Bioinformatics Software Engineer

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 engineeringAPIs, libraries, data models, and 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 Responsibilities:

  • Develop and maintain scalable pipelines for genomic data processing (single-cell WGS/RNA, long-read, Illumina)
  • Build reusable software components, APIs, and data models supporting genomic workflows
  • Optimize workflows for HPC and cloud computing environments
  • Contribute to the operation and evolution of a multi-petabyte sequencing data platform spanning thousands of samples
  • Collaborate closely with biologists and clinicians to translate research and clinical needs into robust software solutions
  • Write and maintain documentation for software deployment, operation, and user support
  • Participate in code reviews and design discussions, emphasizing maintainability and best practices

Required Skills:

  • 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

Nice-to-Have Experience:

  • Experience with cloud computing platforms (e.g., AWS, GCP)
  • Exposure to CI/CD systems (e.g., GitHub Actions, GitLab CI)
  • Some experience with frontend or web-based systems, particularly maintaining existing interfaces (not a primary focus)\
  • Prior experience working with genomic, biomedical, or clinical data

Desired Attributes:

  • Enjoys writing clean, well-structured, and maintainable software
  • Able to navigate large codebases and make meaningful contributions quickly
  • Comfortable working both independently and collaboratively
  • Values software engineering best practices (testing, documentation, version control)
  • Motivated to learn cancer biology and genomics
  • Strong written and verbal communication skills

Why This Environment Is Unique:

  • Access to rare pediatric cancer cohorts
  • Close integration with clinical teams, enabling translational research
  • Opportunity to shape core infrastructure used by many labs and studies
  • Work that directly impacts how genomic data are analyzed for real patients

Education & Experience:

  • Bachelor’s or Master’s degree in Computer Science, Bioinformatics, or a related field
  • 2+ years of relevant professional or research experience

Additional Information:

  • Location: Macklowe Building, 323 East 61st Street, New York, NY 10065
  • Schedule: Flexible in-person, average 4 days a week onsite
  • Pay Range: $130,000-$180,000
  • Visa sponsorship is available for eligible candidates for this role.

How to Apply:

If you are interested, please email mcphera1@mskcc.org and include the following:

  • A link to your github and a description of 1 or 2 repos that exemplify your software engineering skills
  • Your CV attached to the email.