Yijun Ruan

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.

FEDRANN improves long-read overlap detection using dimensionality reduction and approximate nearest neighbors, outperforming existing methods on real data.

The paper improves gene expression prediction models by incorporating protein-mediated spatial chromatin interactions, resulting in significant performance gains across multiple cell lines.

The paper introduces a graph-theoretic algorithm to identify CTCF-mediated chromatin loops that are linked in 3D space using ChIA-PET data, finding non-random linked regions with distinct centrality metrics.

The paper models chromatin folding using explosive percolation theory and shows that 80% of loops are needed for 3D condensation across cell lines.

ChIA-PIPE is a fully automated pipeline for analyzing and visualizing ChIA-PET data, including quality assessment and visualization tools.

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.

This study investigates how PML/RARα alters chromatin topology and transcription in APL cells, revealing its role in repressing myeloid differentiation genes.

This paper develops a new electron microscopy method to visualize 3D chromatin folding at ultra-resolution in human cells and finds high heterogeneity in chromatin structures.

The paper shows that KDM7A and UTX demethylate repressive histone marks to enable NF-κB-dependent inflammatory gene activation in endothelial cells.

pyBedGraph is a Python package that rapidly computes summary statistics for genomic signal tracks, outperforming existing tools by up to 245 times.

The paper introduces MIA-Sig, an algorithm to de-noise chromatin interaction data and identify topological domains and inter-domain contacts.

This study examines how structural variants in 26 human populations affect 3D chromatin structure and gene transcription, showing a link between chromatin loops and transcriptional variation.

The paper uses super-resolution microscopy to visualize a chromatin loop in human cells and validates the results with Hi-C data.

ChIA-DropBox is a computational pipeline for analyzing ChIA-Drop data, reconstructing chromatin complexes, and visualizing multiplex chromatin interactions.

The paper provides multi-genomic maps of the EndoC-βH1 cell model to define gene regulatory programs in human pancreatic β cells and identifies allelic effects on cis-regulatory elements.

The paper identifies three span intervals of tandem duplications in TDP tumors and links them to specific gene mutations and pathways, showing TP53 and BRCA1 loss drives short-span TDPs.

This paper introduces a method to analyze multiplex chromatin interactions with single-molecule precision and shows they contribute to topologically associated domains and gene regulation.