The McPherson and Shah Labs are seeking a talented and self-driven 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, 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.
Pay: $130,000.00 - $180,000.00 per year
Benefits:
Work Location: In person
