Quanming Shi

This study uses somatic mutations to track marrow-derived cell infiltration into the human brain, finding widespread microglia replenishment and a protective link between clonal hematopoiesis and Alzheimer's disease.

A genome-wide plasmid screen, Retain-seq, identifies thousands of CpG-rich promoter-like human elements that tether episomes to mitotic chromosomes, shape ecDNA structure, and lose function when methylated.

The paper identifies enhancer-like elements on ecDNA in colorectal cancer that are derived from transposable elements and are functionally active in cancer cell fitness.

This paper develops a method to fluorescently label and track non-repetitive genomic loci in live human cells, showing gene-specific chromatin dynamics independent of transcription.

The paper shows that ecDNA-borne PVT1 fusions stabilize oncogenic mRNAs by interacting with SRSF1, enhancing RNA stability and supporting MYC dependency in cancer.

The paper identifies autoantibody hotspots on the XIST RNP complex in female-biased autoimmune diseases and links them to clinical outcomes.

This study introduces CRISPRai, a bidirectional epigenetic editing system, to investigate gene regulation hierarchies and interactions in T cells and hematopoietic lineage transcription factors.

This paper introduces ENTER-seq, a method using engineered lentiviral particles to systematically discover receptor-ligand interactions and map TCR specificity in single cells.

This study shows XIST is required in adult human B cells to silence X-linked immune genes and identifies TRIM28 as a B cell-specific XIST cofactor involved in X-inactivation and atypical B cell formation.

This study shows Spen binds to endogenous retroviral RNAs and recruits chromatin silencing machinery, linking RNA-mediated retrovirus silencing to X chromosome inactivation.

The paper shows that YAP-dependent transcription is activated by cycles of rapid nuclear-cytoplasmic shuttling, not just nuclear enrichment, and identifies factors that induce these cycles.

This study identifies factors that determine Satb1 binding-site selectivity, showing its preference for nucleosome-dense regions and its mechanosensitive interactions with DNA.

This paper introduces a fluorogenic nanobody array tag, ArrayG, enabling prolonged single molecule imaging in live cells with reduced background and improved photo-stability.