Bioinformatics Engineer: Bioinformatics Core

Memorial Sloan-Kettering Cancer Center (MSKCC) is a world-renowned organization dedicated to the progressive control and cure of cancer through programs of patient care, research, and education. The Bioinformatics Core (BIC) at MSKCC in New York City is seeking a Bioinformatics Engineer to perform next-generation sequence 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 (approx. 15 members from diverse disciplines) with several active collaborators, and in concert with other Bioinformatics and Software Engineers.

BIC facilitates scientific discoveries by supporting basic and clinical research groups throughout MSKCC. It is responsible for processing and analysis of high throughput next-generation sequencing data, a high performance computing facility, building training programs, and developing web-based tools.

In this role you will design, develop and operate computational pipelines for the analysis of next-generation sequencing data. Work will include both large-scale projects and small custom jobs that span a wide variety of analysis problems.


  • Master’s or equivalent in Computer Science, Bioinformatics or Mathematics
  • At least 3 years of Bioinformatics software development required
  • Thorough experience with the following:
    • Advanced skills in Perl or Python
    • Next-generation analysis toolkits (PICARD, GATK, samtools, etc.)
    • UNIX/Linux environment
  • Desirable experience:
    • Java or C/C++
    • R
    • Clustered computing
    • Relational databases (e.g. Oracle, MySQL)

MSKCC 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.

We offer an excellent salary and comprehensive benefits, including tuition reimbursement. Please visit our website at and apply on-line with job id: 3633.

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