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 with 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 enable 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 assist 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
