Alexander Yu Rudensky

SPP1hi macrophages in RA synovial fibrin deposits promote tissue hyperplasia.

ArchVelo models gene regulation and infers cell trajectories using scATAC-seq and scRNA-seq data, improving accuracy and identifying new differentiation trajectories in immune cells.

The paper identifies distal and interchromosomal chromatin interactions in T cells using a new algorithm and links them to gene regulation through epigenomic analysis.

The paper identifies two distinct regulatory T cell subsets in colorectal cancer with opposing roles in tumor growth and prognosis.

This study shows that regulatory T cells modulate peripheral neuron activation to restrain skin inflammation by expressing Penk, a precursor for endogenous opioids.

The paper uses spatial transcriptomics and a new method called DeepTopics to identify distinct cellular patterns in RA synovium, revealing divergent ectopic lymphoid structures.

ChromaFold predicts 3D chromatin contact maps from scATAC-seq data, outperforming bulk-based methods and enabling cell-type-specific interaction analysis.

Starfysh integrates spatial transcriptomics and histology to analyze tumor microenvironments, identifying disease-specific spatial hubs and immune interactions in breast cancers.

The paper defines a shared differentiation trajectory of CD8 T cell dysfunction across cancer and infection using ATAC-seq and RNA-seq data from multiple studies.

This study identifies ZFP36 RNA-binding proteins as regulators of T-cell activation and anti-viral immunity, showing they restrain T-cell expansion and effector functions.