@jef.works - Dr. Jean Fan

09 Sep 2026 13:24 +0000

Excited to share a substantial update to our preprint on STARIT (Spatial Transcriptomics As Rasterized Image Tensors), a framework for enabling computer vision AI analysis of spatial transcriptomics data for characterizing subcellular heterogeneity. Preprint: v2 https://www.biorxiv.org/content/10.64898/2025.12.18.695193v2.full

01 Sep 2026 14:06 +0000

Our paper on spatial transcriptomic profiling of cold ischemia in mouse kidneys is now published open-access in Genome Biology: https://link.springer.com/article/10.1186/s13059-026-04167-y We hope these insights help us understand cold-storage injury in kidney transplants + inform future temporal ST analyses. Congrats team 🥳

04 Aug 2026 00:01 +0000

I'm currently running the most sophisticated agentic network (pregnancy). Within the span of 40 weeks, my biological agents (cells) will read 3 billion letters of instructions (DNA) to autonomously assemble a new human being. When will AI agents catch up? 😉 #biologyisamazing

26 Jul 2026 23:42 +0000

Continuing my observations of the neoliberal academic ecosystem with more post-tenure shenanigans, here is a video of my commentary on artificial intelligence among university professors: youtu.be/SNsIHRmTb44 https://youtu.be/SNsIHRmTb44

23 Jul 2026 15:09 +0000

Check out our updated preprint on STcompare w/ more benchmarks vs other spatial transcriptomics comparison methods, demo robustness to alignment error, etc. Preprint v2: https://www.biorxiv.org/content/10.1101/2025.11.21.689847v2.full New tutorials: https://jef.works/STcompare/index.html [contains quote post or other embedded content]

21 Jul 2026 17:54 +0000

In this @nature.com news article, I reflect on the last 10 years of spatial transcriptomics to highlight the feedback loop between industry and academia in our unified efforts to push the boundaries of science towards improving human health: https://www.nature.com/articles/d41586-026-02212-1.epdf?sharing_token=LvFy-fFjEyQoLLFRo1z4TtRgN0jAjWel9jnR3ZoTv0N3-zuVQSCnN8p1CLjLKT4J95BIHaXzBgdC3AAyGVx_wXmHDpeWtw3umBgM1xNqpnjrr2oOod84AuznqVpPHD9ejaf4ieW_X-mC9xFWIvJI5XOUAtHHSIs_3355C3V3Gls%3D

16 Jul 2026 20:23 +0000

Many of us profs are struggling w/ AI use by students. But a source of frustration I didn't anticipate: AI use by colleagues. Because if I had wanted an AI’s opinion, I too can prompt ChatGPT 🙄 More in my reflection on "Artificial Intelligence among University Professors" https://jean.fan/2026/07/16/artificial-intelligence-among-university-professors.html

06 Jul 2026 13:33 +0000

Happy 20th birthday to PLOS Computational Biology 🎂 In this perspective, as an editor for the Genomics section, I offer a data-driven reflection on how genomics research within the journal has evolved over the years by analyzing trends in submitted research papers: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1014471

02 Jul 2026 15:59 +0000

Thick-tissue spatial transcriptomics with 3DEEP-HybISS in skin enabled pseudotemporal molecular mapping of hair follicle organogenesis via natural asynchrony of follicle development: https://www.cell.com/cell/fulltext/S0092-8674%2826%2900702-6 Explore the data for yourself: https://jef.works/CellCarto-3DEEP/ Congrats to @kalhorlab + team

30 May 2026 00:38 +0000

As academic audit culture grows (now NIH pre-approvals for conferences and foreign collaborators), I hope students will remember there is another way: an academia built around mutual trust and obligation through collective effort. My take on the neoliberal academic ecosystem: youtu.be/PGO4qgfm7DU https://youtu.be/PGO4qgfm7DU

04 May 2026 15:17 +0000

In this blog post, I demo how I went from a question ➡️ "how have gas prices changed in different regions across the US over time?" ➡️ to using AI to find relevant data ➡️ to using AI to vibe code this data visualization to answer my question: https://jef.works/blog/2026/05/04/gas-prices-over-time/ Try it out for yourself!

23 Apr 2026 01:52 +0000

Before cameras, only painters could "capture reality." After, people said cameras would replace painters. But painting evolved. Now, people say AI will replace programmers. So, I reflect on things painting in the age of cameras can teach us about coding in the age of AI: https://jean.fan/2026/04/22/art-can-teach-us-about-ai.html

20 Apr 2026 15:56 +0000

We've updated our preprint characterizing the spatiotemporal impact of cold ischemia in mouse kidney to better understand the molecular underpinnings of cold-storage injury in kidney transplants. Check it out: https://www.biorxiv.org/content/10.1101/2025.05.25.654911v2.full.pdf+html 🧵👇

16 Apr 2026 23:24 +0000

What's your "scientific origin story"? In this video essay, I share mine from a keynote to graduating high school students: youtu.be/JXXIilLEmSg Every story has an origin, including yours. Through education, you gain the skills to shape this story & choose which parts you may one day like to share. https://youtu.be/JXXIilLEmSg

