Senior Software Engineer

Research & Development United States


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Senior Software Engineer - Remote or San Diego, CA


We’re a different kind of biotech company.  And we’re here to make a difference.


Prometheus Biosciences, Inc. (Nasdaq: RXDX), is a clinical-stage biotechnology company pioneering a precision medicine approach for the discovery, development, and commercialization of novel therapeutic and companion diagnostic products for the treatment of immune-mediated diseases. 


The Company’s precision medicine platform, Prometheus360™, combines proprietary machine learning-based analytical approaches with one of the world’s largest gastrointestinal bioinformatics databases to identify novel therapeutic targets and develop therapeutic candidates to engage those targets. Prometheus Biosciences was named Best Places to Work by Biospace in 2022 and is headquartered in San Diego, CA. 



Data Science & Engineering (DSE) at Prometheus Biosciences, Inc. is looking for a full-stack software engineer with experience in back-end infrastructure, databases and big data.  Experience (or at least a strong interest) in bioinformatics, biology and machine learning is a strong plus.


DSE is a software and methods group that develops computational and machine learning approaches to discover new drug targets, validate biomarkers and develop companion diagnostics.  We’re a small, remote team where members have a chance to wear multiple hats, contribute to the needs across R&D, collaborate with experts from diverse backgrounds and build expertise in the underlying science and technology.


This position can be fully remote, the ideal candidate will be self-motivated and able to work effectively with a remote-first team.



  • Provide expertise as we make organization-wide decisions about data formats, cloud infrastructure for compute and storage, and the rest of our tech stack.
  • Help create a cloud infrastructure that enables:
    • Scientists and computational biologists to perform queries, load large quantities of data for processing, and track the provenance of their results;
    • Collaborators at academic institutions, and scientists at Prometheus Biosciences, to send us data continuously as we enroll more patients and generate more data;
    • Other non-developers to perform queries, summarize statistics, and visualize data (font-end) from our consolidated database.
  • Build automated ETL workflows that ingest, clean, and harmonize complex, multi-modal data from a variety of sources and formats into a single source of truth in the cloud.
  • Work with Computational Biologists to implement and improve bioinformatics pipelines to run more efficiently.
  • Work with logistics, data curation, and sample management experts to organize and harmonize all of our data.
  • Review other developer's code, provide feedback, and integrate suggestions from others.
  • Write clear, accessible, and effective documentation that targets users with various levels of technical and scientific knowledge.
  • Support, train, and mentor engineers and data scientists.
  • Collaborate with scientists (immunologists, cell and molecular biologists, etc.) across Prometheus Biosciences.


Education and Experience

  • 5+ years of software engineering experience with a focus on data infrastructure.
  • A technical degree (such as Computer Science, Computer Engineering, Biomedical Engineering, Electrical Engineering, Mathematics, Physics, Statistics) or equivalent experience.
  • Fluent in Python and SQL and feel at home in a remote Linux server session.
  • Familiar with cloud compute and storage (such as GCP, Azure, and AWS).
  • Passionate about collaborative development tools and workflow (GitHub issues and PRs, code review, unit tests, listing, etc.).
  • Comfortable with (and in fact, prefers) asynchronous communication and a documentation-first mindset.


Additional Experience - Nice-to-haves

  • Experience with R and other bioinformatics tools.
  • Knowledge about statistics and machine learning.
  • Experience with Pandas, Athena, RedShift, Apache Spark.
  • Experience with Docker, Kubernetes, and CI/CD.
  • Familiarity with infrastructure-as-code (Terraform, CloudFormation, Helm).
  • Experience with human genetics, genomics, immunology, or any biomedical discipline.


Skills and Abilities

  • Self-motivated with excellent planning, problem-solving, organizational and communication skills including presenting data to all levels of the organization.
  • High integrity, be able to inspire trust and exhibit the highest level of ethics.
  • Entrepreneurial, enjoys working in a fast-paced, smaller-company environment.
  • Willingness to travel, depending on business needs.