Bioinformatics Software Engineer


Bioinformatics 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 want to apply your superb programming and analytical skills towards a cancer cure, 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 imaging with multiplexed molecular quantification. 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 profiling of patient samples, with the goal of improving immunotherapy and precision medicine. Join us if you want to make an impact!

As a Bioinformatics Software Engineer, you will:

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


  • Bachelor’s or Master’s degree with strong coding and 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 working with genomic sequence data and processing pipelines is a big plus
  • Experience designing large software tools, writing efficient code, Git workflows
  • Proficiency working in cloud and HPC environments
  • Analytical, reasoning, mathematical and problem-solving skills
  • Knowledge of algorithms and statistics
  • Proficiency in Python (including building distributable Python modules)
  • Preference for experience maintaining large databases; proficiency in SQL

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