Staff Software Engineer, Bioinformatics

The Role 

GeneDx, the world’s leading genomics diagnostics company, is seeking a Senior Software Engineer/Bioinformatician for our Bioinformatics Platform team. 

As a Senior Software Engineer, you will work with other engineers and bioinformaticians in our team to deliver faster, cheaper, more reliable, more scalable, and more accurate bioinformatics software into our production diagnostics platform. You will lead technical design and implementation efforts to improve our bioinformatics workflow and bioinformatics algorithms; executing using the best practices and principles of modern software engineering. You will lead analytical validation efforts in support of new pipeline development and existing pipeline improvements. When working with non-technical team members, you’ll understand their root cause needs and be able to propose novel technical solutions. Additionally, you will collaborate with and support other data scientists and software engineers in their code development and assist in establishing best practices within the team.

As a senior engineer, you own strategic initiatives of the team and be comfortable coordinating work including other senior staff. Your breadth of engineering knowledge will allow you to make and review plans for complex projects that may include other engineering specialties (e.g. devops). You will be empowered and trusted to make critical decisions where mistakes could lead to serious delay or cancelation of an initiative. You will be expected to find resourceful and creative solutions to hard problems and support your teammates in doing the same.

Experience, Traits, and Skills 

• Proficiency in Python; comfortable with working in other similar languages  .
• Experience building/consuming API calls/responses and ETL functions.
• Experience with AWS services, Docker, Kubernetes, Helm, CI/CD, automated testing, and data logging suites/toolsets.
• Good understanding of general software engineering patterns, best practices, and methods.
• 8+ years professional experience (industry setting) designing and supporting robust applications using modern object-oriented frameworks.
• Able to define and execute work across platforms over multiple quarters, as a technical project lead and contributor.
• Have developed novel bioinformatics algorithms and products.
• Track record of influential publications or leadership of scientific collaborations.
• Successful history of delivering scalable production software.  
• Excellent communication skills; ability to work collaboratively with other development teams.
• Knowledge of bioinformatics pipeline scalability, observability, and cost efficiency.
• Be able to lead, coordinate, and execute validation efforts for new products.
• Deep understanding of technical implementation of complex variant calling - structural variants beyond copy number.
• Ability to improve existing variant calling algorithms.
• Technical knowledge of NGS and non-NGS laboratory assays.
• Prior experience working in a CAP/CLIA regulated setting.
• Prior experience preparing for a CAP/CLIA inspection.
• Understanding of assay panel design considerations.
• Able to coordinate and execute efforts for modifications to existing bioinformatics products.
• Experience troubleshooting wet-lab and dry-lab issues.
• Strong understanding of bayesian statistics and ML in relation to common bioinformatics applications.
• Familiarity with samtools, gatk, picard, vcftools, bedtools.
• Familiarity with bioinformatics workflow management tools and concepts.
• PhD strongly preferred.

The Responsibilities 

• Design, write, and maintain high quality and robust software applications and services to meet team goals.
• Design novel algorithms in support of new product offerings, lead analytical validation efforts in support of existing pipeline improvements.
• Collaborate with teammates and product managers in developing development roadmaps and sprint planning.
• Lead establishment and adherence to robust and compliant software development best practices.
• Participate in software quality testing and validation.
• Participate in cross-functional development with other teams.
• Contribute to continuous improvement in the operating model of the team.
• Level up your teammates to bring deeper understanding of technical know-how across teams.
• Ensure quality technical implementation within our platform.
• Your code is peer-reviewed through the pull request process. You lead reviews of others’ work.
• Produce high quality code that meets company coding standards and is clearly written and documented so that other software developers can work with it.

The Objectives 

• Delivery of a cost-efficient, reliable, and scalable bioinformatics platform.
• You are an active and vital contributor to your team and your co-workers’ success and well-being.
• Bioinformatics platform is scalable, cost controlled, reliable, and engineered with modern software engineering best practices.
• Bioinformatics software is modular and evolvable, allowing easy implementation of algorithmic improvements.