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    Opportunity: (Senior) Staff Scientist, Computational Biology / Bioinformatics @ New York Stem Cell Foundation -- New York, NY (US)
    Submitted by Human Resources; posted on Friday, January 05, 2024

    The New York Stem Cell Foundation (NYSCF) Research Institute is a growing and successful nonprofit whose mission is to accelerate cures for the diseases of our time through stem cell research.

    As a (Senior) Staff Scientist, Computational Biology / Bioinformatics, you will be responsible for building custom tools and developing novel algorithms for analyzing genomic and (single-cell) transcriptomic data created at the NYSCF Research Institute. Your expertise should encompass a strong foundation in statistics, deep/machine learning and data science, coupled with in-depth knowledge of molecular biology and genetics. You will also have experience building pipelines for high-throughput molecular sequencing technologies and a proven track record of data analysis method development. We encourage applications from individuals with knowledge of stem cell / developmental biology or any diseases studied at NYSCF. In this role, you will report to the VP, Computational Biology.

    What you'll do:
    • Develop deep/machine learning models for the integration and interrogation of multimodal data sets comprising molecular sequencing, health records, microscopic imaging, and other modalities
    • Create tools for the optimization of cell fate engineering protocols and screening experiments
    • Maintain and improve tools for ancestry inference from genotyping arraysImprove the detection of genomic abnormalities from sequencing and genotyping data to support QC of cell line production
    • Prototype, develop, deploy, and document pipelines for quality control, analysis and annotation of high-throughput sequencing data
    • Keep track of recent developments in computational biology, benchmark newly published methods and incorporate them into gold standard pipelines
    • Develop and implement novel data visualization strategies to summarize results and QC features
    • Migrate data storage and analysis pipelines to cloud-computing infrastructure (AWS)
    • Connect molecular profiling data with cell line metadata database
    • Support experimental groups with data organization and analysis and advise on experiment design for sequencing and other high-throughput assays
    • Report new methods and scientific results in presentations and publications
    What we're looking for:
    • PhD in Biology, Bioinformatics, Genomics, Computational Biology or a similar field, or MS degree and 5+ years of relevant work experience
    • A firm grasp of statistics, deep/machine learning and bioinformatics
    • Programming experience in Python and/or R and knowledge of software design principles
    • Experience with Linux command line tools and shell scripts
    • Basic database skills (SQL) and experience with database integration
    • Grasp of molecular biology and genetics
    • Knowledge of sequencing technologies such as (single-cell) RNA-seq, WGS/WES, ATAC-seq, etc.
    • Familiarity with standard tools for QC, alignment, quantification and downstream analysis of sequencing data
    • Ability to work in a multi-disciplinary environment of computational biologists, wetlab biologists and translational scientists
    • Familiarity with cloud computing infrastructures (ideally AWS)
    • Experience with visualization tools such as matplotlib or ggplot2 is a plus
    • Knowledge of or a keen interest in stem cell and disease biology is a plus
    • Level will be commensurate with experience
    The base starting salary range for the Staff Scientist position is $85,000 - $110,000 USD. The base starting salary range for the Senior Staff Scientist position is $110,000 - $150,000 USD. NYSCF has a 35-hour workweek. The (Senior) Staff Scientist level is classified as exempt. Multiple factors, including your experience, determine final offer amounts and levels and may vary from the amounts listed above.

    At NYSCF, we believe diversity in all forms makes us a better team, and we celebrate it. Yet studies have shown that women, people of color, and other minoritized individuals in STEM may be less likely to apply to jobs where they do not meet all of the criteria. Therefore, if you are excited about this role but your past experience does not align perfectly with every qualification in the job description, we encourage you to apply anyways. You may be just the right candidate for this or other roles.

    We offer all full-time employees a comprehensive benefits package that goes into effect on the first of the month following your start date. It includes a choice of medical, dental, and vision insurance (with 100% of the premiums paid for employees and subsidies for any dependents), 403b retirement plan with 5% employer match (immediate vesting schedule which starts after your first 90 days), short and long term insurance, life insurance, inclusive paid parental leave program, pretax transit and parking, legal aid benefits and wellness benefits. Our paid time off includes vacation, sick, personal days, flexible holidays, summer flex program, and all company holidays. If a visa is required, NYSCF will cover all of those costs. Relocation will sometimes be necessary; therefore, we will provide you with an allowance.

    In compliance with federal law, all persons hired will be required to verify identity and eligibility to work in the United States and complete the required employment eligibility verification upon hire.

    NYSCF is an equal opportunity employer, and we value diversity in our organization. We provide equal opportunities to all applicants for employment without discrimination or harassment based on race, color, religion, sex (including pregnancy, childbirth, or related medical conditions), sexual orientation, gender identity or expression, age, disability, national origin, marital or domestic/civil partnership status, genetic information, citizenship status, veteran status, or any other characteristic protected by law.

    The position is based at our location in Manhattan.

    Recruitment Phishing Scams:

    Fake job advertisements and offers are increasingly appearing on the internet. If you have encountered a job posting or have been approached with a job offer that you suspect may be fraudulent, we strongly recommend you do not respond and report it to the Federal Trade Commission ( and the FBI at You can also contact our team jobs[at] to report details of your experience.

    Please be mindful of the following:
    • NYSCF will only reach out to you through an email address.
    • Other than your email address or telephone number, which you may provide via a job application portal, NYSCF will never ask you to provide personally identifiable information about yourself (such as a Social Security Number or Driver's License Number) via a messaging application (like that used on the LinkedIn platform or Microsoft Teams or Zoom).
    • NYSCF will conduct interviews face-to-face over Zoom or in person.
    • All job postings will be listed on NYSCF's official career page ( If someone contacts you about a job or position that is not listed on the official career page, please contact the NYSCF recruitment team at the contact information below.
    • If you have any questions regarding the validity of a recruitment inquiry or an interview, please contact the NYSCF's recruitment team at jobs[at] to confirm before proceeding.
    Apply Here:


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