Rui Jiang - RankMe

106 papers B 3Misc 2Journal 87Unranked 14

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Harnessing LLMs to decode genetic perturbations. Nat. Comput. Sci. Zijing Gao, Rui Jiang
2025	J	`jnl`	A phenotype-based AI pipeline outperforms human experts in differentially diagnosing rare diseases using EHRs. npj Digit. Medicine Xiaohao Mao, Yu Huang, Ye Jin, Lun Wang, Xuanzhong Chen, Honghong Liu, Xinglin Yang, Haopeng Xu, Xiaodong Luan, Ying Xiao, Siqin Feng, Jiahao Zhu, Xuegong Zhang, Rui Jiang, Shuyang Zhang, Ting Chen
2025	J	`jnl`	CASHeart: A database of single cells chromatin accessibility for the human heart. Quant. Biol. Qun jiang, Xiaoyang Chen, Zijing Gao, Jinmeng Jia, Shengquan Chen, Rui Jiang
2025	J	`jnl`	Deep multiple instance learning on heterogeneous graph for drug-disease association prediction. Comput. Biol. Medicine Yaowen Gu, Si Zheng, Bowen Zhang, Hongyu Kang, Rui Jiang, Jiao Li
2025	J	`jnl`	Label Informed Contrastive Pretraining for Node Importance Estimation on Knowledge Graphs. IEEE Trans. Neural Networks Learn. Syst. Tianyu Zhang, Chengbin Hou, Rui Jiang, Xuegong Zhang, Chenghu Zhou, Ke Tang, Hairong Lv
2025	J	`jnl`	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. Briefings Bioinform. Si Zheng, Yaowen Gu, Yuzhen Gu, Yelin Zhao, Liang Li, Min Wang, Rui Jiang, Xia Yu, Ting Chen, Jiao Li
2025	J	`jnl`	Prediction of mortality in intensive care unit with short-term heart rate variability: Machine learning-based analysis of the MIMIC-III database. Comput. Biol. Medicine Lexin Huang, Zixuan Dou, Fang Fang, Boda Zhou, Ping Zhang, Rui Jiang
2024	J	`jnl`	A transformer-based weakly supervised computational pathology method for clinical-grade diagnosis and molecular marker discovery of gliomas. Nat. Mac. Intell. Rui Jiang, Xiaoxu Yin, Pengshuai Yang, Lingchao Cheng, Juan Hu, Jiao Yang, Ying Wang, Xiaodan Fu, Li Shang, Liling Li, Wei Lin, Huan Zhou, Fufeng Chen, Xuegong Zhang, Zhongliang Hu, Hairong Lv
2024	J	`jnl`	Accurate Annotation for Differentiating and Imbalanced Cell Types in Single-Cell Chromatin Accessibility Data. IEEE ACM Trans. Comput. Biol. Bioinform. Yuhang Jia, Siyu Li, Rui Jiang, Shengquan Chen
2024	J	`jnl`	Cofea: correlation-based feature selection for single-cell chromatin accessibility data. Briefings Bioinform. Keyi Li, Xiaoyang Chen, Shuang Song, Lin Hou, Shengquan Chen, Rui Jiang
2024	J	`jnl`	Discrete latent embedding of single-cell chromatin accessibility sequencing data for uncovering cell heterogeneity. Nat. Comput. Sci. Xuejian Cui, Xiaoyang Chen, Zhen Li, Zijing Gao, Shengquan Chen, Rui Jiang
2024	J	`jnl`	Label Informed Contrastive Pretraining for Node Importance Estimation on Knowledge Graphs. CoRR Tianyu Zhang, Chengbin Hou, Rui Jiang, Xuegong Zhang, Chenghu Zhou, Ke Tang, Hairong Lv
2024	J	`jnl`	collectNET: a web server for integrated inference of cell-cell communication network. Database J. Biol. Databases Curation Yan Pan, Zijing Gao, Xuejian Cui, Zhen Li, Rui Jiang
2024	J	`jnl`	scPRAM accurately predicts single-cell gene expression perturbation response based on attention mechanism. Bioinform. Qun jiang, Shengquan Chen, Xiaoyang Chen, Rui Jiang
