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... 🧵👇
- Conventional analysis methods to identify cell-types and states in molecular resolution spatial transcriptomics data rely on tallying the number of molecules per gene per segmented cell, overlooking subcellular heterogeneity that can play important functional roles in defining cell states.
- We developed STARIT (Spatial Transcriptomics As Rasterized Image Tensors) as an alternative way to represent molecular resolution spatial transcriptomics data to incorporate subcellular molecular organization.
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View full threadCongrats to @deevelazquez.bsky.social for leading this work 👏 🥳 🎉 Dee is applying to PhD programs so if you’re recruiting graduate students, definitely check out STARIT. Preprint: www.biorxiv.org/content/10.6... Software: github.com/JEFworks-Lab...
- 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 🧵👇
- Comparative analysis of spatial transcriptomics datasets can be performed using traditional non-spatial differential gene expression analysis but these approaches can miss cases where a gene has similar gene expression magnitude despite having distinct spatial expression patterns.
- STcompare provides orthogonal insights to such differential expression analysis by incorporating spatial information by enabling two differential spatial comparison tests: one based on spatial correlation, and one based on spatial fold change.
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View full threadCongrats to Kalen Clifton and Vivien Jiang for leading this work! 👏 🥳 🎉 Both will soon be looking for postdoc (Kalen) and PhD (Vivien) opportunities so if you’re recruiting, definitely check out their work: www.biorxiv.org/content/10.1...
- 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 👇)
- When interviewing for faculty positions, it can feel like there's a "right answer" to "win". But the reality is: there’s no perfect script. Teach your ideas with clarity and enthusiasm. Trust that your genuine self will resonate more than performing what you think others want. Find your fit! 🍀
- 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 FanWrapping 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
- Deep learning can predict gene expression from H&E, but performance varies widely, highlighting the need for further investigation into factors that impact prediction performance. Our study assesses the impact of training data quality on the predictive performance. 2/n
- We train identical models using matched ST datasets from different technologies (Visium vs Xenium) with unique technical constraints that impact data quality. We find that the predictive performance across genes is 38% higher when trained on Xenium data compared to Visium data. 3/n
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View full threadCongratulations to Caleb Hallinan for leading this work in collaboration with CJ Lucas @jhu.edu @hopkinsengineer.bsky.social
- 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"
- I would also like to note that, given the results presented in our paper, previous results presented in the publication describing the Xenium technology and demonstrated using this gene panel (Janesick et al, Nature Communication, December 2023) are in part erroneous. However...
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View full threadSee the previous preprint post for more details: bsky.app/profile/jef....
- 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
- 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
