Dory identifies differential spatial patterns in chromatin tracing data by analyzing structural differences between groups, linking changes to gene regulation.

Genome biology · Sep 3, 2026Peer-reviewedBioinformatics

Perturb-tracing enables high-content screening of multiscale 3D genome regulators

Yubao Cheng, Mengwei Hu, Bing Yang, Tyler B Jensen, Yuan Zhang, Tianqi Yang, Ruihuan Yu, Zhaoxia Ma, Jonathan S. D. Radda, Shengyan Jin, Chongzhi Zang, Siyuan S. Wang

The paper introduces Perturb-tracing, a high-content screening platform to identify regulators of 3D chromatin organization, discovering new factors that influence chromatin folding and nuclear architecture.

Nature Methods · Apr 10, 2025Peer-reviewedGenetics

Interpreting ruminant specific conserved non-coding elements by developmental gene regulatory network

Xiangyu Pan, Zhaoxia Ma, Xinqi Sun, Hui Li, Tingting Zhang, Chen Zhao, Nini Wang, Rasmus Heller, Wing Hung Wong, Wen Wang, Yu Jiang, Yong Wang

The paper identifies ruminant-specific conserved non-coding elements and develops a method to interpret their regulatory roles in rumen development using gene regulatory networks.

bioRxiv · Nov 8, 2021 · PreprintGenomics