Xiaotao Wang

Hidden genetic diversity in 320 nearly-complete East Asian genome assemblies

The paper presents 320 nearly-complete East Asian genome assemblies, revealing new genetic diversity and structural variations not present in existing global pangenomes.

Deciphering complete archaic introgression sequences in modern human genomes

The paper introduces ASMaid, a method to detect archaic introgression sequences in human genomes, revealing more complete and diverse archaic segments than previous methods.

Boosting the detection of enhancer-promoter loops via novel normalization methods for chromatin interaction data

Raichu improves enhancer-promoter loop detection in Hi-C data by enhancing sensitivity and recovering missed loops compared to ICE normalization.

Multifaceted roles of cohesin in regulating transcriptional loops

This study investigates cohesin's role in transcriptional loops and DNA replication using human cells, finding that cohesin loss affects long-range chromatin interactions and up-regulates early initiation zone genes.

An integrated view of the structure and function of the human 4D nucleome

The paper integrates 4D Nucleome data to analyze 3D genome structure and function in human cells, revealing chromatin domains, loops, and interactions, and showing how genetic variants affect genome folding.

Tri-omic mapping revealed concerted dynamics of 3D epigenome and transcriptome in brain cells

The paper introduces a tri-omic method to study 3D epigenome and transcriptome dynamics in brain cells across mouse lifespan, revealing distinct genomic mechanisms in neurons and non-neuronal cells.

Chemically Induced Nuclear Pore Complex Protein Degradation via E3 Ligase TRIM21

This study identifies small-molecule ligands for TRIM21, an E3 ligase, demonstrating their ability to degrade nuclear pore complex proteins and induce cell death in cancer cells.

EagleC Explorer: A desktop application for interactively detecting and visualizing SVs and enhancer hijacking on Hi-C contact maps

EagleC Explorer is a desktop tool for visualizing and detecting structural variations and enhancer hijacking in Hi-C data, enabling interactive analysis in cancer studies.

HiCLift: A fast and efficient tool for converting chromatin interaction data between genome assemblies

HiCLift converts chromatin interaction data between genome assemblies efficiently, outperforming re-mapping approaches in speed while maintaining accuracy.

Extreme structural heterogeneity rewires glioblastoma chromosomes to sustain patient-specific transcriptional programs

The paper maps structural variants and neoloops in glioblastoma stem cells to show how they sustain tumor-specific transcriptional programs and identify patient-specific vulnerabilities.

Fast alignment and preprocessing of chromatin profiles with Chromap

Chromap provides a fast and accurate method for aligning and preprocessing chromatin profiles, outperforming existing tools in speed while maintaining alignment accuracy.

Subtype-specific epigenomic landscape and 3D genome structure in bladder cancer

This study identifies subtype-specific epigenomic and 3D genome structures in bladder cancer, linking NPAS2 to luminal subtype regulation and clinical outcomes.

A supervised learning framework for chromatin loop detection in genome-wide contact maps

This paper introduces Peakachu, a Random Forest framework for chromatin loop detection in Hi-C data, showing improved identification of short-range interactions across multiple platforms and species.