Andy Y. Chen

Regulation of immune signal integration and memory by inflammation-induced chromosome conformation

This study shows that inflammation-induced changes in 3D genome conformation regulate immune signal integration and transcriptional memory in macrophages.

Clonal lineage tracing of innate immune cells in human cancer

The paper uses mtDNA mutations to trace clonal relationships of innate immune cells in cancer, showing myeloid clones are linked to monocytes and have distinct epigenetic profiles.

A unified genetic perturbation language for human cellular programming

CRISPR-All enables genome-scale, combinatorial genetic perturbations in human cells, revealing additive functional improvements through multiplexed modifications.

Cis-Regulatory Element and Transcription Factor Circuitry Required for Cell-Type Specific Expression of FOXP3

The paper identifies cis-regulatory elements and transcription factors controlling FOXP3 expression in human Tregs and Tconvs, revealing mechanisms that restrict FOXP3 to Tregs in mice.

Functional memory T cells are derived from exhausted clones and expanded by checkpoint blockade

This study shows that exhausted T cells can form functional memory T cells after antigen clearance, and checkpoint blockade expands these memory clones.

Evolutionarily guided transcription factor design programs novel T cell states

This paper designs novel transcription factors using evolutionary principles to generate T cell states with enhanced functionality.