Ryan Thompson
Assistant Professor Of Medicine at Icahn School of Medicine at Mount Sinai
Village/Town of Mount Kisco, New York, United States
Summary
👤
Senior🎓
Top SchoolRyan Thompson is an Assistant Professor of Medicine and computational biologist with 16 years of experience applying statistics, mathematics, and software engineering to large-scale NGS and microarray datasets. He builds reproducible workflows and reusable analysis tools that emphasize rigorous statistical design, clear visualization, and practical deployment—work that spans from improving clinical biomarker classifiers to epigenetic and transcriptomic systems biology. A prolific open-source contributor, he has improved tooling across bioinformatics and developer ecosystems, including contributions to Snakemake’s cluster robustness and popular Emacs projects like Magit and Swiper. He mentors biologists and programmers alike, translating complex biological questions into maintainable code and testable analyses, and has a track record of turning methodological advances into clinical and research impact. An unexpected thread through his career is deep engagement with developer ergonomics (Emacs tooling and test automation), reflecting an engineer’s eye for productivity as well as science.
16 years of coding experience
3 years of employment as a software developer
University of California, San DiegoDoctor of Philosophy (Ph.D.), Bioinformatics, Doctor of Philosophy (Ph.D.), Bioinformatics at The Scripps Research InstituteHigh School, High School at Scotch Plains/Fanwood High SchoolBachelor’s Degree, Biology, General, Bachelor’s Degree, Biology, General at University of Virginia
English, German
Stackoverflow
41,408reputation
3.7mreached
151answers
169questions
subprocess
top-1%
r
top-5%
python
top-5%
Github Skills (32)
ivy10
git10
python10
package-management10
testing10
command-line-arguments10
magit10
subprocess10
emacs-lisp10
command-line-parser10
emacs10
argument-parsing10
workflow-management10
completions10
scripting9
Programming languages (20)
Github contributions (5)
dimitri/el-get
Oct 2011 - Mar 2014
Manage the external elisp bits and pieces upon which you depend!
Role in this project:
Full-stack Developer
Full-stack DeveloperContributions:445 commits, 17 comments, 2 issues in 2 years 5 months
Contributions summary:Ryan's contributions center around enhancing the functionality and maintainability of `el-get`, a package management system for Emacs. Their work includes fixing bugs, such as stale references, and adding features like support for specifying the installation branch and handling different GitHub URL formats for various VCS types. The user also improved the build process by removing unnecessary shell-quoting, migrating to the "http-tar" methods, and addressing versioning and dependency issues. Their commits involved changes to recipe files, and core elisp code.
elispspacemacsmagitemacsbits
magit/magit
Jan 2012 - May 2019
It's Magit! A Git Porcelain inside Emacs.
Role in this project:Software Developer (Emacs/Magit Plugin Developer)
Software Developer (Emacs/Magit Plugin Developer)Contributions:15 commits, 3 PRs, 22 comments in 7 years 5 months
Contributions summary:Ryan primarily contributed to the `magit/magit` repository by developing and improving functionality related to the `git-wip` plugin. Their work included adding new features like `magit-wip-mode`, enhancing the font-locking of the first line in commit messages, and addressing issues like buffer read-only errors in rebase mode. The user also made various other improvements, including fixes for whitespace in yes/no questions and correcting how branch names are handled.
porcelainmagitemacsgit-porcelainemacs-lisp
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