Senior Bioinformatics Engineer page is loaded Senior Bioinformatics Engineer Apply locations 160 Fifth Avenue, New York, NY time type Full time posted on Posted 12 Days Ago job requisition id R0001635 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.
About UsThe Simons Foundation is a private foundation established in 1994 in New York City by Jim and Marilyn Simons. With an annual grants and programs budget of $450 million, the foundation's mission is to advance the frontiers of
research in mathematics and the basic sciences.
The foundation pursues its mission through its grant-making division, comprising programs in Autism & Neuroscience, Mathematics & Physical Sciences, Life Sciences, Science, Society & Culture, and through its internal research division, the Flatiron Institute.
The Mathematics & Physical Sciences program supports work in mathematics, theoretical computer science and theoretical physics. The Life Sciences program works to advance basic research in life sciences, with, among other efforts, large grant programs in ocean ecology and in the origins of life.
The mission of Simons Foundation Autism Research Initiative (SFARI) is to improve the understanding, diagnosis, and treatment of individuals on the autism spectrum. The Neuroscience Collaborations support and convene scientists to address fundamental questions about brain function.
In 2016, the foundation launched the Flatiron Institute (FI), a multidisciplinary institute whose mission is to advance scientific research through
computational methods, including data analysis, modeling and simulation. The FI hosts scientists and collaborating expert programmers who work to create, deploy and support new state-of-the-art computational methods.
Science, Society & Culture supports and promotes scientific literacy in society generally. Specifically, the program supports the nonprofit Math for America and the independent science news sites, Quanta Magazine and The Transmitter. This program's Science Sandbox initiative seeks to unlock scientific thinking in all people, so that science becomes a more integral part of culture.
SALARY AND BENEFITS
In addition to competitive salaries, the Simons Foundation provides employees with an outstanding benefits package.
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.
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