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

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

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 🧵👇

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...

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

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 👇)

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

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

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 👋

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

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 🧵👇

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!

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

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...

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

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

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

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

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

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

I got a used Nikon Labophot #microscope to do some fun #scienceathome! Check out this video of bird bath water I was able to take through the microscope with my phone. Still learning to identify protozoan microorganisms though! #scienceisforeveryone 📽️ www.youtube.com/shorts/0X0nt...

Just got my Presidential Early Career Award #PECASE certificate in the mail! 🎉 Grateful for #NSF grants that power our #BiomedicalResearch. Words remind us that federally funded research creates valuable public goods that help us reach our full potential. #ScienceMatters #FundResearch #AcademicSky

In our latest study, we use #spatialtranscriptomics to characterize cold ischemic injury at multiple time points modeling a kidney transplant setting to reveal compartment-specific changes Check out the preprint: www.biorxiv.org/content/10.1... 🧵👇 1/n

To supplement my students' learning, I made this brief explanation + demo on how to analyze #spatialtranscriptomics data to identify spatially variable genes using Moran's I #dataanalysis #Rstats Code along: www.youtube.com/watch?v=aaAN... #AcademicSky #codetutorials #Bioinformatics

Another semester done 🥳🥂 In this blog post, I reflect on how I chose to accommodate a student who wanted to miss class to attend a political rally, and how I promote the ideologies of freedom of speech and democracy through my teaching of computer science: jean.fan/2025/05/05/i... #AcademicSky

Are you interested in learning about the intersection of #AI and molecular #biology? Come to our @keystonesymposia.bsky.social this September in beautiful Santa Fe! keysym.us/KSAIBio26 #KSAIBio26 Scholarship + short talk deadline May 20 so apply soon! Look forward to seeing you there! #AcademicSky

In this #codetutorial blog post, I demonstrate a multi-sample integrative #dataanalysis of VisiumHD #spatialtranscriptomics data using geometric sketching with Harmony in Seurat to identify transcriptionally similar tissue structures. Try it out for yourself: jef.works/blog/2025/04... #AcademicSky

👏 A huge thank-you to Jean Fan (@jef.works) from @jhu.edu @hopkinsengineer.bsky.social for an outstanding IICD Seminar on evidence of off-target probe binding. Watch the recording here: youtu.be/OhYAFJ3o1mM?... #CancerResearch #SpatialOmics #MathematicalOncology

We identify evidence of off-target probe binding in the 10x Genomics #Xenium v1 Human Breast Gene Expression Panel, compromising the accuracy of resulting #singlecell #spatialtranscriptomics profiles See our preprint for more details: www.biorxiv.org/content/10.1... #AcademicSky 🧵👇 1/n

Our #bionformatics #dataviz #Rstats package scatterbar for visualizing cell-type proportions in spot-resolution #spatialtranscriptomics data is now published! Try it out! Paper: academic.oup.com/bioinformati... Code: cran.r-project.org/web/packages... Tutorials: jef.works/scatterbar/ #AcademicSky

Honored to receive the Presidential Early Career Award for Scientists and Engineers (PECASE): www.whitehouse.gov/ostp/news-up... #NSFfunded #AcademicSky #womeninSTEM For aspiring young scientists and engineers #PhDLife looking for guidance/advice, I wanted to offer a 🧵 on what I did:

Yeah I'm on sab[ #brat ]ical Made a Guess/Technologic #parody for #PhDlife 📽️ Academique: youtube.com/shorts/hvJ4X... "Write it, read it, fix it, save it, Send it to reviewers, quick, rewrite it. Trash it, change it, pay it, print it. Send it to your friends, yeah I think they'll cite it."

Made a #short about my internal conflicts on academic publishing #AcademicSky #PhDlife "Stop asking me where I want to publish our paper. I don't care...I just want people to read it. And maybe learn from it. Even build on it. Ok?" Is this #hopecore or #hopelesscore youtube.com/shorts/GV7NJ...

Our #bionformatics #Rstats method CRAWDAD for quantifying cell-type spatial relationships across length scales in #singlecell #spatialomics data is now published! Paper: www.nature.com/articles/s41... Code: github.com/JEFworks-Lab... 🥳🥂 #AcademicSky Previous 🧵 summary: bsky.app/profile/jef....

Every year, I give my lab (and myself) a "mini-sabbatical" to pursue creative endeavors outside of regular work/studies. So I spent some time reflecting on my thoughts on #AI + the role of professors in this AI transformation via a short film 📽️: www.youtube.com/watch?v=6MPs... #AcademicSky

In this student-requested video, I demo the process of making a high quality publication-ready figure (from making a mockup to enhancing visual similarity in Illustrator) and narrate my general process. Follow along and try it out for yourself: www.youtube.com/watch?v=L9qo... #phdlife #AcademicSky