iiinova — where your digital self keeps evolving

Dr. Jean Fan @jef.works · 22/09/2026

Our paper on STcompare to identify spatially differential genes is now published: academic.oup.com/bioinformati... In this blog post, I apply STcompare to identify spatially sexually dimorphic genes in mouse kidneys using both vibe coding and trad coding. Follow along: jef.works/blog/2026/09...

020

Dr. Jean Fan @jef.works · 09/09/2026

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 www.biorxiv.org/content/10.6...

biorxiv.org

Spatial Transcriptomics As Rasterized Image Tensors (STARIT) characterizes cell states with subcellular molecular heterogeneity

Imaging-based spatially resolved transcriptomics (imSRT) technologies provide high-throughput molecular-resolution spatial characterization of genes within cells. Conventional analysis methods to iden...

152

Dr. Jean Fan @jef.works · 01/09/2026

Our paper on spatial transcriptomic profiling of cold ischemia in mouse kidneys is now published open-access in Genome Biology: link.springer.com/article/10.1... We hope these insights help us understand cold-storage injury in kidney transplants + inform future temporal ST analyses. Congrats team 🥳

040

Dr. Jean Fan @jef.works · 04/08/2026

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

0192

Dr. Jean Fan @jef.works · 27/07/2026

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

youtu.be

Artificial Intelligence among University Professors

YouTube video by Prof. Jean Fan

072

Dr. Jean Fan @jef.works · 21/07/2026

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...

0208

Dr. Jean Fan @jef.works · 16/07/2026

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...

073

Dr. Jean Fan @jef.works · 06/07/2026

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...

journals.plos.org

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...

041

Dr. Jean Fan @jef.works · 02/07/2026

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

050

Dr. Jean Fan @jef.works · 30/05/2026

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

youtu.be

University Professors in the Neoliberal Academic Ecosystem

YouTube video by Prof. Jean Fan

070

Dr. Jean Fan @jef.works · 04/05/2026

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!

020

Dr. Jean Fan @jef.works · 23/04/2026

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...

030

Dr. Jean Fan @jef.works · 20/04/2026

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... 🧵👇

121

Dr. Jean Fan @jef.works · 17/04/2026

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.

youtu.be

Writing your scientific origin story #videoessay #graduation #keynote

YouTube video by Prof. Jean Fan

000

Dr. Jean Fan @jef.works · 01/04/2026

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-scientist.com

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.

010

Dr. Jean Fan @jef.works · 15/03/2026

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...

jean.fan

Jean Fan | Personal site

Personal website of Prof. Jean Fan

3171

Dr. Jean Fan @jef.works · 02/03/2026

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... 🧵👇

4103

Dr. Jean Fan @jef.works · 25/02/2026

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

132

Dr. Jean Fan @jef.works · 22/02/2026

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...

130

Dr. Jean Fan @jef.works · 19/02/2026

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

13012

Dr. Jean Fan @jef.works · 22/01/2026

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

083

Dr. Jean Fan @jef.works · 17/01/2026

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

020

Dr. Jean Fan @jef.works · 15/01/2026

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...

093

Dr. Jean Fan @jef.works · 13/01/2026

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/

0162

Dr. Jean Fan @jef.works · 12/01/2026

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...

140

Dr. Jean Fan @jef.works · 11/01/2026

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...

062

Dr. Jean Fan @jef.works · 09/01/2026

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!

1284

Dr. Jean Fan @jef.works · 07/01/2026

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

youtube.com

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

YouTube video by Prof. Jean Fan

010

Dr. Jean Fan @jef.works · 06/01/2026

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!

072

Dr. Jean Fan @jef.works · 05/01/2026

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

youtu.be

Come Take A Portrait With Me | a short film

YouTube video by Prof. Jean Fan

031

Dr. Jean Fan @jef.works · 22/12/2025

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... 🧵👇

161

Dr. Jean Fan @jef.works · 03/12/2025

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 🧵👇

1143

Dr. Jean Fan @jef.works · 22/10/2025

In this journal club commentary, I reflect on an older paper from the Campbell group @sangerinstitute.bsky.social showing how normal skin is full cancer mutations yet stays healthy to highlight the opportunity to revisit this question using new spatial omics tech: www.nature.com/articles/s41...

nature.com

Revisiting the somatic mutation theory of cancer pathogenesis - Nature Reviews Genetics

Jean Fan recounts a 2015 paper by Martincorena et al. that revealed oncogenic mutations in normal tissues, also highlighting how the latest spatial technologies can now be used to study the spatial co...

