Software Engineer: Bioinformatics Applications and Developer Tools

  • Mountain View, CA, USA
  • Full-time
  • Department: Engineering

Company Description

DNAnexus is the leading cloud-based SaaS company serving the global life science community. DNAnexus’ health informatics platform serves customers across a spectrum of industries — government, biopharmaceutical, clinical diagnostics, healthcare, and academic research in 33 countries with compliant protection of data, privacy, and intellectual property. The platform provides a secure and collaborative environment where genomics, multi-omics, and real world data can be combined with clinical data at scale, providing new insights that can lead to improved diagnostics, new targeted therapies and better patient care.

Job Description

Core components of our platform are the apps and developer tools we provide our users to create and run their analyses. As a software engineer of these applications, you will be responsible for creating products on the DNAnexus platform with the aim of delivering the best user and developer experience possible. You will contribute enhancements to our public library of apps and enable performance testing of these tools to make them highly available, scalable, fault tolerant and responsive. You will also be contributing to compilers for running workflows on DNAnexus that are written in open languages such as  WDL, CWL and Nextflow. To build these tools you will work closely with scientists and bioinformaticians within the company.


  • Design and build scalable applications and pipelines specifically targeted to the cloud environment
  • Identify scalability/reliability limits in both our system as well as the 3rd party technologies
  • Design and run performance testing of applications and pipelines
  • Maintain and upgrade the applications on a regular basis
  • Work closely with architect and product manager to build features
  • Understand domain-specific needs and work closely with product manager and other team members to implement them


  • Bachelors, Masters, or Ph.D. in a computational or scientific degree
  • (e.g. Computer Science, Computational Biology)
  • Ability to develop reusable, well-tested software
  • Ability to work with systems-level tools in a Unix environment (e.g. file systems, containers)
  • Fluency in Python. Fluency in one of Scala, Java, Go, R desired
  • Experience using Linux and comfortable working in a Unix shell
  • Experience with performance analysis and related skills enabling objective evaluation of tools and technologies
  • Ability to present and discuss technical designs and topics with other developers
  • Ability to write documentation that accurately and meaningfully captures designs and implementation details
  • Ability to work well within a distributed team of developers, peer review code, and own components of our platform
  • Demonstrated ability to pick up new technologies and quickly adapt to new paradigms
  • Attention to detail and working with the user’s experience in mind
  • Interest in scientific applications and topics, including cutting-edge multi-omics analysis methods
  • Solid computer science background, including algorithmic complexity
  • Passion for and knowledge of various developer tools and trends

Desired Skills and Experience:

  • Experience developing products using Amazon Web Services and Microsoft Azure
  • Knowledge of networks and system architecture for web services
  • Experience in bioinformatics or computational biology and familiarity with commonly used tools, e.g. BWA, GATK, PLINK, GWAS tools, genomic data visualization tools
  • Experience in applying workflow automation tools such as Docker, WDL, CWL, Nextflow and Snakemake
  • Familiarity with big data analytics technologies including Spark, and an understanding of relational database concepts
  • Familiarity with compilers and modern programming language paradigms
  • Interest in current practices in DevOps, continuous integration, and testing

Additional Information

Based in Mountain View, California, DNAnexus is experiencing rapid growth and is searching for the best talent to join our team. We recently completed a $100 million financing round to advance our growth globally to further serve leading healthcare and life science organizations. Key investors include Google Ventures, Perceptive Advisors, Northpond Ventures, TPG Biotech, and Foresite Capital.

If you are interested in joining our team, please apply today! 

All your information will be kept confidential according to EEO guidelines.

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