Nikhil Kumar
Bioinformatics Engineer
New York, New York, United States
Summary
🤩
Rockstar🎓
Top SchoolNikhil Kumar is a Bioinformatics Engineer based in New York with 12 years of experience building production-grade genomic analysis pipelines and scientific data platforms. At Memorial Sloan Kettering he designs portable, large-scale workflows using CWL, Singularity and the TOIL executor while also developing full-stack pipeline and metadata services with Django, PostgreSQL, Elixir, and Phoenix LiveView. He is an active open-source contributor to key workflow infrastructure—improving stability, CWL import handling, and batch system integrations in the widely used toil project—which reflects his attention to reliability and operability. Earlier roles at Merck and Harvard Medical School yielded practical ML-driven publication recommendation tooling and a 50% faster algorithm for 2D genomic data, respectively. Comfortable across backend, DevOps and data visualization, he blends computational biology domain knowledge with software engineering rigor to deliver reproducible, scalable analysis. An oft-overlooked strength is his habit of contributing robust tests and error handling to upstream projects, raising quality for downstream users.
12 years of coding experience
Bachelor of Science (B.S.), Biomedical/Medical Engineering, 3.77, Bachelor of Science (B.S.), Biomedical/Medical Engineering, 3.77 at Rutgers University-New Brunswick
English
Github Skills (15)
ccl10
lsf10
workflow-engine10
aws10
python10
testing10
kubernetes9
batch-processing9
kubernetes-pods9
batchfile9
batch9
docker8
dockers8
slurm8
yaml7
Programming languages (14)
Github contributions (5)
DataBiosphere/toil
Jan 2019 - Oct 2021
A WDL, CWL and Python API supporting easy-to-use workflow engine. It is scalable, efficient and cross-platform (Linux/macOS).
Role in this project:
Back-end Developer & DevOps Engineer
Back-end Developer & DevOps EngineerContributions:25 commits, 8 PRs, 21 comments in 2 years 9 months
Contributions summary:Nikhil primarily focused on improving the stability and functionality of the `toil` workflow engine. Their contributions included adding tests for various import methods (HTTP, HTTPS, S3) and addressing issues related to CWL (Common Workflow Language) file imports, including handling different file schemes. Additionally, the user refactored the LSF (Load Sharing Facility) batch system integration, enhancing its robustness by incorporating JSON parsing, error handling, and version detection. Furthermore, the user made enhancements to memory management and UUID generation, reinforcing the overall reliability of the system.
linuxmacospythonwdlworkflow-engine
mskcc/phylowgs
Feb 2024 - Apr 2026
Application for inferring subclonal composition and evolution from whole-genome sequencing data.
Contributions:7 releases, 9 pushes, 1 branch in 2 years 2 months
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