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Simons Foundation
  • Position Number: 4880040
  • Location: New York, NY
  • Position Type: Laboratory and Research

Bioinformatics Data Manager

SFARI Cohorts and Data Collections
Since its beginning, SFARI (Simons Foundation Autism Research Initiative) has partnered with families and clinical centers across the country to build large and diverse cohorts of well-characterized individuals with autism or with specific genetic alterations associated with neurodevelopmental risk. These include the Simons Simplex Collection (SSC), Simons Searchlight, Autism Inpatient Collection, and SPARK. The principles of community-based participatory research have been key to all cohort activities. The Simons Foundation Informatics group manages the collection and distribution of large-scale aggregate and deidentified clinical and genomic data from these cohorts, which are made available to autism researchers through SFARI Base, a clearinghouse for autism and autism-related research data and biospecimens supported by SFARI.

Bioinformatics Data Manager
The Bioinformatics group at the Simons Foundation is seeking a dedicated full-time bioinformatics data manager. The ideal candidate has outstanding attention to detail, with experience in data science or bioinformatics, and will be at the forefront of the Foundation's open data initiatives.

This critical position is responsible for overseeing an extensive and ever-expanding collection of genomics (over 170K whole-exomes and genomes) and biomedical data across Simons Foundation autism cohorts and neuroscience collaborations. The data manager will be instrumental in enhancing data accessibility and utility for both internal staff and external investigators, aligning with the principles of open data and science. The data manager will be part of the bioinformatics team and will collaborate with informatics' engineering team, the SFARI science team, and external investigators.

Key responsibilities include meticulous handling and processing of incoming data, such as genomic sequencing or biosensor data, as well as performing detailed quality control checks and downstream bioinformatics analyses. Additionally, the candidate will be responsible for preparing regular data releases and facilitating coordination among different teams, contributing to the Foundation's dynamic and collaborative environment.

Data releases
Maintain the Bioinformatics quality control pipeline, used to verify consistency with phenotypic data and ensure the integrity of released genomic data
Execute existing variant calling pipelines, which will be included in data releases
Package whole-exome and whole-genome data for regular curated and rapid releases
Manage ad hoc genetic data releases for various SFARI cohorts and datasets

Data organization
Coordinate data receipt from external investigators, vendors, and research groups
Perform incoming data cleaning, including deidentifying sample identifiers, organizing data files, and ensuring consistent metadata
Manage the organization of raw, cleaned, and released data on our local cluster environment
Harmonize our large collection of heterogeneous datasets hosted on SFARI Base

Data sharing and support
Support data sharing for SFARI investigators and collaborations, such as the Autism Rat Consortium (ARC), and Simons Sex Differences Collaboration (SSDC)
Respond promptly to dataset questions from external investigators
Support data access for cloud platforms

B.S. or M.S. in data science, bioinformatics, or a related discipline.

Required Experience
At least 4+ years' relevant work experience
Extensive experience with Linux/bash
Experience working in an HPC environment
Experience with Python
Experience with version control using git / GitHub
Basic skills in data analysis and statistics
Strong organizational skills and outstanding attention to detail
Effective oral and written communicator
Ability to thrive in collaborative environments

Desired Experience
Enthusiasm for open science and collaboration
Experience with genomics data processing and analysis
Experience writing technical documentation
Experience with cloud storage solutions (AWS, Google Cloud, Terra)
Working knowledge of SQL
Familiarity with data privacy and security regulations in the healthcare or research domain

Cover letter stating your interest in the position.
Links to code repositories or GitHub, if available

The full-time annual compensation range for this position is $130,000 – $145,000, 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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