An adaptive classifier system tree for extending genetics-based machine learning in a dynamic environment. - Dongcheng Hu; Rui Jiang 001; Yupin Luo (Artif. Life Robotics, 2000)

Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy. - Rui Jiang 001; Hua Yang; Fengzhu Sun; Ting Chen 006 (BMC Bioinform., 2006)

Optimal Adaptive Controller for Multidimensional Armax Model. - Rui Jiang 001; Kueiming Lo (Cybern. Syst., 2007)

Accelerating Genome-Wide Association Studies Using CUDA Compatible Graphics Processing Units. - Rui Jiang 001; Feng Zeng; Wangshu Zhang; Xuebing Wu; Zhihong Yu (IJCBS, 2009)

A Comparative Study of Ensemble Learning Approaches in the Classification of Breast Cancer Metastasis. - Wangshu Zhang; Feng Zeng; Xuebing Wu; Xuegong Zhang; Rui Jiang 001 (IJCBS, 2009)

Align human interactome with phenome to identify causative genes and networks underlying disease families. - Xuebing Wu; Qifang Liu; Rui Jiang 001 (Bioinform., 2009)

A random forest approach to the detection of epistatic interactions in case-control studies. - Rui Jiang 001; Wanwan Tang; Xuebing Wu; Wenhui Fu (BMC Bioinform., 2009)

Bayesian Models and Gibbs Sampling Strategies for Local Graph Alignment and Motif Identification in Stochastic Biological Networks. - Ting Chen 006; Rui Jiang 001; Fengzhu Sun (Commun. Inf. Syst., 2009)

DOPCA: A New Method for Calculating Ontology-Based Semantic Similarity. - Mingxin Gan; Xue Dou; Daoping Wang; Rui Jiang 001 (ACIS-ICIS, 2011)

Integrating sequence conservation features and a domain-domain interaction network to detect disease-associated nsSNPs. - Rui Jiang 001; Jiaxin Wu 005 (BIBM Workshops, 2011)

A genetic algorithm for optimizing subnetwork markers for the study of breast cancer metastasis. - Jiaxin Wu 005; Mingxin Gan; Rui Jiang 001 (ICNC, 2011)

Uncover disease genes by maximizing information flow in the phenome-interactome network. - Yong Chen; Tao Jiang 001; Rui Jiang 001 (Bioinform., 2011)

Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering. - Xiaolin Hao; Rui Jiang 001; Ting Chen (Bioinform., 2011)

Integrating multiple protein-protein interaction networks to prioritize disease genes: a Bayesian regression approach. - Wangshu Zhang; Fengzhu Sun; Rui Jiang 001 (BMC Bioinform., 2011)

Constructing a gene semantic similarity network for the inference of disease genes. - Rui Jiang 001; Mingxin Gan; Peng He (BMC Syst. Biol., 2011)

DomainRBF: a Bayesian regression approach to the prioritization of candidate domains for complex diseases. - Wangshu Zhang; Yong Chen; Fengzhu Sun; Rui Jiang 001 (BMC Syst. Biol., 2011)

Prioritisation of candidate Single Amino Acid Polymorphisms using one-class learning machines. - Jiaxin Wu 005; Mingxin Gan; Rui Jiang 001 (Int. J. Comput. Biol. Drug Des., 2011)

A Max-Flow-Based Approach to the Identification of Protein Complexes Using Protein Interaction and Microarray Data. - Jianxing Feng; Rui Jiang 001; Tao Jiang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Improving Recommendation Performance through Ontology-Based Semantic Similarity. - Mingxin Gan; Xue Dou; Rui Jiang 001 (ICICA (LNCS), 2012)

Ontology-Based Genes Similarity Calculation with TF-IDF. - Yue Huang; Mingxin Gan; Rui Jiang 001 (ICICA (LNCS), 2012)

