dbWGFP: a database and web server of human whole-genome single nucleotide variants and their functional predictions. - Jiaxin Wu 005; Mengmeng Wu; Lianshuo Li; Zhuo Liu; Wanwen Zeng; Rui Jiang 001 (Database J. Biol. Databases Curation, 2016)

Integrating embeddings of multiple gene networks to prioritize complex disease-associated genes. - Mengmeng Wu; Wanwen Zeng; Wenqiang Liu; Yijia Zhang 001; Ting Chen 006; Rui Jiang 001 (BIBM, 2017)

Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding. - Xu Min; Wanwen Zeng; Ning Chen 002; Ting Chen 006; Rui Jiang 001 (Bioinform., 2017)

Predicting enhancers with deep convolutional neural networks. - Xu Min; Wanwen Zeng; Shengquan Chen; Ning Chen 002; Ting Chen 006; Rui Jiang 001 (BMC Bioinform., 2017)

Mimvec: a deep learning approach for analyzing the human phenome. - Mingxin Gan; Wenran Li; Wanwen Zeng; Xiaojian Wang; Rui Jiang 001 (BMC Syst. Biol., 2017)

Prediction of enhancer-promoter interactions via natural language processing. - Wanwen Zeng; Mengmeng Wu; Rui Jiang 001 (BMC Genom., 2018)

EnDisease: a manually curated database for enhancer-disease associations. - Wanwen Zeng; Xu Min; Rui Jiang 001 (Database J. Biol. Databases Curation, 2019)

Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network. - Wanwen Zeng; Yong Wang; Rui Jiang 001 (Bioinform., 2020)

IRIS: A method for predicting in vivo RNA secondary structures using PARIS data. - Jianyu Zhou; Pan Li; Wanwen Zeng; Wenxiu Ma; Zhipeng Lu 002; Rui Jiang 001; Qiangfeng Cliff Zhang; Tao Jiang 001 (Quant. Biol., 2020)

SilencerDB: a comprehensive database of silencers. - Wanwen Zeng; Shengquan Chen; Xuejian Cui; Xiaoyang Chen; Zijing Gao; Rui Jiang 001 (Nucleic Acids Res., 2021)

scGraph: a graph neural network-based approach to automatically identify cell types. - Qijin Yin; Qiao Liu 008; Zhuoran Fu; Wanwen Zeng; Boheng Zhang; Xuegong Zhang; Rui Jiang 001; Hairong Lv (Bioinform., 2022)

Deep generative modeling and clustering of single cell Hi-C data. - Qiao Liu 008; Wanwen Zeng; Wei Zhang 241; Sicheng Wang; Hongyang Chen; Rui Jiang 001; Mu Zhou; Shaoting Zhang 001 (Briefings Bioinform., 2023)

HiChIPdb: a comprehensive database of HiChIP regulatory interactions. - Wanwen Zeng; Qiao Liu 008; Qijin Yin; Rui Jiang 001; Wing Hung Wong (Nucleic Acids Res., 2023)

DeepDrug: A general graph-based deep learning framework for drug-drug interactions and drug-target interactions prediction. - Qijin Yin; Rui Fan; Xusheng Cao; Qiao Liu 008; Rui Jiang 001; Wanwen Zeng (Quant. Biol., 2023)

Inferring Gene Regulatory Network Based on scATAC-seq Data with Gene Perturbation. - Wei Shao; Yuti Liu; Shuang Zhang; Shuang Chen; Qiao Liu 008; Jianyu Zhou; Wanwen Zeng (BIBM, 2024)