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...

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Dr. Jean Fan @jef.works · 09/09/2026

Using real imaging-based spatial transcriptomics (MERFISH) data of bacteria, STARIT identifies cells with similar overall exp magnitude but distinct subcellular organization: showing more punctuated vs diffuse transcript localization for flagellar subunits, with potential functional consequences.

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Dr. Jean Fan @jef.works · 09/09/2026

In this updated preprint, we show STARIT can delineate smooth trajectories with continuous changes in subcellular localization, is robust to partial volume capture under certain conditions, and is compatible with a range of AI feature extractors.

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Dr. Jean Fan @jef.works · 09/09/2026

Imaging-based spatial transcriptomics is often represented as cell-level gene counts, overlooking subcellular spatial variation. STARIT creates an image-based representation, allowing us to use computer vision AI models to identify cell states with distinct subcellular localization patterns.

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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 🥳

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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

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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...

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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...

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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

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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!

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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...

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Dr. Jean Fan @jef.works · 20/04/2026

We also improved our interactive website to explore this data and results so take a look for yourself: jef.works/CellCarto-Co... Congrats to Sami Singh, Dee Velazquez, with Hamid Rabb + team 🎉

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Dr. Jean Fan @jef.works · 20/04/2026

Our spatiotemporal molecular analysis reveals an unexpected metabolic response: genes involved in oxygen-dependent oxidative phosphorylation are upregulated in the hypoxic inner medulla, a region that typically relies on glycolysis. Now corroborated by protein-level evidence from immunofluorescence.

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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... 🧵👇

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Dr. Jean Fan @jef.works · 02/03/2026

To put this Mentorship Index to the test, I applied it to evaluate 2 colleagues 😜 h-index: Manolis wins (170 vs 88) M10-index: Lior wins (106 vs 38) Both have invested in achieving different kinds of accomplishments, which can be reflected in these different metrics.

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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... 🧵👇

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Dr. Jean Fan @jef.works · 25/02/2026

We previously showed how improving data quality (molecular detection sensitivity, imaging resolution, etc) provides an orthogonal strategy to tuning model architecture in spatial transcriptomics-based predictive modeling. But data imputation intended to improve data quality led to overfitting. 2/n

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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

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Dr. Jean Fan @jef.works · 22/02/2026

I walk through how I vibe → inspect → rethink → hand-fix logic errors → visualize → zero in on genes with quantifiably different spatial patterns between Visium and Xenium that suggest off-target binding. STcompare: github.com/JEFworks-Lab... Additional reading: elifesciences.org/reviewed-pre...

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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...

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Dr. Jean Fan @jef.works · 19/02/2026

We also now demonstrate how to leverage tissue-specific gene expression from atlasing resources like HuBMAP to assess how off-target binding might affect observed gene expression profiles in a specific tissue of interest for custom gene panels.

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Dr. Jean Fan @jef.works · 19/02/2026

We now clarify the differences between these probe sequences in a new supplementary note. Importantly, this impacts our interpretation of observed results to provide stronger evidence of putative imperfect sequence homology based off-target probe binding.

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Dr. Jean Fan @jef.works · 19/02/2026

Previously, we used the publicly available Xenium v1 Human Breast Panel probe sequences from the 10x website (pre-April 2025). We now understand that this file erroneously included extra probe sequences that aren't actually used.

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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

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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

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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

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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...

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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/

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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...

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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...

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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!

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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!

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Dr. Jean Fan @jef.works · 22/12/2025

Using real bacterial-MERFISH spatial transcriptomics data, we demonstrate how STARIT can delineate rotational variation not distinguishable by conventional gene count analysis.

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Dr. Jean Fan @jef.works · 22/12/2025

Using real osmFISH spatial transcriptomics data, we demonstrate how STARIT can identify comparable cell-types to conventional gene count clustering analysis, with analogous differential feature analysis to give comparable insights to differential expression analysis.

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Dr. Jean Fan @jef.works · 22/12/2025

Using simulated data, we demonstrate that STARIT can distinguish transcriptionally distinct cell-types and further separates cell states based on subcellular transcript localization, which conventional gene count analysis fails to capture.

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Dr. Jean Fan @jef.works · 22/12/2025

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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Dr. Jean Fan @jef.works · 22/12/2025

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.

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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... 🧵👇

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Dr. Jean Fan @jef.works · 03/12/2025

Finally, we apply STcompare to spatial transcriptomics data of healthy control and diseased acute kidney injury tissue to discover potentially disease-relevant changes in spatial gene expression patterns.

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Dr. Jean Fan @jef.works · 03/12/2025

We also apply STcompare to real spatial transcriptomics data of biological replicates to confirm high spatial correspondence for spatially variable genes as well as identify some genes that maintain spatial patterning but change in magnitude potentially indicative of batch effects.

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Dr. Jean Fan @jef.works · 03/12/2025

Using simulated data, we demonstrate how STcompare provides distinct insights from bulk differential gene expression analysis and robustly controls for false positives even in the presence of spatial autocorrelation common in spatial transcriptomics data.

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Dr. Jean Fan @jef.works · 03/12/2025

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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Dr. Jean Fan @jef.works · 03/12/2025

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.

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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 🧵👇

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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

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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 👋

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Dr. Jean Fan @jef.works · 09/09/2025

Likewise, to pinpoint what imaging data quality factors may drive these performance differences, we simulated lower-resolution images by applying Gaussian blur to the H&E images to demonstrate that image resolution has a measurable impact on performance and interpretability. 6/n

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Dr. Jean Fan @jef.works · 09/09/2025

Further, we demonstrate how imputation methods intended to rescue sparsity and noise boost performance when evaluated on the held-out test set but decreases performance when evaluated on an independent replicate, suggesting overfitting that limit robustness and generalizability. 5/n

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Dr. Jean Fan @jef.works · 09/09/2025

To pinpoint what molecular data quality factors may drive these performance differences, we performed a series of in silico ablation experiments in which we systematically decrease molecular data to show sparsity and noise as drivers of decreased performance. 4/n

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Dr. Jean Fan @jef.works · 09/09/2025

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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