Senior Bioinformatics Engineer

Simons Foundation
Job Location
170 Fifth Ave
7th Floor
New York, NY 10010
Job Description


The Simons Foundation in New York City is seeking a Senior Bioinformatics Engineer to develop and support whole exome sequencing and genome sequencing 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.


Main Functions and Responsibilities

  • 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




  • Doctoral degree in bioinformatics, computational sciences or related field.
  • Over five years’ work experience in bioinformatics
  • Experience with next-generation sequencing data
  • Experience in Linux/Unix cluster environment
  • Advanced programming skills in Python/Java
  • 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



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


The Simons Foundation is an Equal Opportunity Employer, M/F/D/V.

About Our Organization

The Simons Foundation’s mission is to advance the frontiers of research in mathematics and the basic sciences. Cofounded in New York City by Jim and Marilyn Simons, the foundation celebrated its 20th anniversary in 2014. The Simons Foundation at its core exists to support basic — or discovery-driven — scientific research, undertaken in pursuit of understanding the phenomena of our world. The foundation’s support of scientists generally takes the form of direct grants to individual investigators and projects, through their academic institutions. The foundation makes grants in four areas: Mathematics and Physical Sciences, Life Sciences, autism research (SFARI) and Education & Outreach. In 2013 the foundation also launched an internal research division, the Simons Center for Data Analysis. The Simons Foundation seeks to create strong collaborations and foster cross-pollination of ideas between investigators, as these interactions often lead to unexpected breakthroughs and new understanding. In an effort to directly foster such interaction between scientists, in 2012 the foundation launched a new collaborative funding model, the Simons Collaborations, which bring funded investigators — sometimes from different disciplines — together to work on a timely and important problem. To date, five Simons Collaborations have been launched in and across mathematics, physics and the life sciences. The Simons Center for Data Analysis similarly functions to unite scientists, usually across disciplines, for collaboration.

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