Bioinformatics Engineer III

Our mission is to make biology easier to engineer. Ginkgo is constructing, editing, and redesigning the living world in order to answer the globe’s growing challenges in health, energy, food, materials, and more. Our bioengineers make use of an in-house automated foundry for designing and building new organisms.

Ginkgo Bioworks is a publicly traded (NYSE: $DNA), high-growth biotechnology company based in Boston’s Seaport District, that is redesigning the living world to solve some of the globe’s growing challenges in health, energy, food, material, and more. Our mission to “make biology easier to engineer” is poised to disrupt multiple industries by leveraging our innovative data, automation, and scale capabilities in biological engineering.

Ginkgo believes that if we are to grow a thriving, sustainable bioeconomy, we must also grow a new market in biosecurity. Our biosecurity and public health initiative, Concentric by Ginkgo, launched a nationwide emergency response to the COVID-19 pandemic, providing end-to-end pathogen monitoring services to schools, communities, and travelers. As we continue to scale Concentric, our work is also evolving into new and exciting directions, from global expansion to the integration of new technologies and capabilities, including our Traveler-Based Genomic Surveillance Plan with the CDC.

We are seeking a motivated Bioinformatics Engineer/Test Engineer 2/3 to join our growing Biosecurity Team and be a part of implementing innovative biosecurity solutions. Your responsibilities will include engineering pipelines, analyzing sequencing data, and supporting the development of long-term biosecurity initiatives. In this role you will interface with key teams in the Ginkgo Bioworks Foundry and Biosecurity Divisions to ensure program success through high quality deliverables and innovative offerings. You bring subject matter expertise in bioinformatics, pipeline development, and high performance computing to help the Biosecurity Division’s growing bioinformatics programs; you are a cross-functional team player, bringing diverse perspectives to our interdisciplinary team, and poised to develop the future of biosecurity.

Responsibilities

• Support Ginkgo’s Biosecurity Teams with your technical expertise in bioinformatics
• Design, build, test, deploy, and maintain bioinformatics pipelines
• Interface with software engineers to create and implement NGS data analysis pipelines for production use
• Collaborate cross-functionally with wet and dry-lab operators on experimental design and analysis to optimize new analytic approaches using NGS technologies
• Effectively communicate scientific results to technical and non-technical audiences
• Assist with shaping Ginkgo and Concentric’s overall direction as a company and support its evolving needs, as necessary

Minimum Requirements

• BS with 4+years OR MS with 2+ years OR PhD with 1+ year of experience
• 2 years of relevant industry experience is required
• Proficient in at least one software programming language (Python)
• Proficient in workflow management software (Nextflow, Docker)
• Proficient in pipeline development on AWS infrastructure
• Proficient in best practices for collaborative software development (GitHub, version control systems, CI/CD, test-driven development, and good documentation habits)
• First-hand technical experience in at least two of the following disciplines: bioinformatics, computer science, mathematics, genome assembly & annotation, statistics, probabilistic modeling, machine learning, or quantitative modeling of biological systems
• Demonstrated ability to meet the demands of multiple concurrent projects, and work efficiently in a fast-paced, high-growth environment
• Ability to adapt to changing priorities and pivot as needed in a fast-paced environment
• Superb communication skills, with the ability to effectively convey project plans and complex technical details to a wide range of internal teams, executive leadership, and external customers
• Strong curiosity for, and comfort working in, areas of biology & biosecurity previously unknown to you (and, at times, unknown to your peers)

Preferred Capabilities and Experience

• Experience analyzing and benchmarking outputs from multiple sequencing technologies: Illumina, Oxford Nanopore, PacBio, Hi-C
• Direct sequencing and bioinformatics experience with varied pathogen types (e.g. viral, bacterial, fungal) or engineered organisms
• Experience with many or all of the following: Python, bash/unix scripting, Snakemake, Nextflow, airflow, CWL, relational databases (SQL), GraphQL, distributed computing (AWS/Google Cloud), Docker, software version control (git)
• Data and Database Management: SQL, AWS, Snowflake
• Technical program management skills, JIRA, SCRUM, and agile methodologies

Total compensation for this role is market driven, with a starting salary of $110k+, as well as company stock awards. Base pay is ultimately determined based on a candidate's skills, expertise, and experience. We also offer a comprehensive benefits package including medical, dental & vision coverage, health spending accounts, voluntary benefits, leave of absence policies, Employee Assistance Program, 401(k) program with employer contribution, 8 paid holidays in addition to a full-week winter shutdown and unlimited Paid Time Off policy.

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• Ginkgo Bioworks CEO on scaling up Covid-19 testing: ‘If we try, we can win’ (CNBC)
• Ginkgo raises $70 million to ramp up COVID-19 testing for employers, universities (Boston Globe)
• Ginkgo Bioworks Redirects Its Biotech Platform to Coronavirus (Wall Street Journal)
• Ginkgo Bioworks Provides Support on Process Optimization to Moderna for COVID-19 Response (PRNewswire)
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