2023	J	`jnl`	Building digital life systems for future biology and medicine. Quant. Biol. Xuegong Zhang, Lei Wei, Rui Jiang, Xiaowo Wang, Jin Gu, Zhen Xie, Hairong Lv
2023	J	`jnl`	Deep generative modeling and clustering of single cell Hi-C data. Briefings Bioinform. Qiao Liu, Wanwen Zeng, Wei Zhang, Sicheng Wang, Hongyang Chen, Rui Jiang, Mu Zhou, Shaoting Zhang
2023	J	`jnl`	DeepDrug: A general graph-based deep learning framework for drug-drug interactions and drug-target interactions prediction. Quant. Biol. Qijin Yin, Rui Fan, Xusheng Cao, Qiao Liu, Rui Jiang, Wanwen Zeng
2023	J	`jnl`	HiChIPdb: a comprehensive database of HiChIP regulatory interactions. Nucleic Acids Res. Wanwen Zeng, Qiao Liu, Qijin Yin, Rui Jiang, Wing Hung Wong
2023	J	`jnl`	Improving artificial intelligence pipeline for liver malignancy diagnosis using ultrasound images and video frames. Briefings Bioinform. Yiming Xu, Bowen Zheng, Xiaohong Liu, Tao Wu, Jinxiu Ju, Shi-jie Wang, Yufan Lian, Hongjun Zhang, Tong Liang, Ye Sang, Rui Jiang, Guangyu Wang, Jie Ren, Ting Chen
2023	Misc	`conf`	Time-Aware Multiway Adaptive Fusion Network for Temporal Knowledge Graph Question Answering. ICASSP Yonghao Liu, Di Liang, Fang Fang, Sirui Wang, Wei Wu, Rui Jiang
2023	J	`jnl`	Time-aware Multiway Adaptive Fusion Network for Temporal Knowledge Graph Question Answering. CoRR Yonghao Liu, Di Liang, Fang Fang, Sirui Wang, Wei Wu, Rui Jiang
2023	J	`jnl`	simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data. Bioinform. Chen Li, Xiaoyang Chen, Shengquan Chen, Rui Jiang, Xuegong Zhang
2022	J	`jnl`	CS-CO: A Hybrid Self-Supervised Visual Representation Learning Method for H&E-stained Histopathological Images. Medical Image Anal. Pengshuai Yang, Xiaoxu Yin, Haiming Lu, Zhongliang Hu, Xuegong Zhang, Rui Jiang, Hairong Lv
2022	J	`jnl`	Cell type annotation of single-cell chromatin accessibility data via supervised Bayesian embedding. Nat. Mach. Intell. Xiaoyang Chen, Shengquan Chen, Shuang Song, Zijing Gao, Lin Hou, Xuegong Zhang, Hairong Lv, Rui Jiang
2022	J	`jnl`	DeepCAGE: Incorporating Transcription Factors in Genome-wide Prediction of Chromatin Accessibility. Genom. Proteom. Bioinform. Qiao Liu, Kui Hua, Xuegong Zhang, Wing Hung Wong, Rui Jiang
2022	J	`jnl`	DualGCN: a dual graph convolutional network model to predict cancer drug response. BMC Bioinform. Tianxing Ma, Qiao Liu, Haochen Li, Mu Zhou, Rui Jiang, Xuegong Zhang
2022	J	`jnl`	REDDA: Integrating multiple biological relations to heterogeneous graph neural network for drug-disease association prediction. Comput. Biol. Medicine Yaowen Gu, Si Zheng, Qijin Yin, Rui Jiang, Jiao Li
2022	J	`jnl`	scGraph: a graph neural network-based approach to automatically identify cell types. Bioinform. Qijin Yin, Qiao Liu, Zhuoran Fu, Wanwen Zeng, Boheng Zhang, Xuegong Zhang, Rui Jiang, Hairong Lv
2021	J	`jnl`	DeepCAPE: A Deep Convolutional Neural Network for the Accurate Prediction of Enhancers. Genom. Proteom. Bioinform. Shengquan Chen, Mingxin Gan, Hairong Lv, Rui Jiang
2021	J	`jnl`	Few shot domain adaptation for in situ macromolecule structural classification in cryoelectron tomograms. Bioinform. Liangyong Yu, Ran Li, Xiangrui Zeng, Hongyi Wang, Jie Jin, Ge Yang, Rui Jiang, Min Xu
