Dr. Jean Fan

@JEFworks

Associate prof comp biologist @JHUBME. Founder @cuSTEMized. Editor @PLOSCompBiol. Alum @HarvardDBMI @blairmagnet. Doing art like a science, science like an art.

Baltimore, MD jef.works Joined April 2013

413 Following 8.9K Followers 532 Posts

Latest posts 5

Dr. Jean Fan @JEFworks Oct 22

In this blog post, I put our new faster implementations of STalign + STcompare to the test!

I vibe code to align 200k spatially resolved single cells + perform spatial differential expression analysis in < 1 minute.

Try it out for yourself: jef.works/blog/2026/10/2…

Dr. Jean Fan @JEFworks Oct 19

Thanks to the amazing Kamil Slowikowski (slowkow.com), we've ported our tools STalign + STcompare to C++ so we can now run large spatial transcriptomics alignment + comparison in seconds (vs hours) 🥳🙌

Try it out:
- github.com/JEFworks-Lab/S…
- github.com/JEFworks-Lab/S…

Dr. Jean Fan @JEFworks Oct 13

Our paper on comp method STARIT using comp vision AI analysis of spatial transcriptomics data for unsupervised characterization of subcellular heterogeneity is now published 🥳

🗞️: journals.plos.org/ploscompbiol/a…
💻: github.com/JEFworks-Lab/S…

Congrats to
@dee_velazquez_ and team 👏 🥳

Dr. Jean Fan @JEFworks Oct 11

Continuing my observations of the neoliberal academic ecosystem, here is a video of my commentary on the status of women and feminized pro-social labor in STEM calling for transformative change beyond representation-based affirmative remedies 📽️: youtube.com/watch?v=l6ud-H…

Dr. Jean Fan @JEFworks Sep 22

Our paper on STcompare to identify spatially differential genes is now published 🥳: academic.oup.com/bioinformatics…

In this blog post, I apply STcompare to find spatially sexually dimorphic genes in mouse kidneys using vibe coding vs trad coding.

Follow along: jef.works/blog/2026/09/2…