Dr. Jean Fan
Associate prof comp biologist @JHUBME. Founder @cuSTEMized. Editor @PLOSCompBiol. Alum @HarvardDBMI @blairmagnet. Doing art like a science, science like an art.
- 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
- Reposted by Dr. Jean Fan[Not loaded yet]
- 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 🧵👇
- eLife Assessment: "This valuable study identifies and characterizes probe binding errors in a widely used commercial [ST] platform...The authors provide convincing evidence...[T]his work provides an essential quality control resource that will improve data interpretation"
- 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
