Bioinformatics Software Engineer


Software Engineer – Genomics

We are seeking a strong developer to join Sloan Kettering Institute’s Single Cell Research Initiative (SCRI). The team’s goal is to develop cutting-edge algorithms to interpret the flood of data emerging from single-cell technologies in order to explore questions in tumor heterogeneity, metastasis and the tumor-immune environment. If you would rather apply your superb programming and analytical skills towards a cancer cure than to finance and shopping carts, our dynamic multi-disciplinary team is the place for you. 

SCRI is directed by computational biologist Dr. Dana Pe’er, a pioneer with a strong track record of developing new conceptual approaches and widely used tools in the single-cell analysis field. We collect big biological data, primarily from multi-dimensional single-cell technologies such as single-cell RNA and chromatin sequencing and high-parameter imaging. You will improve computational infrastructure and pipelines and implement algorithms that process, integrate and visualize the multiple data types, allowing data scientists, biologists and clinicians to interact with and interpret the data. A key focus is the single-cell profiling of patient samples, with the goal of improving immunotherapy and precision medicine. Join us if you want to make an impact!

As a Software Engineer, you will:

  • Maintain and test existing SCRI code infrastructure
  • Improve sample database and data intake workflows
  • Evaluate and compare best practices for processing and analyzing different data types
  • Help to implement new software features for processing, visualizing and interpreting data from multiple modalities, including from single-cell and imaging technologies
  • Provide consultation, guidance and training to research scientists using SCRI tools


    • Bachelor’s or Master’s degree with strong machine learning/stats components, or 2+ years of programming experience; OR equivalent experience
    • Bioinformatics/Genomics experience and familiarity with common concepts, terminologies and software currently used in the field
    • Experience designing large software tools and writing efficient code
    • Proficiency in the testing process; ability to debug and modify code and use Git workflows
    • Analytical, reasoning, mathematical and problem-solving skills
    • Knowledge of algorithms and statistics
    • Proficiency in Python (including building distributable Python modules)
    • Proficiency working in cloud and HPC environments

If you are interested in this position, please apply through the MSK Careers portal: