James A. Sharpe

This study induces skeletal muscle, neuronal, and endothelial cells from bovine embryonic stem cells and demonstrates their self-organization into vascularized tissue structures.

LimbLab provides a pipeline for 3D analysis and visualization of limb bud gene expression data, improving workflow efficiency and compatibility with existing tools.

LimbNET provides a collaborative platform for simulating and visualizing gene network patterns in limb development using spatiotemporal data.

This study maps over 85,000 oocytes in mouse ovaries across their reproductive lifespan, revealing spatial patterns and a bimodal size distribution, along with a mathematical model of oocyte activation and loss.

The paper investigates how innate immune responses to Plasmodium falciparum contribute to blood-brain barrier disruption in cerebral malaria using an in vitro model.

The paper develops a limb-mesenchymal organoid system and models to show that digit-like structures form through mechanochemical instabilities involving cell adhesion, chemotaxis, and convergent-extension.

This study shows that Plasmodium falciparum egress products disrupt BBB endothelial junctions and activate JAK-STAT signaling, leading to increased permeability and suggesting therapeutic targets.

The paper develops a theoretical model to predict multiplet types in mx-scRNA-seq and shows that partial stealth multiplets can significantly affect data when labeling is suboptimal.

This study identifies early transcriptional targets of WNT signaling during limb bud and digit development by transiently blocking WNT signaling with small molecule inhibitors.

This study investigates how varying proportions of primed and naive ESCs affect gastruloid formation and AP axial patterning, revealing developmental flexibility in mammalian embryogenesis.

The paper reconstructs spatio-temporal gene expression patterns in developing mouse limbs using static snapshots, enabling analysis of gene dynamics across time.

C3PO reconstructs 3D cell positions after dissociation, enabling spatial transcriptomics with 3D structure preservation.

This paper introduces a method to reconstruct 4D developmental trajectories from 3D images using spherical harmonics, demonstrating its application to mouse limb buds and hearts.

The paper studies AP axis establishment in gastruloids using scRNA-seq and identifies molecular signatures of germ layer commitment and differences between Bra/T+ and Bra/T- populations.

This study identifies cell intercalation as the primary driver of chick limb bud morphogenesis, using in vivo imaging and computational modeling to reveal the role of molecular gradients and tissue fluidity.

ya||a is a GPU-accelerated agent-based model for morphogenesis that simulates mesenchyme and epithelium more efficiently than previous models.

This study develops a method to trace the origins of phenotypic abnormalities by quantifying 3D gene expression patterns in developing organs, revealing subtle gene expression differences in Apert syndrome models.

The paper shows that different gene regulatory networks in E. coli constrain phenotypic variation differently, even when producing the same phenotype.

This study shows EGCG treatment improves facial dysmorphology in DS mouse models and humans but warns against non-prescribed use due to variable outcomes.