ONTraC uses a graph neural network to analyze spatial transcriptomics data, improving trajectory reconstruction and revealing microenvironment-dependent changes in gene regulation and cell interactions during development.

Genome biology · May 8, 2025Peer-reviewedGenomics

Screening of functional maternal-specific chromatin regulators in early embryonic development

Guifen Liu, Yiman Wang, Xiangxiu Wang, Wen Wang, Zheng Cao, Yong Zhang

The paper identifies maternal-specific chromatin regulators in zebrafish embryogenesis using a computational pipeline and F0 homozygous mutation technology.

bioRxiv · Mar 6, 2024 · PreprintDevelopmental Biology

ADNP Modulates SINE B2-Derived CTCF-Binding Sites during Blastocyst Formation in Mouse

Wen Wang, Rui Gao, Dongxu Yang, Mingli Ma, Ruge Zang, Xiangxiu Wang, Chuan Chen, Xiaochen Kou, Yanhong Zhao, Jiayu Chen, Xuelian Liu, Jiaxu Lu, Ben Xu, Juntao Liu, Yanxin Huang, , Yawei Gao

The paper investigates CTCF chromatin occupancy during mouse pre-implantation development and identifies ADNP's role in modulating SINE B2-derived CTCF-binding sites.

Genes & Development · Feb 1, 2024Peer-reviewedDevelopmental Biology

Giotto Suite: a multi-scale and technology-agnostic spatial multi-omics analysis ecosystem

Jiaji George Chen, Joselyn Chávez, Matthew O’Brien, Junxiang Xu, Edward C. Ruiz, Wen Wang, Iqra Amin, Irzam Sarfraz, Pratishtha Guckhool, Adriana Sistig, Guo‐Cheng Yuan, Ruben Dries

Giotto Suite provides a modular, open-source framework for analyzing spatial multi-omics data across scales and technologies.

bioRxiv · Nov 26, 2023 · PreprintBioinformatics