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.

Nature Structural & Molecular Biology · Jan 13, 2026Peer-reviewedGenomics

ChIA-PIPE: A fully automated pipeline for ChIA-PET data analysis and visualization

Byoungkoo Lee, Jiahui Wang, Liuyang Cai, Minji Kim, Sandeep Namburi, Harianto Tjong, Yuliang Feng, Ping Wang, Zhonghui Tang, Ahmed Abbas, Chia‐Lin Wei, Yijun Ruan, Sheng Li

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

Science Advances · Jul 10, 2020Peer-reviewedBioinformatics

Chromatin Topology Reorganization and Transcription Repression by PML/RARα in Acute Promyeloid Leukemia

Ping Wang, Zhonghui Tang, Byoungkoo Lee, Jacqueline Jufen Zhu, Liuyang Cai, Przemysław Szałaj, Simon Zhongyuan Tian, Meizhen Zheng, Dariusz Plewczyński, Xiaoan Ruan, Edison T. Liu, Chia‐Lin Wei, Yijun Ruan

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

Genome biology · May 11, 2020Peer-reviewedGenomics

Ultrastructural Visualization of 3D Chromatin Folding Using Serial Block-Face Scanning Electron Microscopy and In Situ Hybridization (3D-EMISH)

Paweł Trzaskoma, Błażej Ruszczycki, Byoungkoo Lee, Katarzyna Karolina Pels, Katarzyna Krawczyk, Grzegorz Bokota, Andrzej Antoni Szczepankiewicz, Jesse Aaron, Agnieszka Walczak, Małgorzata Alicja Śliwińska, Adriana Magalska, Michał Kadlof, Artur Wolny, Zofia Parteka-Tojek, Sebastian Arabasz, , Grzegorz Marek Wilczynski

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.

Nature Communications · May 1, 2020Peer-reviewedGenomics

Multiplex chromatin interaction analysis by signal processing and statistical algorithms

Minji Kim, Meizhen Zheng, Simon Zhongyuan Tian, Daniel Capurso, Byoungkoo Lee, Jeffrey H. Chuang, Yijun Ruan

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

Genome biology · Nov 25, 2019Peer-reviewedGenomics

Super resolution imaging of a distinct chromatin loop in human lymphoblastoid cells

Jacqueline Jufen Zhu, Zofia Parteka-Tojek, Byoungkoo Lee, Przemysław Szałaj, Ping Wang, Karolina Jodkowska, Jesse Aaron, Teng‐Leong Chew, Dariusz Plewczyński, Yijun Ruan

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

bioRxiv · Apr 29, 2019 · PreprintMolecular Biology

ChIA-DropBox: a novel analysis and visualization pipeline for multiplex chromatin interactions

Simon Zhongyuan Tian, Daniel Capurso, Minji Kim, Byoungkoo Lee, Meizhen Zheng, Yijun Ruan

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

bioRxiv · Apr 18, 2019 · PreprintBioinformatics

Multiplex Chromatin Interaction Analysis with Single-Molecule Precision

Meizhen Zheng, Simon Zhongyuan Tian, Rahul Maurya, Byoungkoo Lee, Minji Kim, Daniel Capurso, Emaly Piecuch, Liang Gong, Jacqueline Jufen Zhu, Chee‐Hong Wong, Chew Yee Ngan, Ping Wang, Xiaoan Ruan, Chia‐Lin Wei, Yijun Ruan

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.

bioRxiv · Jan 25, 2018 · PreprintGenomics