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

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

Artificial Intelligence among University Professors

YouTube video by Prof. Jean Fan

youtu.be

Check out our updated preprint on STcompare w/ more benchmarks vs other spatial transcriptomics comparison methods, demo robustness to alignment error, etc. Preprint v2: www.biorxiv.org/content/10.1... New tutorials: jef.works/STcompare/in...

STcompare: comparative spatial transcriptomics data analysis of structurally matched tissues to characterize differentially spatially patterned genes

Motivation Comparative analysis of spatial transcriptomics (ST) data is needed to identify genes that spatially change in their expression patterns between conditions, such as in diseased versus healt...

biorxiv.org

Dr. Jean Fan@jef.works · 8mo ago

Check out our new preprint on STcompare for identifying spatially differential gene expression patterns at structurally matched locations across spatial transcriptomics datasets. Preprint on bioRxiv: www.biorxiv.org/content/10.1... R package on Github: github.com/JEFworks-Lab... #AcademicSky 🧵👇

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: www.nature.com/articles/d41...

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" jean.fan/2026/07/16/a...

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: journals.plos.org/ploscompbiol...

Another 10 years of PLOS Computational Biology: A data-driven reflection on trends in genomics research

Since the founding of PLOS Computational Biology 20 years ago, genomics research has advanced at a remarkable pace. In this 20th anniversary commentary, as an Editor for the Journal Section of Genomic...

journals.plos.org

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

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

University Professors in the Neoliberal Academic Ecosystem

YouTube video by Prof. Jean Fan

youtu.be

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: jef.works/blog/2026/05... Try it out for yourself!

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: jean.fan/2026/04/22/a...

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: www.biorxiv.org/content/10.1... 🧵👇

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.

Writing your scientific origin story #videoessay #graduation #keynote

YouTube video by Prof. Jean Fan

youtu.be

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 the-scientist.com/the-m-index-... Calculate yours: jef.works/Mentorship-I...

The M-Index: A New Metric Puts Mentorship in the Spotlight | The Scientist

The Mentorship Index aims to provide a quantifiable proxy of how researchers support junior scientists, offering a new way to evaluate academic impact.

the-scientist.com

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: jean.fan/2026/03/15/v...

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: jef.works/Mentorship-I... Blog: jef.works/blog/2026/03... 🧵👇

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: www.biorxiv.org/content/10.1... 🧵1/n

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: jef.works/blog/2026/02...

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: biorxiv.org/content/10.1... 🧵👇1/n

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: jefworks.github.io/online-biosk... Fork to modify: github.com/JEFworks/onl... #JustAcademicThings

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

Thanks to the authors for sharing all components of this beautiful mouse embryo spatial transcriptomics data from cell gene counts to per-molecule coordinates: www.ahajournals.org/doi/full/10.... So I vibe coded an app to explore the 3D subcellular transcript organization: jef.works/CellCarto-Mo...

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/

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": jean.fan/2026/01/12/n...

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...

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: jef.works/SVG-Text-Sta... Try it out! Hope it’s useful!

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: youtube.com/shorts/CnH51... #FunWithCode

Fun With Code: cover of Teardrop by Massive Attack using TidalCycles on Strudel

YouTube video by Prof. Jean Fan

youtube.com

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

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

Come Take A Portrait With Me | a short film

YouTube video by Prof. Jean Fan

youtu.be

Check out our new preprint on STARIT for creating image-based tensor representations of molecular resolution spatial transcriptomics data that can be combined with deep learning computer vision models to recover cell-states based on subcellular heterogeneity: www.biorxiv.org/content/10.6... 🧵👇

Check out our new preprint on STcompare for identifying spatially differential gene expression patterns at structurally matched locations across spatial transcriptomics datasets. Preprint on bioRxiv: www.biorxiv.org/content/10.1... R package on Github: github.com/JEFworks-Lab... #AcademicSky 🧵👇