2021	J	`jnl`	OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions. Nucleic Acids Res. Shengquan Chen, Qiao Liu, Xuejian Cui, Zhan-Ying Feng, Chunquan Li, Xiaowo Wang, Xuegong Zhang, Yong Wang, Rui Jiang
2021	—	`conf`	Self-supervised Visual Representation Learning for Histopathological Images. MICCAI (2) Pengshuai Yang, Zhiwei Hong, Xiaoxu Yin, Chengzhan Zhu, Rui Jiang
2021	J	`jnl`	SilencerDB: a comprehensive database of silencers. Nucleic Acids Res. Wanwen Zeng, Shengquan Chen, Xuejian Cui, Xiaoyang Chen, Zijing Gao, Rui Jiang
2021	J	`jnl`	Simultaneous deep generative modelling and clustering of single-cell genomic data. Nat. Mach. Intell. Qiao Liu, Shengquan Chen, Rui Jiang, Wing Hung Wong
2021	J	`jnl`	stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics. Bioinform. Shengquan Chen, Boheng Zhang, Xiaoyang Chen, Xuegong Zhang, Rui Jiang
2020	J	`jnl`	A Natural Language Processing Pipeline of Chinese Free-Text Radiology Reports for Liver Cancer Diagnosis. IEEE Access Honglei Liu, Yan Xu, Zhiqiang Zhang, Ni Wang, Yanqun Huang, Yanjun Hu, Zhenghan Yang, Rui Jiang, Hui Chen
2020	J	`jnl`	A Natural Language Processing Pipeline of Chinese Free-text Radiology Reports for Liver Cancer Diagnosis. CoRR Honglei Liu, Yan Xu, Zhiqiang Zhang, Ni Wang, Yanqun Huang, Zhenghan Yang, Rui Jiang, Hui Chen
2020	J	`jnl`	A simulated annealing approach for resolution guided homogeneous cryo-electron microscopy image selection. Quant. Biol. Jie Shi, Xiangrui Zeng, Rui Jiang, Tao Jiang, Min Xu
2020	J	`jnl`	DeepCDR: a hybrid graph convolutional network for predicting cancer drug response. Bioinform. Qiao Liu, Zhiqiang Hu, Rui Jiang, Mu Zhou
2020	J	`jnl`	EnClaSC: a novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes. BMC Bioinform. Xiaoyang Chen, Shengquan Chen, Rui Jiang
2020	J	`jnl`	Few shot domain adaptation for in situ macromolecule structural classification in cryo-electron tomograms. CoRR Liangyong Yu, Ran Li, Xiangrui Zeng, Hongyi Wang, Jie Jin, Ge Yang, Rui Jiang, Min Xu
2020	J	`jnl`	Few-shot learning for classification of novel macromolecular structures in cryo-electron tomograms. PLoS Comput. Biol. Ran Li, Liangyong Yu, Bo Zhou, Xiangrui Zeng, Zhenyu Wang, Xiaoyan Yang, Jing Zhang, Xin Gao, Rui Jiang, Min Xu
2020	J	`jnl`	IRIS: A method for predicting in vivo RNA secondary structures using PARIS data. Quant. Biol. Jianyu Zhou, Pan Li, Wanwen Zeng, Wenxiu Ma, Zhipeng Lu, Rui Jiang, Qiangfeng Cliff Zhang, Tao Jiang
2020	J	`jnl`	Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network. Bioinform. Wanwen Zeng, Yong Wang, Rui Jiang
2020	J	`jnl`	Roundtrip: A Deep Generative Neural Density Estimator. CoRR Qiao Liu, Jiaze Xu, Rui Jiang, Wing Hung Wong
2019	J	`jnl`	Automatic localization and identification of mitochondria in cellular electron cryo-tomography using faster-RCNN. BMC Bioinform. Ran Li, Xiangrui Zeng, Stephanie E. Sigmund, Ruogu Lin, Bo Zhou, Chang Liu, Kaiwen Wang, Rui Jiang, Zachary Freyberg, Hairong Lv, Min Xu
2019	J	`jnl`	DeepHistone: a deep learning approach to predicting histone modifications. BMC Genom. Qijin Yin, Mengmeng Wu, Qiao Liu, Hairong Lv, Rui Jiang
