Bioinformatics Software Engineer III

Memorial Sloan Kettering Cancer Center • New York, NY

22h • Hybrid

About The Position

The people of Memorial Sloan Kettering Cancer Center (MSK) are united by a singular mission: ending cancer for life. Our specialized care teams provide personalized, compassionate, expert care to patients of all ages. Informed by basic research done at our Sloan Kettering Institute, scientists across MSK collaborate to conduct innovative translational and clinical research that is driving a revolution in our understanding of cancer as a disease and improving the ability to prevent, diagnose, and treat it. MSK is dedicated to training the next generation of scientists and clinicians, who go on to pursue our mission at MSK and around the globe. Exciting Opportunity at MSK! The McPherson and Shah Labs are seeking a dedicated and determined Bioinformatics Software Engineer to develop and maintain software systems for large-scale genomic data analysis. You will join an interdisciplinary team of computational scientists, molecular biologists, and clinicians working to uncover the molecular foundations of cancer and translate genomic discoveries into improved treatments—particularly for rare and aggressive pediatric cancers. This role is open to mid-level and senior candidates, including individuals with two or more years of professional experience post-undergraduate training, as well as more experienced engineers seeking high ownership and impact. In this role, you will design, build, and maintain software that enables researchers to analyze, visualize, and interpret genomic data at scale. You will work on infrastructure that directly supports large-scale research and translational efforts, including near–real-time analysis of patient tumor samples. The position balances: Pipeline development: ≈40% General software engineering (APIs, libraries, data models, core services): ≈40% Ad-hoc analysis and research-driven code: ≈20% You will contribute across the full software lifecycle—from design and implementation to testing, documentation, and deployment—in a small, highly collaborative team.

Requirements

• Bachelor’s or Master’s degree in Computer Science, Bioinformatics, or a related field.
• 2+ years of relevant professional or research experience.
• Strong proficiency in Python.
• Experience with workflow systems such as Nextflow and/or Snakemake.
• Experience with containerized environments (Docker, Singularity).
• Comfort working in Linux/HPC environments and on the command line (bash).
• Familiarity with Conda-based dependency management.
• Basic familiarity with R.
• Building scalable pipelines for genomic data processing (single-cell WGS/RNA, long-read, Illumina).
• Developing reusable software components, APIs, and data models.
• Optimizing workflows for HPC and cloud computing environments.
• Collaborating with biologists and clinicians to translate research and clinical needs into robust software solutions.
• Writing and maintaining documentation for deployment and user support.
• Participating in code reviews and design discussions, emphasizing maintainability and best practices.

Nice To Haves

• Cloud computing platforms (AWS, GCP).
• CI/CD systems (GitHub Actions, GitLab CI).
• Frontend or web-based systems (basic maintenance).
• Prior experience with genomic, biomedical, or clinical data.

Responsibilities

• Designing, building, and maintaining software that enables researchers to analyze, visualize, and interpret genomic data at scale.
• Working on infrastructure that directly supports large-scale research and translational efforts, including near–real-time analysis of patient tumor samples.
• Pipeline development
• General software engineering (APIs, libraries, data models, core services)
• Ad-hoc analysis and research-driven code
• Contributing across the full software lifecycle—from design and implementation to testing, documentation, and deployment

What This Job Offers

• Job Type: Full-time
• Career Level: Mid Level
• Number of Employees: 5,001-10,000 employees