Wilfred Wong

FourC identifies significant and differential contacts in 4C-seq data using a Bayesian model and Gaussian processes to address duplication and model spatial patterns.

scDIVA transfers fine-grained immune cell type annotations between tumor-immune scRNA-seq datasets by integrating batch correction and detecting novel cell states.

The paper identifies pre-established chromatin regions in human ESCs that enable rapid activation of lineage-specific genes during differentiation.

The paper identifies H3 serine 28 phosphorylation as a mechanism driving chromatin derepression and immune cell fate transitions by disrupting repressive chromatin domains.

The paper identifies two NANOG enhancers in human embryonic stem cells and shows their critical role in maintaining self-renewal and preventing differentiation.

This study shows that cohesin depletion affects locus- and differentiation-specific transcriptional activation and regulatory interactions in mouse ESCs, with some loops and genes being more sensitive than others.

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

The paper identifies a long-range enhancer for ONECUT1 involved in pancreatic differentiation and links a diabetes risk variant to disrupted transcription factor binding.

The paper uses a CRISPRi screen in hESC differentiation to identify enhancers with nonlinear regulatory activity, revealing a CTCF loop-constrained model for improved enhancer prediction.

SCARlink predicts gene expression from chromatin accessibility in single-cell multiome data, identifies enhancers, and enables chromatin potential analysis for developmental trajectories.

HiC-DC+ is a tool for Hi-C/HiChIP interaction calling and differential analysis, showing improved performance in HiChIP benchmarking and revealing 3D organization changes during cohesin perturbation and differentiation.