HiC2Self denoises Hi-C contact maps using self-supervised learning, reconstructing 3D chromatin structures from low-coverage data across bulk and single-cell samples.

Science Advances · Jul 23, 2026Peer-reviewedGenomics

Signaling induced biophysical disruption of repressed chromatin domains drives immune cell fate

Alexia Martínez de Paz, Christopher R. Chin, Mythili Ketavarapu, Yuchen Sun, Matthew R. Marunde, Jeremy T.-H. Chang, Laiba F Khan, John Cohen, Rui Yang, Michael J. Bale, Andrew W. Daman, Vigneshwari E. Kumar, Chenyang Jiang, Dughan J. Ahimovic, Mark Owyong, , Steven Zvi Josefowicz

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

bioRxiv · Dec 11, 2025 · PreprintImmunology

TAD hierarchy restricts poised LTR activation and loss of TAD hierarchy promotes LTR co-option in cancer

Elissa W.P. Wong, Merve Şahin, Rui Yang, UkJin Lee, Dan Li, Yingqian Ada Zhan, Rohan Misra, Fanny V. Tomas, Nawaf Alomran, Alexander Polyzos, Cindy J. Lee, Tuan Trieu, Alexander Martinez‐Fundichely, Thomas Wiesner, Andrew Rosowicz, , Ping Chi

The paper shows that TAD hierarchy restricts LTR activation, and its loss in cancer allows LTRs to act as alternative promoters, driving oncogene activation and transcriptional diversity.

Nature Genetics · Jun 30, 2025Peer-reviewedCancer Biology

ChromaFold predicts the 3D contact map from single-cell chromatin accessibility

Vianne Ran Gao, Rui Yang, Arnav Das, Renhe Luo, Hanzhi Luo, Dylan R. McNally, Ioannis Karagiannidis, Martín A. Rivas, Zhong-Min Wang, Darko Barišić, Alireza Karbalayghareh, Wilfred Wong, Yingqian Ada Zhan, Christopher R. Chin, William Stafford Noble, , Christina S. Leslie

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

Nature Communications · Nov 1, 2024Peer-reviewedBioinformatics

Epiphany: predicting Hi-C contact maps from 1D epigenomic signals

Rui Yang, Arnav Das, Vianne Ran Gao, Alireza Karbalayghareh, William Stafford Noble, Jeffrey A. Bilmes, Christina S. Leslie

Epiphany predicts cell-type-specific Hi-C contact maps from epigenomic signals, showing robust performance across cell types and species.

Genome biology · Jun 6, 2023Peer-reviewedGenomics