and optimization of biological and genomic data. In this role, you will be pivotal to the success of our DELVE platform, leveraging advanced bioinformatics techniques to support our efforts in viral evolution and transformative drug discovery. You will be responsible for designing and implementing robust data pipelines, managing both relational and graph databases, and ensuring the efficient processing of high-throughput experimental datasets such as next-generation sequencing (NGS) data. Your deep understanding of bioinformatics tools, algorithms, and data structures, coupled with your strong programming skills, will be essential in accelerating our discover-test-design-learn cycle. You'll work closely with our interdisciplinary teams of data scientists, biologists, and computational researchers to facilitate seamless data flow and integration, ultimately driving innovative solutions in our cutting-edge therapeutic development.

Key Responsibilities:

• Design and Develop Data Pipelines: Design, construct, and maintain scalable data pipelines to process and analyze a variety of biological datasets. Ensure data integrity and accessibility across various bioinformatics platforms.
• Database Management: Develop, optimize, and manage relational and graph databases, ensuring efficient data storage, retrieval, and analysis. Implement best practices for database security, reliability, and performance.
• Data Integration: Collaborate with Data and Experimental Scientists to integrate diverse datasets, transforming raw data into actionable insights. Facilitate seamless data flow between internal and external data sources.
• Cross-functional Collaboration: Work closely with Data and Experimental Scientists to understand data needs and provide technical support in data management and analysis.
• Automation and Optimization: Identify opportunities for automating routine data processes. Implement solutions to enhance data processing efficiency and data quality controls.
• Documentation and Reporting: Produce thorough documentation of data processes, workflows, and pipeline architecture. Generate reports on data performance metrics and system improvements.

Minimum Qualifications:

• Bachelor’s or Master’s degree in Bioinformatics, Computer Science, Information Technology, Data Science, or a related field with at least 3 years of experience.
• Proven experience as a Data Engineer or in a similar role, preferably in a bioinformatics or life sciences environment.
• Strong proficiency in managing and querying relational databases (e.g., MySQL, PostgreSQL) and graph databases (e.g., Neo4j).
• Experience with data pipeline tools and technologies such as nextflow or similar frameworks.
• Experience with cloud computing platforms, preferably AWS.
• Proficient in programming languages such as Python, or R.
• Experience with bioinformatics tools and libraries.
• Solid understanding of data integration techniques and data warehousing concepts.
• Excellent problem-solving skills and the ability to work independently or as part of a team.
• Strong communication skills, with the ability to convey complex technical concepts to diverse audiences.

Preferred Qualifications:

• Experience with application development packages such as Shiny or Streamlit.
• Experience with electronic lab notebook systems such as Benchling.
• Experience interfacing with lab automation systems.

About Flagship

Flagship Pioneering is a bioplatform innovation company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $90 billion in aggregate value. Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  Flagship has been recognized twice 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, and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com.

Flagship Pioneering is 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.