Simon Ye
Senior Bioinformatics Scientist
San Diego, California, United States
Summary
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Rockstar🎓
Top SchoolSimon Ye is a Senior Bioinformatics Scientist with 15 years of experience blending software engineering and computational biology, currently working across industry roles at Novartis and Kate Therapeutics in Cambridge, MA. He holds a B.S. in Chemistry and Computer Science from Stanford and pursued a Ph.D. at MIT, reflecting deep interdisciplinary training. Early software roles at Google and research positions at Stanford and Sandia underpin strong systems and research instincts applied to translational bioinformatics. Simon contributes to prominent open-source infrastructure—improving build and deployment for the well-known Snakemake workflow manager—demonstrating attention to reproducible, production-ready pipelines. He brings practical DevOps experience (shadow directories, scheduler fixes) to accelerate complex genomic workflows from prototype to regulated environments. Colleagues rely on him to bridge rigorous computational methods with scalable engineering practices that drive therapeutic discovery.
16 years of coding experience
3 years of employment as a software developer
Doctor of Philosophy (Ph.D.), MEMP, Doctor of Philosophy (Ph.D.), MEMP at Massachusetts Institute of TechnologyB. S., Chemistry, Computer Science, B. S., Chemistry, Computer Science at Stanford University
Stackoverflow
167reputation
16kreached
6answers
3questions
Github Skills (17)
python10
cicd10
build-automation10
workflow-management10
testing9
cli8
command-line-interface8
command-line8
dockers7
docker7
inspect6
backbonejs6
preprocessor6
ocr6
inspector6
Programming languages (18)
Github contributions (5)
snakemake/snakemake
Jul 2015 - Nov 2018
This is the development home of the workflow management system Snakemake. For general information, see
Role in this project:
DevOps Engineer
DevOps EngineerContributions:13 commits in 3 years 5 months
Contributions summary:Simon's contributions primarily focused on improving the build and deployment process of the Snakemake workflow management system. They modified the `snakemake` and `executors.py` files to enable shadow directory support, allowing for isolated working directories during rule execution and also introduced the `--keep-shadow` command line argument. Furthermore, the user fixed a bug in the scheduler lock, and addressed issues related to file handling, as well as touch directives.
snakemakereproducibilityworkflow-management
yesimon/metax_bakeoff_2019
Aug 2019 - Sep 2019
Contributions:2 commits, 2 pushes, 1 branch in 1 month
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