Bioinformatics Engineer Lead – Center for Molecular Oncology

Memorial Sloan Kettering Cancer Center
Center for Molecular Oncology
United States NY New York


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 Lead to be a software team manager responsible for engaging in and directing the design and implementation of variant calling pipelines from large-scale genomic data sets. This Bioinformatics Engineer Lead will work 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. The Platform Informatics software team is responsible for developing data analysis pipeline frameworks 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 manager 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
* Interested in enabling open, reproducible research
* Familiar with genomic data and metadata
* Familiar with source control systems, preferably Git.
* Familiar with software testing methodologies and concepts
* An expert with the UNIX/Linux environment and clustered computing
* Someone who thrives in a fast-paced, dynamic environment with changing priorities
* 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 the ability to both contribute and lead a team of technical peers.

You Need:

* Masters, PhD or equivalent in computer science, bioinformatics, computational biology or other applied science with software development experience
* Demonstrated ability to manage software development in a small team environment
* Hands-on expertise running bioinformatics pipelines on genomics data
* Advanced knowledge of scripting and programming languages such as Java, C/C++, Python, Ruby, Perl and bash/csh/ksh
* 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 of CWL (Common Workflow Language)
* Experience running bioinformatics analyses using pipelines on the cloud (AWS and/or Google)
* Ability to apply troubleshooting techniques to resolve complex, cross functional issues
* Strong organizational skills, attention to detail and accuracy
* Excellent written and verbal communication skills to interact with both biologists and IT professionals

Start date

As soon as possible

How to Apply

Via website and email bic-recruit[at]cbio[dot]mskcc[dot]org. Please include #BIO_ENG_LEAD_2018 in the subject line.