2019	J	`jnl`	EnDisease: a manually curated database for enhancer-disease associations. Database J. Biol. Databases Curation Wanwen Zeng, Xu Min, Rui Jiang
2019	J	`jnl`	EpiFIT: functional interpretation of transcription factors based on combination of sequence and epigenetic information. Quant. Biol. Shaoming Song, Hongfei Cui, Shengquan Chen, Qiao Liu, Rui Jiang
2019	J	`jnl`	GLORY: Exploration and integration of global and local correlations to improve personalized online social recommendations. Inf. Syst. Frontiers Mingxin Gan, Lily Sun, Rui Jiang
2019	B	`conf`	Instance Segmentation of Anatomical Structures in Chest Radiographs. CBMS Jie Wang, Zhigang Li, Rui Jiang, Zhen Xie
2019	—	`conf`	Liver Histopathological Image Retrieval Based on Deep Metric Learning. BIBM Pengshuai Yang, Yupeng Zhai, Lin Li, Hairong Lv, Jigang Wang, Chengzhan Zhu, Rui Jiang
2019	B	`conf`	Rule-Based Method to Develop Question-Answer Dataset from Chest X-Ray Reports. CBMS Jie Wang, Hairong Lv, Rui Jiang, Zhen Xie
2019	J	`jnl`	VPAC: Variational projection for accurate clustering of single-cell transcriptomic data. BMC Bioinform. Shengquan Chen, Kui Hua, Hongfei Cui, Rui Jiang
2019	J	`jnl`	hicGAN infers super resolution Hi-C data with generative adversarial networks. Bioinform. Qiao Liu, Hairong Lv, Rui Jiang
2018	J	`jnl`	Chromatin accessibility prediction via a hybrid deep convolutional neural network. Bioinform. Qiao Liu, Fei Xia, Qijin Yin, Rui Jiang
2018	J	`jnl`	FLOWER: Fusing global and local associations towards personalized social recommendation. Future Gener. Comput. Syst. Mingxin Gan, Rui Jiang
2018	J	`jnl`	Guest Editorial for Special Section on the Sixth National Conference on Bioinformatics and System Biology of China. IEEE ACM Trans. Comput. Biol. Bioinform. Xiaodan Fan, Xinglai Ji, Rui Jiang
2018	J	`jnl`	Prediction of enhancer-promoter interactions via natural language processing. BMC Genom. Wanwen Zeng, Mengmeng Wu, Rui Jiang
2018	—	`conf`	Respond-CAM: Analyzing Deep Models for 3D Imaging Data by Visualizations. MICCAI (1) Guannan Zhao, Bo Zhou, Kaiwen Wang, Rui Jiang, Min Xu
2018	J	`jnl`	Respond-CAM: Analyzing Deep Models for 3D Imaging Data by Visualizations. CoRR Guannan Zhao, Bo Zhou, Kaiwen Wang, Rui Jiang, Min Xu
2017	J	`jnl`	A sequence-based method to predict the impact of regulatory variants using random forest. BMC Syst. Biol. Qiao Liu, Mingxin Gan, Rui Jiang
2017	J	`jnl`	Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding. Bioinform. Xu Min, Wanwen Zeng, Ning Chen, Ting Chen, Rui Jiang
2017	—	`conf`	Exploring functional variant using a deep learning framework. CASE Tianyi Sun, Zhuo Liu, Xing-Ming Zhao, Rui Jiang
2017	—	`conf`	Integrating embeddings of multiple gene networks to prioritize complex disease-associated genes. BIBM Mengmeng Wu, Wanwen Zeng, Wenqiang Liu, Yijia Zhang, Ting Chen, Rui Jiang
2017	J	`jnl`	Mimvec: a deep learning approach for analyzing the human phenome. BMC Syst. Biol. Mingxin Gan, Wenran Li, Wanwen Zeng, Xiaojian Wang, Rui Jiang
2017	—	`conf`	PPIM: A protein-protein interaction database for Maize. CASE Guanghui Zhu, Rui Jiang, Xing-Ming Zhao
