Jackson A. Weir

Induced microfold cells are required for the function of pulmonary tertiary lymphoid organs that promote mucosal immunity

This study shows that induced microfold cells are essential for the function of pulmonary tertiary lymphoid organs, which support mucosal immunity against influenza.

Spatiotemporal lineage tracing reveals the dynamic spatial architecture of tumor growth and metastasis

This study uses spatial transcriptomics and lineage tracing to show how tumor subclones drive microenvironmental changes that promote metastasis in a mouse model.

Sample barcoding-associated technical variation in probe-based single-cell RNA sequencing

The paper identifies technical variation caused by probe set barcoding in single-cell RNA sequencing and shows how Flex v2 reduces this issue.

In vivo interrogation of transcriptional and epigenetic regulators of lung epithelial regeneration

The paper identifies Kat8 and the NSL complex as essential for lung epithelial repair and maps transcription factor dependencies in alveolar repair trajectories using SAGE.

Genome-scale spatial mapping of the Hodgkin lymphoma microenvironment identifies tumor cell survival factors

This study identifies IL13 as a survival factor for Hodgkin lymphoma cells by analyzing the tumor microenvironment with spatial and single-cell resolution.

Energy-Regularized Graph Learning for Multiscale Spatial Representation

Glimmer improves spatial representation learning by adaptively learning graphs that balance molecular similarity and spatial proximity across scales, outperforming existing methods in clustering and spatial conservation.

Scalable imaging-free spatial genomics through computational reconstruction

This paper introduces an imaging-free spatial transcriptomics method using molecular diffusion patterns and UMAP to reconstruct spatial data with high fidelity and scalability.

Slide-tags: scalable, single-nucleus barcoding for multi-modal spatial genomics

Slide-tags enables spatial localization of single nuclei for multi-modal spatial genomics, achieving high-resolution mapping and multiomic profiling in various tissues.