Bioinformatics Engineer II

USA-NY-New York
2 weeks ago
Requisition ID
Research - Other

Company Overview

At Memorial Sloan Kettering (MSK), we’re not only changing the way we treat cancer, but also the way the world thinks about it. By working together and pushing forward with innovation and discovery, we’re driving excellence and improving outcomes.


For the 27th year, MSK has been named a top hospital for cancer by U.S. News & World Report. We are proud to be on Becker’s Healthcare list as one of the 150 Great Places to Work in Healthcare in 2016, as well as Glassdoor’s annual Employees’ Choice Awards 2017. We’re treating cancer, one patient at a time. Join us and make a difference every day.

Job Description

Bioinformatics Engineer – Center for Molecular Oncology

The mission of the Center for Molecular Oncology (CMO) is to promote precision oncology through genomic analysis to guide the diagnosis and treatment of cancer patients. The CMO brings together clinicians and scientists throughout MSKCC to conduct large-scale translational research involving molecular characterization of patient tumor specimens in order to identify correlations between genomic features and clinical outcomes.

The Platform Informatics group within the CMO is seeking a Bioinformatics Engineer to perform next-generation sequencing data processing, analysis, and pipeline framework design in a dynamic and exciting academic environment at the nexus of cancer biology, computer science, statistics and clinical research. Work will be performed in a small group atmosphere (approximately 10 members from diverse disciplines) with several active collaborators, and in concert with other Bioinformatics and Software Engineers. Platform Informatics is currently developing data analysis pipelines and analytic platforms on both local high performance computing clusters and cloud-based resources to facilitate research activities and precision health initiatives. This position will directly contribute toward the evolution of our infrastructure design that leverages the Common Workflow Language (CWL) specification and a container-based systems approach that enable compute portability and reproducibility.

You are:

  • A software engineer committed to applying programming skills for research discovery and clinical benefit
  • Interested in the analysis of large genomic datasets and the development of new clinical technologies
  • Hands-on expertise running bioinformatics pipelines on genomics data
  • Familiarity with genomic data and metadata
  • Expertise with UNIX/Linux command line
  • Proficiency with writing Python scripts
  • Advanced knowledge of scripting and programming languages such as Java, C/C++, Python, Ruby, Perl and bash/csh/ksh
  • Familiarity with software testing methodologies and concepts
  • Significant experience with software container technologies such as Docker and/or Singularity
  • Experience with porting programs to Docker/Singularity containers; experience with deploying and using Docker/Singularity containers
  • Experience using CWL (Common Workflow Language) specification
  • Experience running bioinformatics analyses using pipelines on the cloud (AWS and/or Google)
  • A person who enjoys working in a team, is self-motivated, can manage multiple tasks simultaneously, and can solve problems independently
  • Self-directed individual with strong desire to learn and contribute in a team of technical peers.

You have:

  • Masters or equivalent in computer science, bioinformatics, computational biology or other applied science with at least 2 years of software development experience
  • Experience with the UNIX/Linux environment and clustered computing
  • Familiarity with source control systems, preferably Git.
  • Advanced skills in Python
  • Ability to learn and adopt new technology
  • Strong interest in enabling open, reproducible research
  • Ability to apply troubleshooting techniques to resolve complex, cross functional issues
  • Demonstrated ability to work independently and meet deadlines as a member of a team.
  • Strong organizational and troubleshooting abilities, attention to detail and accuracy.
  • Excellent written and verbal communication skills to interact with both biologists and IT professionals




MSK is an equal opportunity and affirmative action employer committed to diversity and inclusion in all aspects of recruiting and employment. All qualified individuals are encouraged to apply and will receive consideration without regard to race, color, gender, gender identity or expression, sexual orientation, national origin, age, religion, creed, disability, veteran status or any other factor which cannot lawfully be used as a basis for an employment decision.  


Federal law requires employers to provide reasonable accommodation to qualified individuals with disabilities. Please tell us if you require a reasonable accommodation to apply for a job or to perform your job. Examples of reasonable accommodation include making a change to the application process or work procedures, providing documents in an alternate format, using a sign language interpreter, or using specialized equipment.


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