2017	J	`jnl`	Predicting enhancers with deep convolutional neural networks. BMC Bioinform. Xu Min, Wanwen Zeng, Shengquan Chen, Ning Chen, Ting Chen, Rui Jiang
2016	J	`jnl`	Construction and Analysis of Functional Networks in the Gut Microbiome of Type 2 Diabetes Patients. Genom. Proteom. Bioinform. Lianshuo Li, Zicheng Wang, Peng He, Shining Ma, Jie Du, Rui Jiang
2016	—	`conf`	DeepEnhancer: Predicting enhancers by convolutional neural networks. BIBM Xu Min, Ning Chen, Ting Chen, Rui Jiang
2016	J	`jnl`	Global inference of disease-causing single nucleotide variants from exome sequencing data. BMC Bioinform. Mengmeng Wu, Ting Chen, Rui Jiang
2016	J	`jnl`	Trinity: Walking on a User-Object-Tag Heterogeneous Network for Personalised Recommendations. J. Comput. Sci. Technol. Mingxin Gan, Lily Sun, Rui Jiang
2016	J	`jnl`	Whole genome sequencing and its applications in medical genetics. Quant. Biol. Jiaxin Wu, Mengmeng Wu, Ting Chen, Rui Jiang
2016	J	`jnl`	dbWGFP: a database and web server of human whole-genome single nucleotide variants and their functional predictions. Database J. Biol. Databases Curation Jiaxin Wu, Mengmeng Wu, Lianshuo Li, Zhuo Liu, Wanwen Zeng, Rui Jiang
2015	J	`jnl`	Differential regulation enrichment analysis via the integration of transcriptional regulatory network and gene expression data. Bioinform. Shining Ma, Tao Jiang, Rui Jiang
2015	J	`jnl`	Pinpointing disease genes through phenomic and genomic data fusion. BMC Genom. Rui Jiang, Mengmeng Wu, Lianshuo Li
2015	J	`jnl`	ROUND: Walking on an object-user heterogeneous network for personalized recommendations. Expert Syst. Appl. Mingxin Gan, Rui Jiang
2014	J	`jnl`	Constructing a Boolean implication network to study the interactions between environmental factors and OTUs. Quant. Biol. Congmin Zhu, Rui Jiang, Ting Chen
2014	J	`jnl`	Integrated Approach in Systems Biology. Comput. Math. Methods Medicine Huiru Zheng, Rui Jiang, Zhongming Zhao
2014	J	`jnl`	Prioritizing protein complexes implicated in human diseases by network optimization. BMC Syst. Biol. Yong Chen, Thibault Jacquemin, Shuyan Zhang, Rui Jiang
2013	J	`jnl`	Constructing a user similarity network to remove adverse influence of popular objects for personalized recommendation. Expert Syst. Appl. Mingxin Gan, Rui Jiang
2013	J	`jnl`	Improving accuracy and diversity of personalized recommendation through power law adjustments of user similarities. Decis. Support Syst. Mingxin Gan, Rui Jiang
2013	—	`conf`	Inferring semantic similarity through correlating information contents of gene ontology terms. BIBM Mingxin Gan, Rui Jiang
2013	J	`jnl`	PyroHMMvar: a sensitive and accurate method to call short indels and SNPs for Ion Torrent and 454 data. Bioinform. Feng Zeng, Rui Jiang, Ting Chen
2013	B	`ed.`	Research in Computational Molecular Biology - 17th Annual International Conference, RECOMB 2013, Beijing, China, April 7-10, 2013. Proceedings RECOMB Minghua Deng, Rui Jiang, Fengzhu Sun, Xuegong Zhang
2012	J	`jnl`	Identification of disease-related nsSNPs via the integration of protein sequence features and domain-domain interaction data. Int. J. Comput. Biol. Drug Des. Rui Jiang, Mingxin Gan, Jiaxin Wu
