Bioinformatics Software Engineer III

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.

Role Overview:

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.

Key Qualifications:

• 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.

Core Skills:

• 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-Have Experience:

• 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.

Additional Information:

• Location: 323 E. 61st, NYC (Macklowe)

• Schedule: Flexible in-person, average 4 days/week onsite, 37.5 hrs.

Helpful Links:

• Compensation Philosophy

• Benefits

The salary for this role falls within MSK’s established range for similar positions and is determined by experience and qualifications. Incentive pay opportunities are available.