Lin An

An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis

The paper integrates epigenomic and transcriptomic data from mouse hematopoiesis to identify regulatory elements and their dynamics across cell types.

S3norm: simultaneous normalization of sequencing depth and signal-to-noise ratio in epigenomic data

S3norm improves normalization of epigenomic data by simultaneously adjusting sequencing depth and signal-to-noise ratio, enhancing the detection of biological variation.

Hierarchical Domain Structure Reveals the Divergence of Activity among TADs and Boundaries

OnTAD identifies hierarchical TAD structures from Hi-C data with improved accuracy and speed, revealing new insights into TAD organization and gene regulation.

Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of mouse hematopoietic cells

The paper integrates GATA transcription factors and epigenomes in mouse hematopoietic cells using IDEAS to map regulatory landscapes and identify candidate cis-regulatory elements.

Snapshot: clustering and visualizing epigenetic history during cell differentiation

Snapshot generates hierarchical visualizations of epigenetic features along cell differentiation hierarchies using epigenomic data from the VISION project.

An Integrative Framework For Detecting Structural Variations In Cancer Genomes

This paper presents an integrative framework to detect structural variants in cancer genomes using multiple methods and finds that non-coding structural variation significantly impacts genome function in cancer cells.

HiCPlus: Resolution Enhancement of Hi-C interaction heatmap

HiCPlus enhances the resolution of Hi-C interaction heatmaps using deep learning, reconstructing high-resolution data from low-resolution inputs.