Identification of disease-related nsSNPs via the integration of protein sequence features and domain-domain interaction data. - Rui Jiang 001; Mingxin Gan; Jiaxin Wu 005 (Int. J. Comput. Biol. Drug Des., 2012)

Inferring semantic similarity through correlating information contents of gene ontology terms. - Mingxin Gan; Rui Jiang 001 (BIBM, 2013)

PyroHMMvar: a sensitive and accurate method to call short indels and SNPs for Ion Torrent and 454 data. - Feng Zeng; Rui Jiang 001; Ting Chen (Bioinform., 2013)

Improving accuracy and diversity of personalized recommendation through power law adjustments of user similarities. - Mingxin Gan; Rui Jiang 001 (Decis. Support Syst., 2013)

Constructing a user similarity network to remove adverse influence of popular objects for personalized recommendation. - Mingxin Gan; Rui Jiang 001 (Expert Syst. Appl., 2013)

Prioritizing protein complexes implicated in human diseases by network optimization. - Yong Chen; Thibault Jacquemin; Shuyan Zhang; Rui Jiang 001 (BMC Syst. Biol., 2014)

Integrated Approach in Systems Biology. - Huiru Zheng; Rui Jiang 001; Zhongming Zhao (Comput. Math. Methods Medicine, 2014)

Constructing a Boolean implication network to study the interactions between environmental factors and OTUs. - Congmin Zhu; Rui Jiang 001; Ting Chen 002 (Quant. Biol., 2014)

Differential regulation enrichment analysis via the integration of transcriptional regulatory network and gene expression data. - Shining Ma; Tao Jiang 001; Rui Jiang 001 (Bioinform., 2015)

Pinpointing disease genes through phenomic and genomic data fusion. - Rui Jiang 001; Mengmeng Wu; Lianshuo Li (BMC Genom., 2015)

ROUND: Walking on an object-user heterogeneous network for personalized recommendations. - Mingxin Gan; Rui Jiang 001 (Expert Syst. Appl., 2015)

DeepEnhancer: Predicting enhancers by convolutional neural networks. - Xu Min; Ning Chen 002; Ting Chen 006; Rui Jiang 001 (BIBM, 2016)

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)

Global inference of disease-causing single nucleotide variants from exome sequencing data. - Mengmeng Wu; Ting Chen 006; Rui Jiang 001 (BMC Bioinform., 2016)

Construction and Analysis of Functional Networks in the Gut Microbiome of Type 2 Diabetes Patients. - Lianshuo Li; Zicheng Wang; Peng He; Shining Ma; Jie Du; Rui Jiang 001 (Genom. Proteom. Bioinform., 2016)

Trinity: Walking on a User-Object-Tag Heterogeneous Network for Personalised Recommendations. - Mingxin Gan; Lily Sun; Rui Jiang 001 (J. Comput. Sci. Technol., 2016)

Whole genome sequencing and its applications in medical genetics. - Jiaxin Wu 005; Mengmeng Wu; Ting Chen 006; Rui Jiang 001 (Quant. Biol., 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)

Exploring functional variant using a deep learning framework. - Tianyi Sun; Zhuo Liu; Xing-Ming Zhao; Rui Jiang 001 (CASE, 2017)

PPIM: A protein-protein interaction database for Maize. - Guanghui Zhu; Rui Jiang 001; Xing-Ming Zhao (CASE, 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)

A sequence-based method to predict the impact of regulatory variants using random forest. - Qiao Liu 008; Mingxin Gan; Rui Jiang 001 (BMC Syst. Biol., 2017)

Respond-CAM: Analyzing Deep Models for 3D Imaging Data by Visualizations. - Guannan Zhao; Bo Zhou 009; Kaiwen Wang; Rui Jiang 001; Min Xu 009 (MICCAI (1), 2018)

Chromatin accessibility prediction via a hybrid deep convolutional neural network. - Qiao Liu 008; Fei Xia 002; Qijin Yin; Rui Jiang 001 (Bioinform., 2018)