01 Apr 2026 14:49 +0000

Check out this article from TheScientist profiling our development of the Mentorship Index as a proxy for a researcher’s contribution to mentoring junior scholars The M-Index: A New Metric Puts Mentorship in the Spotlight https://the-scientist.com/the-m-index-a-new-metric-puts-mentorship-in-the-spotlight-74280 Calculate yours: https://jef.works/Mentorship-Index/

15 Mar 2026 20:13 +0000

Just finished teaching another semester of Genomic Data Visualization! 🥳 This semester, I integrated AI-assisted vibe coding. Some students used AI to excel beyond the mechanics of coding. Others struggled in ways I did not expect. I reflect on my blog: https://jean.fan/2026/03/15/vibe-coding-in-class.html

02 Mar 2026 13:25 +0000

As an alternative to the h-index, I made the Mentorship Index (M-index) to proxy a scientist's contribution to mentoring junior scientists. Ex. M10-index = # last-author publications where the first author had < 10 pubs. Calculate yours: https://jef.works/Mentorship-Index/ Blog: https://jef.works/blog/2026/03/01/mentorship-index/ 🧵👇

25 Feb 2026 15:24 +0000

We previously showed how changing training data alone can improve deep learning prediction of spatial transcriptomics gene expression from histology images by +38% (without any changes to model architecture). We've now updated our preprint w/ expanded results: https://www.biorxiv.org/content/10.1101/2025.09.04.674228v2 🧵1/n

22 Feb 2026 23:39 +0000

In this blog post, I vibe code to apply STcompare to kidneys assayed by two different spatial transcriptomics technologies (Visium vs. Xenium) to identify spatially consistent and differentially patterned genes. Follow along + try it out for yourself: https://jef.works/blog/2026/02/22/vibe-coding-stcompare/

19 Feb 2026 20:26 +0000

We recently updated our paper demonstrating evidence of off-target probe binding affecting the 10x Genomics Xenium spatial transcriptomics platform with key clarifications, new quantifications, and approaches for evaluating custom gene panels: https://biorxiv.org/content/10.1101/2025.03.31.646342v2.full 🧵👇1/n

22 Jan 2026 15:51 +0000

As I'm updating my NIH Biosketch for the N-th time this year, I made a Jekyll theme for students to familiarize themselves with this CV structure while building their online presence. Demo: https://jefworks.github.io/online-biosketch Fork to modify: https://github.com/JEFworks/online-biosketch #JustAcademicThings

17 Jan 2026 19:11 +0000

I never got good at CSS box model (parent-child dynamics, relative/absolute/fixed positions, etc). Vibe coding let me mentally offload those mechanics to refocus on creative design. Made this to showcase my photos of vintage cameras/microscopes/slides. Check it out: microspeci.men

15 Jan 2026 19:45 +0000

Thanks to the authors for sharing all components of this beautiful mouse embryo spatial transcriptomics data from cell gene counts to per-molecule coordinates: https://www.ahajournals.org/doi/full/10.1161/CIRCRESAHA.123.323956 So I vibe coded an app to explore the 3D subcellular transcript organization: https://jef.works/CellCarto-MouseEmbryoMERFISH/

13 Jan 2026 15:10 +0000

I've seen some cool gesture-based point cloud controllers. So I noted the JS libraries used and vibe coded a similar web app to explore the relationship between spatial, UMAP, and PCA embeddings for spatial transcriptomics data. Next level interactivity via 🖐️ Try it out: jef.works/GestureGraph/

12 Jan 2026 16:18 +0000

As a younger prof, I'm seeing generational divides in academia w/ senior colleagues (late 1900s) resisting metrification/audit culture vs. those of us raised in it. So I had fun writing a reflection on "University Professors in the Neoliberal Academic Ecosystem": https://jean.fan/2026/01/12/neoliberal-academic-ecosystem.html

11 Jan 2026 21:07 +0000

Newfound disappointment: receiving shallow peer reviews that are entirely AI-generated. The whole point is critical feedback from YOU as a real expert. If reviewers are outsourcing to AI, I think we've lost the plot 🤷‍♀️ As an editor, I'm definitely keeping better track of reviewers I can trust...

09 Jan 2026 17:00 +0000

When polishing scientific figures for publication, I try to limit fonts and font sizes to reduce visual noise. But doing this by hand is very tedious. So I vibe coded a small web app to standardize text in SVGs: https://jef.works/SVG-Text-Standardizer/ Try it out! Hope it’s useful!

07 Jan 2026 15:29 +0000

I tried to vibe code music in TidalCycles on strudel.cc but got hallucinated garbage (maybe TidalCycles is not well represented in the training data) So I read the documentation and manually coded this cover of Teardrop by Massive Attack: https://youtube.com/shorts/CnH51WmCAdY #FunWithCode

06 Jan 2026 14:05 +0000

The authors did such a great job making this spatial transcriptomics data of ovulating mouse ovaries available: https://www.pnas.org/doi/10.1073/pnas.2317418121 So I vibe coded a web browser app to interactively explore its spatiotemporal gene expression trends: https://jef.works/CellCarto-OvulationSlideseq/ Hope it's useful!

05 Jan 2026 15:08 +0000

Every year, I give my lab (+myself) a "mini-sabbatical" to pursue independent learning. This year, I'm learning to use AI tools. So I made a short film to reflect on life/death + create art in an era where it can feel like AI has usurped the value of self-expression: youtu.be/YJjmKRlmI1Q https://youtu.be/YJjmKRlmI1Q