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Senior Bioinformatics Engineer

Simons Foundation
New York City, New York
$150,000 – $175,000
Closing date
Jul 27, 2024

Senior Bioinformatics Engineer

SPARK, launched by the Simons Foundation in 2016, is the largest study of autism ever undertaken. It is open to all individuals living in the U.S. with a professional diagnosis of autism and their family members. The initiative aims to improve the lives of people with autism by identifying the causes of autism and informing more effective therapies, treatments, services, and supports. Participants share medical and behavioral information through online surveys. They can also choose to provide saliva samples for DNA analysis. This data is made available to researchers worldwide to explore the genetic underpinnings of autism, identify potential subtypes, and power downstream research. SPARK also engages the autism community by offering participants access to the latest research findings and potential opportunities to participate in additional studies.

The Bioinformatics team at the Simons Foundation is seeking a full-time senior bioinformatics engineer. The position will play an integral role in returning genetic results to thousands of SPARK participants, including ASD and secondary health-related variants, as well as work with petabytes of genomics data and develop workflows for a variety of informatics needs across SFARI. The ideal candidate will have experience developing bioinformatics pipelines, coding using software development best practices, and performing reproducible genetic analyses.

The candidate will be responsible for bioinformatics analysis of the SPARK return of genetic results process, including tracking samples from sequencing to return, developing and running analysis workflows, and working with the SPARK return of results (RoR) team on the review and selection of returnable variants. The candidate will also be responsible for packaging SFARI cohort genetic datasets for release in SFARI Base as new sequencing data is received and as other dataset updates are needed.

The senior bioinformatics engineer will report to the Deputy Director of Bioinformatics and will work alongside a growing team, including a software engineer, a data manager, and a data analyst on the Bioinformatics team, as well as with Informatics' engineering team, the SDBR (SFARI Data and Biospecimen Repository) team, and various SFARI cohort teams (SPARK, Searchlight, ABN, etc.).

This is a full-time position based at the Simons Foundation offices in New York City.

Essential Functions & Responsibilities

Return of Genetic Results
• Manage the bioinformatics portion of the return of genetic results process, including delivery of sequencing data, variant analysis, and clinical validation orders
• Track data deliveries of samples sent for sequencing
• Run quality control pipeline to confirm RoR eligibility
• Run variant filtering and annotation pipelines for SNVs/Indels & CNVs
• Coordinate lab confirmation orders for predicted pathogenic variants
• Analyze and summarize statistics for sequencing batches
• Respond to questions from SPARK or lab related to variant predictions/orders

Maintenance and Development of Bioinformatics Pipelines
• Implement new features in existing pipelines, as needed
• Design, develop, and test new bioinformatics pipelines, implementing end-to-end workflows that integrate existing tools, to support the needs and goals of SFARI and Informatics

Data Releases
• Package SFARI cohort genomics datasets for release by performing quality control, integrating data from various sources/versions, and documenting datasets details and methods descriptions
• Answer questions about genomics datasets for data in SFARI Base

• Ph.D. in bioinformatics, computational biology, or related field

Required Skills & Experience
• At least 4+ years of relevant work experience
• Strong Python skills and software development best practices
• Experience with sequencing data (whole exome or whole genome) and related tools
• Experience performing reproducible data analysis
• Experience working in an HPC environment
• Experience with git/github
• Effective oral and written communicator
• Ability to thrive in collaborative environments

Helpful skills
• Project management experience
• Experience analyzing large research datasets (>10,000 individuals)
• Familiarity with core genetics concepts
• Solid understanding of statistical analysis
• Experience generating interactive data visualizations or dashboards
• Desire to continually learn and stay up-to-date with best practices and the latest methods

• Resume / CV
• Cover Letter
• Example code or repositories (e.g., github)

• The full-time annual compensation range for this position is $150,000 – $175,000, depending on experience.
• In addition to competitive salaries, the Simons Foundation provides employees with an outstanding benefits package.

Many of the greatest ideas and discoveries come from a diverse mix of minds, backgrounds and experiences, and we are committed to cultivating an inclusive work environment. The Simons Foundation actively seeks a diverse applicant pool and encourages candidates of all backgrounds to apply. We provide equal opportunities to all employees and applicants for employment without regard to race, religion, color, age, sex, national origin, sexual orientation, gender identity, genetic disposition, neurodiversity, disability, veteran status, or any other protected category under federal, state and local law.

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