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

FLOWER: Fusing global and local associations towards personalized social recommendation. - Mingxin Gan; Rui Jiang 001 (Future Gener. Comput. Syst., 2018)

Guest Editorial for Special Section on the Sixth National Conference on Bioinformatics and System Biology of China. - Xiaodan Fan; Xinglai Ji; Rui Jiang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Liver Histopathological Image Retrieval Based on Deep Metric Learning. - Pengshuai Yang; Yupeng Zhai; Lin Li; Hairong Lv; Jigang Wang; Chengzhan Zhu; Rui Jiang 001 (BIBM, 2019)

Rule-Based Method to Develop Question-Answer Dataset from Chest X-Ray Reports. - Jie Wang 111; Hairong Lv; Rui Jiang 001; Zhen Xie (CBMS, 2019)

Instance Segmentation of Anatomical Structures in Chest Radiographs. - Jie Wang 111; Zhigang Li 004; Rui Jiang 001; Zhen Xie (CBMS, 2019)

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

hicGAN infers super resolution Hi-C data with generative adversarial networks. - Qiao Liu 008; Hairong Lv; Rui Jiang 001 (Bioinform., 2019)

VPAC: Variational projection for accurate clustering of single-cell transcriptomic data. - Shengquan Chen; Kui Hua; Hongfei Cui; Rui Jiang 001 (BMC Bioinform., 2019)

Automatic localization and identification of mitochondria in cellular electron cryo-tomography using faster-RCNN. - Ran Li; Xiangrui Zeng; Stephanie E. Sigmund; Ruogu Lin; Bo Zhou 009; Chang Liu 031; Kaiwen Wang; Rui Jiang 001; Zachary Freyberg; Hairong Lv; Min Xu 009 (BMC Bioinform., 2019)

DeepHistone: a deep learning approach to predicting histone modifications. - Qijin Yin; Mengmeng Wu; Qiao Liu 008; Hairong Lv; Rui Jiang 001 (BMC Genom., 2019)

GLORY: Exploration and integration of global and local correlations to improve personalized online social recommendations. - Mingxin Gan; Lily Sun; Rui Jiang 001 (Inf. Syst. Frontiers, 2019)

EpiFIT: functional interpretation of transcription factors based on combination of sequence and epigenetic information. - Shaoming Song; Hongfei Cui; Shengquan Chen; Qiao Liu 008; Rui Jiang 001 (Quant. Biol., 2019)

A Natural Language Processing Pipeline of Chinese Free-Text Radiology Reports for Liver Cancer Diagnosis. - Honglei Liu; Yan Xu; Zhiqiang Zhang; Ni Wang; Yanqun Huang; Yanjun Hu; Zhenghan Yang; Rui Jiang 001; Hui Chen 010 (IEEE Access, 2020)

DeepCDR: a hybrid graph convolutional network for predicting cancer drug response. - Qiao Liu 008; Zhiqiang Hu; Rui Jiang 001; Mu Zhou (Bioinform., 2020)

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)

EnClaSC: a novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes. - Xiaoyang Chen; Shengquan Chen; Rui Jiang 001 (BMC Bioinform., 2020)

Roundtrip: A Deep Generative Neural Density Estimator. - Qiao Liu 008; Jiaze Xu; Rui Jiang 001; Wing Hung Wong (CoRR, 2020)

A Natural Language Processing Pipeline of Chinese Free-text Radiology Reports for Liver Cancer Diagnosis. - Honglei Liu; Yan Xu; Zhiqiang Zhang; Ni Wang; Yanqun Huang; Zhenghan Yang; Rui Jiang 001; Hui Chen 010 (CoRR, 2020)

Few shot domain adaptation for in situ macromolecule structural classification in cryo-electron tomograms. - Liangyong Yu; Ran Li; Xiangrui Zeng; Hongyi Wang; Jie Jin; Ge Yang 002; Rui Jiang 001; Min Xu 009 (CoRR, 2020)

