Yaqiang Cao

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.

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.

cLoops improves 3D genomic loop detection by analyzing paired-end tags directly, showing less distance bias and higher enrichment than existing tools.