Prediction of Protein Secondary Structure Based on Residue Pairs. - Xin Liu; Li-Mei Zhang; Wei-Mou Zheng (J. Bioinform. Comput. Biol., 2004)

Clustering of Amino Acids for Protein Secondary Structure Prediction. - Wei-Mou Zheng (J. Bioinform. Comput. Biol., 2004)

Relation between weight matrix and substitution matrix: motif search by similarity. - Wei-Mou Zheng (Bioinform., 2005)

Protein secondary structure prediction by combining hidden Markov models and sliding window scores. - Wei-Mou Zheng (Int. J. Bioinform. Res. Appl., 2005)

Test Data Sets and Evaluation of Gene Prediction Programs on the Rice Genome. - Heng Li; Jin-Song Liu; Zhao Xu; Jiao Jin; Lin Fang; Lei Gao; Yu-Dong Li; Zi-Xing Xing; Shao-Gen Gao; Tao Liu; Hai-Hong Li; Yan Li; et al. (J. Comput. Sci. Technol., 2005)

A Protein Structural Alphabet and Its Substitution Matrix CLESUM. - Wei-Mou Zheng; Xin Liu (Trans. Comp. Sys. Biology, 2005)

DRTF: a database of rice transcription factors. - Ge Gao; Yingfu Zhong; Anyuan Guo; Qihui Zhu; Wen Tang; Wei-Mou Zheng; Xiaocheng Gu; Liping Wei; Jingchu Luo (Bioinform., 2006)

An Amino Acid Substitution Matrix for Protein Conformation Identification. - Xin Liu; Wei-Mou Zheng (J. Bioinform. Comput. Biol., 2006)

TreeFam: a curated database of phylogenetic trees of animal gene families. - Heng Li 002; Avril Coghlan; Jue Ruan; Lachlan James M. Coin; Jean-Karim Hériché; Lara Osmotherly; Ruiqiang Li; Tao Liu; Zhang Zhang 002; Lars Bolund; Gane Ka-Shu Wong; Wei-Mou Zheng; et al. (Nucleic Acids Res., 2006)

A cross-species alignment tool (CAT). - Heng Li 002; Liang Guan; Tao Liu; Yiran Guo; Wei-Mou Zheng; Gane Ka-Shu Wong; Jun Wang 004 (BMC Bioinform., 2007)

The Use of a Conformational Alphabet for Fast Alignment of Protein Structures. - Wei-Mou Zheng (ISBRA, 2008)

ClEPaps: Fast Pair Alignment of protein Structures Based on conformational Letters. - Sheng Wang 001; Wei-Mou Zheng (J. Bioinform. Comput. Biol., 2008)

Counting of oligomers in Sequences Generated by Markov Chains for DNA Motif Discovery. - Gao Shan; Wei-Mou Zheng (J. Bioinform. Comput. Biol., 2009)

Incorporating Ab Initio energy into threading approaches for protein structure prediction. - Mingfu Shao; Sheng Wang 001; Chao Wang; Xiongying Yuan; Shuai Li; Wei-Mou Zheng; Dongbo Bu (BMC Bioinform., 2011)

Self-organizing approach for meta-genomes. - Jianfeng Zhu; Wei-Mou Zheng (Comput. Biol. Chem., 2014)

Loop-corrected belief propagation for lattice spin models. - Hai-Jun Zhou; Wei-Mou Zheng (CoRR, 2015)

FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition. - Chao Wang; Haicang Zhang; Wei-Mou Zheng; Dong Xu 002; Jianwei Zhu; Bing Wang; Kang Ning 001; Shiwei Sun; Shuai Cheng Li 001; Dongbo Bu (Bioinform., 2016)

Improving protein fold recognition by extracting fold-specific features from predicted residue-residue contacts. - Jianwei Zhu; Haicang Zhang; Shuai Cheng Li 001; Chao Wang; Lupeng Kong; Shiwei Sun; Wei-Mou Zheng; Dongbo Bu (Bioinform., 2017)

Improving prediction of burial state of residues by exploiting correlation among residues. - Hai'e Gong; Haicang Zhang; Jianwei Zhu; Chao Wang; Shiwei Sun; Wei-Mou Zheng; Dongbo Bu (BMC Bioinform., 2017)

Constructing effective energy functions for protein structure prediction through broadening attraction-basin and reverse Monte Carlo sampling. - Chao Wang; Yi Wei; Haicang Zhang; Lupeng Kong; Shiwei Sun; Wei-Mou Zheng; Dongbo Bu (BMC Bioinform., 2019)

Predicting protein inter-residue contacts using composite likelihood maximization and deep learning. - Haicang Zhang; Qi Zhang; Fusong Ju; Jianwei Zhu; Yujuan Gao; Ziwei Xie; Minghua Deng; Shiwei Sun; Wei-Mou Zheng; Dongbo Bu (BMC Bioinform., 2019)

Correction to: Predicting protein inter-residue contacts using composite likelihood maximization and deep learning. - Haicang Zhang; Qi Zhang; Fusong Ju; Jianwei Zhu; Yujuan Gao; Ziwei Xie; Minghua Deng; Shiwei Sun; Wei-Mou Zheng; Dongbo Bu (BMC Bioinform., 2019)

ISSEC: inferring contacts among protein secondary structure elements using deep object detection. - Qi Zhang; Jianwei Zhu; Fusong Ju; Lupeng Kong; Shiwei Sun; Wei-Mou Zheng; Dongbo Bu (BMC Bioinform., 2020)

Seq-SetNet: directly exploiting multiple sequence alignment for protein secondary structure prediction. - Fusong Ju; Jianwei Zhu; Qi Zhang; Guozheng Wei; Shiwei Sun; Wei-Mou Zheng; Dongbo Bu (Bioinform., 2022)

ProALIGN: Directly Learning Alignments for Protein Structure Prediction via Exploiting Context-Specific Alignment Motifs. - Lupeng Kong; Fusong Ju; Wei-Mou Zheng; Jianwei Zhu; Shiwei Sun; Jinbo Xu; Dongbo Bu (J. Comput. Biol., 2022)

Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms. - Bin Huang; Lupeng Kong; Chao Wang; Fusong Ju; Qi Zhang; Jianwei Zhu; Tiansu Gong; Haicang Zhang; Chungong Yu; Wei-Mou Zheng; Dongbo Bu (Genom. Proteom. Bioinform., 2023)

Accurate and efficient protein sequence design through learning concise local environment of residues. - Bin Huang; Tingwen Fan; Kaiyue Wang; Haicang Zhang; Chungong Yu; Shuyu Nie; Yangshuo Qi; Wei-Mou Zheng; Jian Han; Zheng Fan; Shiwei Sun; Sheng Ye; et al. (Bioinform., 2023)