Ken Kamiya
morphoDE asks a deliberately simple question: where two cell types meet, the boundary bulges outward in some places and caves inward in others—do the cells on a bulge express different genes than the cells in a dent?
Core trick
Gene expression is compared between convex and concave interface regions, against a null that shuffles shape while keeping cell-type biology fixed.
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Description
morphoDE asks a deliberately simple question: where two cell types meet, the boundary bulges outward in some places and caves inward in others—do the cells on a bulge express different genes than the cells in a dent? We tested it across 11 published 3D spatial-transcriptomics datasets and 126 interface–strata, from a human lymph-node tumor to an Arabidopsis leaf.
The correspondence holds almost everywhere: 125 of 126 interface–strata carry signal that survives a geometry-breaking null (which shuffles the shape while keeping the biology fixed), signal appears in all 11 datasets, and 16 reach a perfect 12/12 in species sharing no common ancestry. On the human tumor the difference is 93% within a single cell type—convex bulges carry immune and cholesterol programs, concave dents carry hypoxia and invasion (PTHLH, KRT17).
Why it matters: interface shape and cell state are linked as a general property of tissue architecture, not a tumor quirk—giving a geometry-readable spatial map of cell state, from cancer to plants.
README excerpt
# morphoDE — Bulge vs. Dent: a cross-species test of interface geometry → gene expression
*morphoDE = **morpho**logy × **d**ifferential **e**xpression: does the shape of a cell-type interface (its bulges and dents) correspond to a difference in gene expression?*
**Do the convex ("bulge") and concave ("dent") parts of a cell-type interface
express different genes?** We tested this deliberately naive hypothesis across
**11 spatial-transcriptomics datasets and 126 interface–strata**, from a human
tumor to a plant leaf, and found the correspondence holds almost everywhere — it
is a general property of tissue architecture, not a tumor-specific phenomenon,
and it is reproducible across developmental stages, regeneration time points, and
individual specimens of the same organism.
> Built with **Claude Science** for the 2026 *Built with Claude: Life Sciences*
> hackathon (Researcher Track). The biological question and the public datasets
> predate the event; **the analysis in this repository was carried out during the
> hackathon.**
*Each dot is one interface–stratum: the number of top differential-expression
genes (out of 12) whose bulge-vs-dent signal survives a geometry-breaking null.
Rows are ordered phylogenetically (vertebrates → invertebrates → plant). Red =
human tumor, blue = animal, green = plant; short vertical line = per-species
median; hollow = zero survivors. Signal is present a