Keji Zhao

Ryder normalizes epigenomic bigWig tracks against stable internal reference regions such as invariant CTCF sites, correcting background and signal separately, recovering expected perturbation effects that depth-only normalization obscured.

This study shows Bhlhe40 promotes GM-CSF and inhibits IL-10 in ILC2s, enhancing eosinophil recruitment during type 2 immune responses.

This paper shows that anti-CTLA-4 antibodies destabilize intratumor Tregs via TGF-β signaling, enhancing anti-tumor immunity and immunotherapy.

This study identifies the Bhlhe40-Pou2af1 axis as a transcriptional regulator of CXCR5 expression in Tfh cells, independent of the Bcl6-Blimp1 pathway.

This paper describes a method to rapidly enrich neoantigen-specific CD8 T cells from peripheral blood, achieving frequencies comparable to tumor-infiltrating lymphocytes over 28 days.

This study shows that the Drosophila SET1 histone methyltransferase regulates male germline stem cell maintenance and differentiation by coordinating JAK-STAT and BMP signaling pathways.

This study shows that the N-terminal amino acid difference between H3 and H3.3 in Drosophila male germline stem cells affects their inheritance patterns and function in stem cell maintenance and differentiation.

Hi-TrAC identifies active sub-TADs with median size 100 kb, revealing fractal nesting of super-enhancers and their disruption by Cohesin and H3K4me1 perturbations.

Hi-TrAC identifies high-resolution chromatin loops and reveals TFs' roles in organizing long- and short-range chromatin structures.

cLoops2 provides a comprehensive tool for analyzing 3D chromatin interactions, including loop detection and annotation, with open-source code available on GitHub.

The paper identifies BRDT binding sites in gene units during spermatogenesis and links them to specific transcription factors and epigenetic features that regulate gene expression.

The paper uses multi-omic data from hybrid mice to reveal symmetrical positioning of homologous chromosomes in the 3D nucleus and epigenetic regulation differences between B6 and Cast strains.

ACT-seq is a new method for mapping histone modifications and chromatin proteins in single cells, using antibody-guided chromatin tagmentation to streamline the process.