Simons Foundation: Senior Bioinformatics Engineer

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.

POSITION SUMMARY

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

MINIMUM QUALIFICATIONS

Education

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

REQUIRED APPLICATION MATERIALS

Resume / CV

Cover Letter

Example code or repositories (e.g., github)

COMPENSATION AND BENEFITS

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.

THE SIMONS FOUNDATION'S DIVERSITY COMMITMENT

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.

To apply, visit: https://simonsfoundation.wd1.myworkdayjobs.com/en-US/simonsfoundationcareers/job/Senior-Bioinformatics-Engineer_R0001635

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