2012	—	`conf`	Improving Recommendation Performance through Ontology-Based Semantic Similarity. ICICA (LNCS) Mingxin Gan, Xue Dou, Rui Jiang
2012	—	`conf`	Ontology-Based Genes Similarity Calculation with TF-IDF. ICICA (LNCS) Yue Huang, Mingxin Gan, Rui Jiang
2011	J	`jnl`	A Max-Flow-Based Approach to the Identification of Protein Complexes Using Protein Interaction and Microarray Data. IEEE ACM Trans. Comput. Biol. Bioinform. Jianxing Feng, Rui Jiang, Tao Jiang
2011	Misc	`conf`	A genetic algorithm for optimizing subnetwork markers for the study of breast cancer metastasis. ICNC Jiaxin Wu, Mingxin Gan, Rui Jiang
2011	J	`jnl`	Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering. Bioinform. Xiaolin Hao, Rui Jiang, Ting Chen
2011	J	`jnl`	Constructing a gene semantic similarity network for the inference of disease genes. BMC Syst. Biol. Rui Jiang, Mingxin Gan, Peng He
2011	—	`conf`	DOPCA: A New Method for Calculating Ontology-Based Semantic Similarity. ACIS-ICIS Mingxin Gan, Xue Dou, Daoping Wang, Rui Jiang
2011	J	`jnl`	DomainRBF: a Bayesian regression approach to the prioritization of candidate domains for complex diseases. BMC Syst. Biol. Wangshu Zhang, Yong Chen, Fengzhu Sun, Rui Jiang
2011	J	`jnl`	Integrating multiple protein-protein interaction networks to prioritize disease genes: a Bayesian regression approach. BMC Bioinform. Wangshu Zhang, Fengzhu Sun, Rui Jiang
2011	—	`conf`	Integrating sequence conservation features and a domain-domain interaction network to detect disease-associated nsSNPs. BIBM Workshops Rui Jiang, Jiaxin Wu
2011	J	`jnl`	Prioritisation of candidate Single Amino Acid Polymorphisms using one-class learning machines. Int. J. Comput. Biol. Drug Des. Jiaxin Wu, Mingxin Gan, Rui Jiang
2011	J	`jnl`	Uncover disease genes by maximizing information flow in the phenome-interactome network. Bioinform. Yong Chen, Tao Jiang, Rui Jiang
2009	—	`conf`	A Comparative Study of Ensemble Learning Approaches in the Classification of Breast Cancer Metastasis. IJCBS Wangshu Zhang, Feng Zeng, Xuebing Wu, Xuegong Zhang, Rui Jiang
2009	J	`jnl`	A random forest approach to the detection of epistatic interactions in case-control studies. BMC Bioinform. Rui Jiang, Wanwan Tang, Xuebing Wu, Wenhui Fu
2009	—	`conf`	Accelerating Genome-Wide Association Studies Using CUDA Compatible Graphics Processing Units. IJCBS Rui Jiang, Feng Zeng, Wangshu Zhang, Xuebing Wu, Zhihong Yu
2009	J	`jnl`	Align human interactome with phenome to identify causative genes and networks underlying disease families. Bioinform. Xuebing Wu, Qifang Liu, Rui Jiang
2009	J	`jnl`	Bayesian Models and Gibbs Sampling Strategies for Local Graph Alignment and Motif Identification in Stochastic Biological Networks. Commun. Inf. Syst. Ting Chen, Rui Jiang, Fengzhu Sun
2007	J	`jnl`	Optimal Adaptive Controller for Multidimensional Armax Model. Cybern. Syst. Rui Jiang, Kueiming Lo
2006	J	`jnl`	Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy. BMC Bioinform. Rui Jiang, Hua Yang, Fengzhu Sun, Ting Chen
2000	J	`jnl`	An adaptive classifier system tree for extending genetics-based machine learning in a dynamic environment. Artif. Life Robotics Dongcheng Hu, Rui Jiang, Yupin Luo