This paper presents a haplotype-resolved telomere-to-telomere pig genome, revealing new protein-coding loci and enabling xenograft cell state analysis and interspecies chimerism compatibility scoring.

bioRxiv · Apr 6, 2026 · PreprintGenomics

A Phospho-Switch for Cell Fate Control

jin ming, xianzhuang liu, Zexiao Jia, Wei Shi, Jiajun Li, Shikun Wang, yulin chen, Shixian Lin, yu liang, peng guo, Hanqing Zhao, Yuxiang Yao, Ruona Shi, Xiaofei Zhang, Yuanyue Shan, , Duanqing Pei

The paper identifies a phospho-switch in SALL4 that controls cell fate by modulating BAF complex interaction in response to BMP4-DUSP9 signaling, causing developmental defects when disrupted.

bioRxiv · Feb 23, 2026 · PreprintDevelopmental Biology

BioLogical: a universal analysis framework for biosystem logical dynamic

Yuxiang Yao, Dong Liu, Zheting Zhang, Chengchen Zhao, Duanqing Pei

BioLogical is an R package for analyzing biosystem logical dynamics, capable of multi-valued logical analysis, order parameter calculation, and system simulation.

Computational and Structural Biotechnology Journal · Dec 6, 2025Peer-reviewedSystems Biology

Role of genetic frustrations in cell reprogramming

Yuxiang Yao, Jieying Zhu, Wenfei Li, Duanqing Pei

This study investigates the role of genetic frustration in cell reprogramming by constructing a Boolean genetic network model and shows its critical role in initiating cell fate transitions.

bioRxiv · Jan 31, 2025 · PreprintSystems Biology

Canalization and competition: the cornerstone of genetic network's dynamic stability and evolution

Yuxiang Yao, Zi‐Gang Huang, Duanqing Pei

This study investigates how regulatory modes in gene networks contribute to dynamic stability and evolution by analyzing their impact on system criticality.

bioRxiv · May 13, 2024 · PreprintSystems Biology