Few-shot learning for classification of novel macromolecular structures in cryo-electron tomograms. - Ran Li; Liangyong Yu; Bo Zhou 009; Xiangrui Zeng; Zhenyu Wang; Xiaoyan Yang; Jing Zhang 062; Xin Gao 001; Rui Jiang 001; Min Xu 009 (PLoS Comput. Biol., 2020)

A simulated annealing approach for resolution guided homogeneous cryo-electron microscopy image selection. - Jie Shi; Xiangrui Zeng; Rui Jiang 001; Tao Jiang 001; Min Xu 009 (Quant. Biol., 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)

Self-supervised Visual Representation Learning for Histopathological Images. - Pengshuai Yang; Zhiwei Hong; Xiaoxu Yin; Chengzhan Zhu; Rui Jiang 001 (MICCAI (2), 2021)

stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics. - Shengquan Chen; Boheng Zhang; Xiaoyang Chen; Xuegong Zhang; Rui Jiang 001 (Bioinform., 2021)

Few shot domain adaptation for in situ macromolecule structural classification in cryoelectron tomograms. - Liangyong Yu; Ran Li; Xiangrui Zeng; Hongyi Wang; Jie Jin; Ge Yang 002; Rui Jiang 001; Min Xu 009 (Bioinform., 2021)

DeepCAPE: A Deep Convolutional Neural Network for the Accurate Prediction of Enhancers. - Shengquan Chen; Mingxin Gan; Hairong Lv; Rui Jiang 001 (Genom. Proteom. Bioinform., 2021)

OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions. - Shengquan Chen; Qiao Liu 008; Xuejian Cui; Zhan-Ying Feng; Chunquan Li; Xiaowo Wang; Xuegong Zhang; Yong Wang; Rui Jiang 001 (Nucleic Acids Res., 2021)

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

Simultaneous deep generative modelling and clustering of single-cell genomic data. - Qiao Liu 008; Shengquan Chen; Rui Jiang 001; Wing Hung Wong (Nat. Mach. Intell., 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)

DualGCN: a dual graph convolutional network model to predict cancer drug response. - Tianxing Ma; Qiao Liu 008; Haochen Li 003; Mu Zhou; Rui Jiang 001; Xuegong Zhang (BMC Bioinform., 2022)

REDDA: Integrating multiple biological relations to heterogeneous graph neural network for drug-disease association prediction. - Yaowen Gu; Si Zheng 001; Qijin Yin; Rui Jiang 001; Jiao Li 001 (Comput. Biol. Medicine, 2022)

DeepCAGE: Incorporating Transcription Factors in Genome-wide Prediction of Chromatin Accessibility. - Qiao Liu 008; Kui Hua; Xuegong Zhang; Wing Hung Wong; Rui Jiang 001 (Genom. Proteom. Bioinform., 2022)

CS-CO: A Hybrid Self-Supervised Visual Representation Learning Method for H&E-stained Histopathological Images. - Pengshuai Yang; Xiaoxu Yin; Haiming Lu; Zhongliang Hu; Xuegong Zhang; Rui Jiang 001; Hairong Lv (Medical Image Anal., 2022)

Cell type annotation of single-cell chromatin accessibility data via supervised Bayesian embedding. - Xiaoyang Chen; Shengquan Chen; Shuang Song 006; Zijing Gao; Lin Hou; Xuegong Zhang; Hairong Lv; Rui Jiang 001 (Nat. Mach. Intell., 2022)

Time-Aware Multiway Adaptive Fusion Network for Temporal Knowledge Graph Question Answering. - Yonghao Liu; Di Liang; Fang Fang; Sirui Wang; Wei Wu 014; Rui Jiang 001 (ICASSP, 2023)

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)

