Staff Software Engineer/Bioinformatician

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.

Pay Transparency, Budgeted Range$183,664—$229,580 USD

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Science - Minded, Patient - Focused. 

At GeneDx, we create, follow, and are informed by cutting-edge science. With over 20 years of expertise in diagnosing rare disorders and diseases, and pioneering work in the identification of new disease-causing genes, our commitment to genetic disease detection, discovery, and diagnosis is based on sound science and is focused on enhancing patient care.

Experts in what matters most. 

With hundreds of genetic counselors, MD/PhD scientists, and clinical and molecular genomics specialists on staff, we are the industry’s genetic testing experts and proud of it. We share the same goal as healthcare providers, patients, and families: to provide clear, accurate, and meaningful answers we all can trust.

SEQUENCING HAS THE POWER TO SOLVE DIAGNOSTIC CHALLENGES.

From sequencing to reporting and beyond, our technical and clinical experts are providing guidance every step of the way:

TECHNICAL EXPERTISE

• High-quality testing: Our laboratory is CLIA certified and CAP accredited and most of our tests are also New York State approved.
• Advanced detection: By interrogating genes for complex variants, we can identify the underlying causes of conditions that may otherwise be missed.

CLINICAL EXPERTISE

• Thorough analysis: We classify variants according to our custom adaptation of the most recent guidelines. We then leverage our rich internal database for additional interpretation evidence.
• Customized care: Our experts review all test results and write reports in a clear, concise, and personalized way. We also include information for research studies in specific clinical situations.
• Impactful discovery: Our researchers continue working to find answers even after testing is complete. Through both internal research efforts and global collaborations, we have identified and published hundreds of new disease-gene relationships and developed novel tools for genomic data analysis. These efforts ultimately deliver more diagnostic findings to individuals.

Learn more About Us here.

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 Benefits include:

• Paid Time Off (PTO)
• Health, Dental, Vision and Life insurance
• 401k Retirement Savings Plan
• Employee Discounts
• Voluntary benefits

GeneDx is an Equal Opportunity Employer.

All privacy policy information can be found here.