021

Dr. Jean Fan @jef.works · 13/10/2025

What is RNA velocity in situ? ChatGPT kept getting it wrong... So I made this video explaining how RNA velocity in situ infers gene expression dynamics by distinguishing nuclear vs. cytoplasmic expression in spatial transcriptomics data: youtu.be/z9Oxf1hvum0 #AcademicSky

youtu.be

RNA velocity in situ infers gene expression dynamics using spatial transcriptomics data

YouTube video by Prof. Jean Fan

2268

Dr. Jean Fan @jef.works · 06/10/2025

Looking to prep for faculty job interviews? Try my Academic Interview Simulator: Faculty Edition. About as realistic as dating sims are to real dating 🤣: www.youtube.com/watch?v=dzv-... (I'm tinkering w/ AI. Inspired by the Rising Stars workshop for post-docs I just served on. Real advice 👇)

youtube.com

Academic Interview Simulation: Faculty Edition (mockup gameplay) #datingsim #parody #aivideo

YouTube video by Prof. Jean Fan

160

Dr. Jean Fan @jef.works · 27/09/2025

In this blog post, I use #RStats to explore publicly available ICE arrest data. #Dataviz shows recent trend where ICE are primarily targeting/locating people without criminal records in communities. Code along and take a look for yourself: jef.works/blog/2025/09... #CodeTutorial

0122

Reposted by Dr. Jean Fan

Keystone Symposia @keystonesymposia.bsky.social · 18/09/2025

Wrapping up AI in Molecular Biology, we celebrate 3 Future of Science Fund Award winners: @ryantheshark.bsky.social (@ucberkeleyofficial.bsky.social), Lucy Luo (@nufeinbergmed.bsky.social) & Reet Mishra. Their work shows the bright future of science! 🌟 #KSAIBio26 @drkbio.bsky.social @jef.works

073

Dr. Jean Fan @jef.works · 16/09/2025

Greetings from beautiful Sante Fe for the AI in Molecular Biology @keystonesymposia.bsky.social #KSAIBio26 Excited to bring together academic and industry leaders in this emerging field to organize, shape trends, influence policy, discuss challenges If you're around, please come say hi 👋

0122

Dr. Jean Fan @jef.works · 09/09/2025

High costs motivate efforts to predict spatial transcriptomics from H&E images w/ deep learning. In our recent preprint, we show that noise, sparsity & resolution in ST data impact performance, highlighting the importance of training data quality: www.biorxiv.org/content/10.1... 🧵1/n

1113

Dr. Jean Fan @jef.works · 29/08/2025

Our paper identifying evidence of off-target probe binding in the 10x Genomics Xenium Breast Gene Panel is now available as a reviewed preprint at #eLife elifesciences.org/reviewed-pre... We look forward to revising the paper to incorporate reviewer recommendations and other updates 🧵👇

2358

Dr. Jean Fan @jef.works · 19/08/2025

Final call for posters @keystonesymposia.bsky.social on AI in molecular biology. Deadline August 21 Beyond talks, our program also includes panel discussions on challenges + opportunities for innovation + responsibility in AI-driven biology: keysym.us/KSAIBio26 Hope u can join the conversation!

051

Dr. Jean Fan @jef.works · 31/07/2025

In this interview, I explain how university research, when funded by independent #NIH #NSF federal grants, brings oversight to biotech to fuel innovation while keeping science transparent, reliable, and in service of the public good: hub.jhu.edu/2025/07/30/j... #ResearchMatters

hub.jhu.edu

University labs help power America's biotech innovation ecosystem

Hopkins researcher Jean Fan and her team create open-source tools that help bridge the gap between academic discoveries and life-saving treatments. Cuts to federal funding threaten to break this criti...

0269

Dr. Jean Fan @jef.works · 24/07/2025

People are being arrested by ICE. What countries are they from? I analyze public data from deportationdata.org/data/ice.html to find increased arrests for immigrants from many countries #FirstTheyCame Code so you can reproduce these trends for yourself: gist.github.com/JEFworks/1f0...

041

Dr. Jean Fan @jef.works · 20/07/2025

I visualize trends in #ICE #immigration arrests and encounters over time and across select US cities using public data from deportationdata.org/data/ice.html Here is the #RStats #ggplot code so you can visualize the #dataviz trends in your own city: gist.github.com/JEFworks/0c7... #codetutorial

0174

Dr. Jean Fan @jef.works · 17/07/2025

I received some old microscopy slides from the 1800s, when at-home microscopes made it possible to look at hidden worlds of diatoms, polycystina, and other teeny tiny things. I made this website so people today can take a look too: microspeci.men Enjoy! #scienceisforeveryone #microscopy #HistSci

66418

Dr. Jean Fan @jef.works · 12/07/2025

I use #ggplot #gganimate #Rstats to visualize spatiotemporal trends in public ICE detention data. Watch ICE detention increase over time: more detainees (bigger dots), more non-criminals (blue → red), and more jails far from the border in 2025. Code #gist: gist.github.com/JEFworks/899... #DataViz

11410

Dr. Jean Fan @jef.works · 10/07/2025

In this blog post, I use #RStats to analyze ICE detention data. #Datavisualization shows record numbers of detainees without any criminal records. Further more/bigger ICE facilities are popping up far from the border. Code along and take a look for yourself: jef.works/blog/2025/07... #CodeTutorial

2249

Dr. Jean Fan @jef.works · 08/07/2025

How it started vs. How it's going #Tenured Grateful to all those who've been a part of this journey so far. But the fun is just getting started 💪 Curious to find out just what this privilege of tenure can enable. Let's see how we can put it to the test. Feel free to share ideas 😉 #AcademicSky

0271

Dr. Jean Fan @jef.works · 24/06/2025

I received this Victorian (~1850s) #microscope slide of a butterfly as a gift and was inspired to make a little video about it #sciart #microscopy 📽️ youtube.com/shorts/vVKCk... Apparently back then, people had microscopes at home as a form of entertainment! #scienceisforeveryone

041