Improving artificial intelligence pipeline for liver malignancy diagnosis using ultrasound images and video frames. - Yiming Xu; Bowen Zheng; Xiaohong Liu 007; Tao Wu; Jinxiu Ju; Shi-jie Wang; Yufan Lian; Hongjun Zhang; Tong Liang; Ye Sang; Rui Jiang 001; Guangyu Wang; et al. (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)

simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data. - Chen Li; Xiaoyang Chen; Shengquan Chen; Rui Jiang 001; Xuegong Zhang (Bioinform., 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)

Building digital life systems for future biology and medicine. - Xuegong Zhang; Lei Wei; Rui Jiang 001; Xiaowo Wang; Jin Gu; Zhen Xie; Hairong Lv (Quant. Biol., 2023)

Cofea: correlation-based feature selection for single-cell chromatin accessibility data. - Keyi Li; Xiaoyang Chen; Shuang Song 006; Lin Hou; Shengquan Chen; Rui Jiang 001 (Briefings Bioinform., 2024)

Machine learning-enabled virtual screening indicates the anti-tuberculosis activity of aldoxorubicin and quarfloxin with verification by molecular docking, molecular dynamics simulations, and biological evaluations. - Si Zheng 001; Yaowen Gu; Yuzhen Gu; Yelin Zhao; Liang Li; Min Wang; Rui Jiang 001; Xia Yu; Ting Chen; Jiao Li 001 (Briefings Bioinform., 2024)

A transformer-based weakly supervised computational pathology method for clinical-grade diagnosis and molecular marker discovery of gliomas. - Rui Jiang 001; Xiaoxu Yin; Pengshuai Yang; Lingchao Cheng; Juan Hu; Jiao Yang; Ying Wang; Xiaodan Fu; Li Shang; Liling Li; Wei Lin; Huan Zhou; et al. (Nat. Mac. Intell., 2024)

Accurate Annotation for Differentiating and Imbalanced Cell Types in Single-Cell Chromatin Accessibility Data. - Yuhang Jia; Siyu Li; Rui Jiang 001; Shengquan Chen (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)

collectNET: a web server for integrated inference of cell-cell communication network. - Yan Pan 014; Zijing Gao; Xuejian Cui; Zhen Li; Rui Jiang 001 (Database J. Biol. Databases Curation, 2024)

Discrete latent embedding of single-cell chromatin accessibility sequencing data for uncovering cell heterogeneity. - Xuejian Cui; Xiaoyang Chen; Zhen Li; Zijing Gao; Shengquan Chen; Rui Jiang 001 (Nat. Comput. Sci., 2024)

Deep multiple instance learning on heterogeneous graph for drug-disease association prediction. - Yaowen Gu; Si Zheng 001; Bowen Zhang; Hongyu Kang; Rui Jiang 001; Jiao Li 001 (Comput. Biol. Medicine, 2025)

Prediction of mortality in intensive care unit with short-term heart rate variability: Machine learning-based analysis of the MIMIC-III database. - Lexin Huang; Zixuan Dou; Fang Fang; Boda Zhou; Ping Zhang; Rui Jiang 001 (Comput. Biol. Medicine, 2025)

A phenotype-based AI pipeline outperforms human experts in differentially diagnosing rare diseases using EHRs. - Xiaohao Mao; Yu Huang; Ye Jin; Lun Wang; Xuanzhong Chen; Honghong Liu; Xinglin Yang; Haopeng Xu; Xiaodong Luan; Ying Xiao; Siqin Feng; Jiahao Zhu; et al. (npj Digit. Medicine, 2025)

CASHeart: A database of single cells chromatin accessibility for the human heart. - Qun Jiang; Xiaoyang Chen; Zijing Gao; Jinmeng Jia; Shengquan Chen; Rui Jiang 001 (Quant. Biol., 2025)

Label Informed Contrastive Pretraining for Node Importance Estimation on Knowledge Graphs. - Tianyu Zhang; Chengbin Hou; Rui Jiang 001; Xuegong Zhang; Chenghu Zhou; Ke Tang 001; Hairong Lv (IEEE Trans. Neural Networks Learn. Syst., 2025)