Using Phylogenetic Relationships to Improve the Inference of Transcriptional Regulatory Networks. - Xiuwei Zhang 002; Maryam Zaheri; Bernard M. E. Moret (BMEI (1), 2008)

Boosting the Performance of Inference Algorithms for Transcriptional Regulatory Networks Using a Phylogenetic Approach. - Xiuwei Zhang 002; Bernard M. E. Moret (WABI, 2008)

Improving Inference of Transcriptional Regulatory Networks Based on Network Evolutionary Models. - Xiuwei Zhang 002; Bernard M. E. Moret (WABI, 2009)

Refining transcriptional regulatory networks using network evolutionary models and gene histories. - Xiuwei Zhang 002; Bernard M. E. Moret (Algorithms Mol. Biol., 2010)

ProPhyC: A Probabilistic Phylogenetic Model for Refining Regulatory Networks. - Xiuwei Zhang 002; Bernard M. E. Moret (ISBRA, 2011)

Transcriptional Regulatory Networks across Species - Evolution, Inference, and Refinement. - Xiuwei Zhang 002 (2011)

Refining Regulatory Networks through Phylogenetic Transfer of Information. - Xiuwei Zhang 002; Bernard M. E. Moret (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

NEMo: An Evolutionary Model with Modularity for PPI Networks. - Min Ye; Gabriela C. Racz; Qijia Jiang; Xiuwei Zhang 002; Bernard M. E. Moret (ISBRA, 2016)

Maximum likelihood reconstruction of ancestral networks by integer linear programming. - Vaibhav Rajan; Ziqi Zhang; Carl Kingsford; Xiuwei Zhang 002 (Bioinform., 2021)

GRNUlar: A Deep Learning Framework for Recovering Single-Cell Gene Regulatory Networks. - Harsh Shrivastava 001; Xiuwei Zhang 002; Le Song; Srinivas Aluru (J. Comput. Biol., 2022)

CLARIFY: cell-cell interaction and gene regulatory network refinement from spatially resolved transcriptomics. - Mihir Bafna; Hechen Li; Xiuwei Zhang 002 (Bioinform., 2023)