DSNetax: a deep learning species annotation method based on a deep-shallow parallel framework. - Hongyuan Zhao; Suyi Zhang; Hui Qin; Xiaogang Liu; Dongna Ma; Xiao Han; Jian Mao; Shuangping Liu (Briefings Bioinform., 2024)

GKNnet: an relational graph convolutional network-based method with knowledge-augmented activation layer for microbial structural variation detection. - Fengyi Guo; Yuanbo Li; Hongyuan Zhao; Xiaogang Liu; Jian Mao; Dongna Ma; Shuangping Liu (Briefings Bioinform., 2025)

FungiLT: A Deep Learning Approach for Species-Level Taxonomic Classification of Fungal ITS Sequences. - Kai Liu; Hongyuan Zhao; Dongliang Ren; Dongna Ma; Shuangping Liu; Jian Mao (Comput., 2025)