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Bioinformatics Engineer

Simons Foundation
Job Location
New York, NY
New York, NY 10010
United States
Job Description



The Simons Foundation in New York City is seeking a Bioinformatics/Senior Bioinformatics Engineer (dependent upon experience) to develop and support whole exome and genome sequence data analysis pipelines in both research and operational modalities. This position will report to the Director of Data and Analytics in the informatics group and will work with other engineers and analysts in the informatics group, as well as with clinical and basic research teams at the foundation.



  • Design, develop and operate computational pipelines for next-generation sequencing data
  • Work on both large-scale projects and small custom tasks that span a wide variety of analysis problems
  • Develop new and/or improve upon existing algorithms for variant detection (SNPs and indels) and structural variant detection (CNVs, inversions and translocations) for clinical research purposes
  • Develop and maintain a knowledge base of variants and annotations discovered in processing of samples





  • Master’s degree or higher in bioinformatics, computational sciences or related field.


Required Attributes

  • Over 3+ years’ work experience in research-and-development setting in bioinformatics
  • Experience with next-generation sequencing data
  • Experience in Linux/Unix cluster environment
  • Advanced programming skills in Python
  • Strong background in algorithm development, statistical methods, machine learning and distributed computing.
  • Extensive knowledge of computational genomics and experience with high-throughput data analysis
  • Outstanding personal initiative and the ability to work effectively as part of a team
  • Excellent verbal and written communication skills


Desirable Experience

  • Familiarity with C++, Perl, Matlab and R is desirable.
  • Familiarity with databases — relational and noSQL — cloud computing and web services is desirable.


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 provides 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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