Computing Configuration Space Obstacles using Polynomial Transforms. - Wenjie Shu 001; Zhiqiang Zheng 005 (ICRA, 2004)

Selection of antisense oligonucleotides based on multiple predicted target mRNA structures. - Xiaochen Bo; Shaoke Lou; Daochun Sun; Wenjie Shu 001; Jing Yang; Shengqi Wang (BMC Bioinform., 2006)

RDMAS: a web server for RNA deleterious mutation analysis. - Wenjie Shu 001; Xiaochen Bo; Rujia Liu; Dongsheng Zhao; Zhiqiang Zheng 005; Shengqi Wang (BMC Bioinform., 2006)

RSRE: RNA structural robustness evaluator. - Wenjie Shu 001; Xiaochen Bo; Zhiqiang Zheng 005; Shengqi Wang (Nucleic Acids Res., 2007)

A novel representation of RNA secondary structure based on element-contact graphs. - Wenjie Shu 001; Xiaochen Bo; Zhiqiang Zheng 005; Shengqi Wang (BMC Bioinform., 2008)

EvoRSR: an integrated system for exploring evolution of RNA structural robustness. - Wenjie Shu 001; Ming Ni; Xiaochen Bo; Zhiqiang Zheng 005; Shengqi Wang (BMC Bioinform., 2009)

De novo identification of replication-timing domains in the human genome by deep learning. - Feng Liu 054; Chao Ren; Hao Li 035; Pingkun Zhou; Xiaochen Bo; Wenjie Shu 001 (Bioinform., 2016)

BiRen: predicting enhancers with a deep-learning-based model using the DNA sequence alone. - Bite Yang; Feng Liu 054; Chao Ren; Zhangyi Ouyang; Ziwei Xie; Xiaochen Bo; Wenjie Shu 001 (Bioinform., 2017)

Deep Learning and Its Applications in Biomedicine. - Chensi Cao; Feng Liu 054; Hai Tan; Deshou Song; Wenjie Shu 001; Weizhong Li 001; Yiming Zhou; Xiaochen Bo; Zhi Xie (Genom. Proteom. Bioinform., 2018)

LIVE: a manually curated encyclopedia of experimentally validated interactions of lncRNAs. - Gaole An; Jiaqi Sun; Chao Ren; Zhangyi Ouyang; Lingyun Zhu; Xiaochen Bo; Shaoliang Peng; Wenjie Shu 001 (Database J. Biol. Databases Curation, 2019)

Predicting CRISPR-Cas9 Off-target with Self-supervised Neural Networks. - Dong Chen 013; Wenjie Shu 001; Shaoliang Peng (BIBM, 2020)

Predicting functional elements and variants effects in non-coding regions based on deep learning. - Yunhao Liu 001; Shaoliang Peng; Wenjie Shu 001; Bin Jiang 006; Chao Yang 015; Kun Xie (HealthCom, 2020)

Design of prime-editing guide RNAs with deep transfer learning. - Feng Liu 054; Shuhong Huang; Jiongsong Hu; Xiaozhou Chen; Ziguo Song; Junguo Dong; Yao Liu; Xingxu Huang; Shengqi Wang; Xiaolong Wang; Wenjie Shu 001 (Nat. Mac. Intell., 2023)