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    Opportunity: Bioinformatics Data Manager @ Simons Foundation -- New York, NY (US)
    Submitted by Ryan V; posted on Wednesday, December 20, 2023

    DESCRIPTION

    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 de-identified 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.

    ESSENTIAL FUNCTIONS / RESPONSIBILITIES

    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

    MINIMUM QUALIFICATIONS

    Education:
    • 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

    COMPENSATION & BENEFITS

    • 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.

    HOW TO APPLY

    To apply, visit: https://apptrkr.com/4878759

    Required application materials:
    • Resume
    • Cover letter stating your interest in the position.
    • Links to code repositories or GitHub, if available

    POLICY

    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.

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