Are you passionate about using technology to solve life-impacting challenges? Help us change how the world treats Cancer! We can provide you with the opportunity to make a difference in your career.
The Cell-Free DNA (cfDNA) Informatics Team in the MSK Center for Molecular Oncology (CMO) is looking for a talented and self-driven 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. The team develops 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. You will contribute toward the evolution of the current infrastructure design that leverages the Common Workflow Language (CWL) specification and a container-based systems approach that enables compute portability and reproducibility.
You will:
- Work and collaborate with a top-notch team of researchers, software engineers and clinicians to build a platform for streamlining and automating genomic data analysis.
- Implement and follow the standard methodologies in software development, code versioning, software testing and deployment and assists in unit/functional regression, and system testing.
- Take part in technical discussion including but not limited to code reviews, product design, and build/release management.
- Process and analyze data from high-throughput next-generation sequencing.
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
- Someone who thrives in a fast-paced, dynamic environment with changing priorities
- Able to apply troubleshooting techniques to resolve complex, cross functional issues
- 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 to 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
- Experience with SQL/NoSQL databases like MySQL or MongoDB
- Hands-on expertise running bioinformatics pipelines on genomics data on-prem (LSF/SLURM) or in cloud (AWS/AZURE)
- Familiar with software container technologies such as Docker and/or Singularity
- Experience using CWL (Common Workflow Language)
- Strong interest in enabling open, reproducible research
- Strong organizational and troubleshooting abilities, attention to detail and accuracy.
- Excellent written and verbal communication skills to interact with both biologists and IT professionals