Rui Jiang

According to our database, Rui Jiang authored at least 93 papers between 2000 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

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

Nat. Comput. Sci., May, 2024

collectNET: a web server for integrated inference of cell-cell communication network.

Yan Pan, Zijing Gao, Xuejian Cui, Zhen Li, Rui Jiang

Database J. Biol. Databases Curation, January, 2024

Accurate Annotation for Differentiating and Imbalanced Cell Types in Single-Cell Chromatin Accessibility Data.

Yuhang Jia, Siyu Li, Rui Jiang, Shengquan Chen

IEEE ACM Trans. Comput. Biol. Bioinform., 2024

A transformer-based weakly supervised computational pathology method for clinical-grade diagnosis and molecular marker discovery of gliomas.

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

Nat. Mac. Intell., 2024

Label Informed Contrastive Pretraining for Node Importance Estimation on Knowledge Graphs.

Tianyu Zhang, Chengbin Hou, Rui Jiang, Xuegong Zhang, Chenghu Zhou, Ke Tang, Hairong Lv

CoRR, 2024

2023

Building digital life systems for future biology and medicine.

Xuegong Zhang, Lei Wei, Rui Jiang, Xiaowo Wang, Jin Gu, Zhen Xie, Hairong Lv

Quant. Biol., September, 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, Rui Jiang, Wanwen Zeng

Quant. Biol., September, 2023

simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data.

Chen Li, Xiaoyang Chen, Shengquan Chen, Rui Jiang, Xuegong Zhang

Bioinform., August, 2023

HiChIPdb: a comprehensive database of HiChIP regulatory interactions.

Wanwen Zeng, Qiao Liu, Qijin Yin, Rui Jiang, Wing Hung Wong

Nucleic Acids Res., January, 2023

Improving artificial intelligence pipeline for liver malignancy diagnosis using ultrasound images and video frames.

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

Briefings Bioinform., January, 2023

Deep generative modeling and clustering of single cell Hi-C data.

Qiao Liu, Wanwen Zeng, Wei Zhang, Sicheng Wang, Hongyang Chen, Rui Jiang, Mu Zhou, Shaoting Zhang

Briefings Bioinform., January, 2023

Time-Aware Multiway Adaptive Fusion Network for Temporal Knowledge Graph Question Answering.

Yonghao Liu, Di Liang, Fang Fang, Sirui Wang, Wei Wu, Rui Jiang

Proceedings of the IEEE International Conference on Acoustics, 2023

2022

Cell type annotation of single-cell chromatin accessibility data via supervised Bayesian embedding.

Xiaoyang Chen, Shengquan Chen, Shuang Song, Zijing Gao, Lin Hou, Xuegong Zhang, Hairong Lv, Rui Jiang

Nat. Mach. Intell., 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, Hairong Lv

Medical Image Anal., 2022

DeepCAGE: Incorporating Transcription Factors in Genome-wide Prediction of Chromatin Accessibility.

Qiao Liu, Kui Hua, Xuegong Zhang, Wing Hung Wong, Rui Jiang

Genom. Proteom. Bioinform., 2022

REDDA: Integrating multiple biological relations to heterogeneous graph neural network for drug-disease association prediction.

Yaowen Gu, Si Zheng, Qijin Yin, Rui Jiang, Jiao Li

Comput. Biol. Medicine, 2022

DualGCN: a dual graph convolutional network model to predict cancer drug response.

Tianxing Ma, Qiao Liu, Haochen Li, Mu Zhou, Rui Jiang, Xuegong Zhang

BMC Bioinform., 2022

scGraph: a graph neural network-based approach to automatically identify cell types.

Qijin Yin, Qiao Liu, Zhuoran Fu, Wanwen Zeng, Boheng Zhang, Xuegong Zhang, Rui Jiang, Hairong Lv

Bioinform., 2022

2021

Simultaneous deep generative modelling and clustering of single-cell genomic data.

Qiao Liu, Shengquan Chen, Rui Jiang, Wing Hung Wong

Nat. Mach. Intell., 2021

SilencerDB: a comprehensive database of silencers.

Wanwen Zeng, Shengquan Chen, Xuejian Cui, Xiaoyang Chen, Zijing Gao, Rui Jiang

Nucleic Acids Res., 2021

OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions.

Shengquan Chen, Qiao Liu, Xuejian Cui, Zhan-Ying Feng, Chunquan Li, Xiaowo Wang, Xuegong Zhang, Yong Wang, Rui Jiang

Nucleic Acids Res., 2021

DeepCAPE: A Deep Convolutional Neural Network for the Accurate Prediction of Enhancers.

Shengquan Chen, Mingxin Gan, Hairong Lv, Rui Jiang

Genom. Proteom. 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, Rui Jiang, Min Xu

Bioinform., 2021

stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics.

Shengquan Chen, Boheng Zhang, Xiaoyang Chen, Xuegong Zhang, Rui Jiang

Bioinform., 2021

Self-supervised Visual Representation Learning for Histopathological Images.

Pengshuai Yang, Zhiwei Hong, Xiaoxu Yin, Chengzhan Zhu, Rui Jiang

Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2021 - 24th International Conference, Strasbourg, France, September 27, 2021

2020

IRIS: A method for predicting in vivo RNA secondary structures using PARIS data.

Jianyu Zhou, Pan Li, Wanwen Zeng, Wenxiu Ma, Zhipeng Lu, Rui Jiang, Qiangfeng Cliff Zhang, Tao Jiang

Quant. Biol., 2020

A simulated annealing approach for resolution guided homogeneous cryo-electron microscopy image selection.

Jie Shi, Xiangrui Zeng, Rui Jiang, Tao Jiang, Min Xu

Quant. Biol., 2020

Few-shot learning for classification of novel macromolecular structures in cryo-electron tomograms.

Ran Li, Liangyong Yu, Bo Zhou, Xiangrui Zeng, Zhenyu Wang, Xiaoyan Yang, Jing Zhang, Xin Gao, Rui Jiang, Min Xu

PLoS Comput. Biol., 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, Rui Jiang, Min Xu

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, Hui Chen

CoRR, 2020

Roundtrip: A Deep Generative Neural Density Estimator.

Qiao Liu, Jiaze Xu, Rui Jiang, Wing Hung Wong

CoRR, 2020

EnClaSC: a novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes.

Xiaoyang Chen, Shengquan Chen, Rui Jiang

BMC Bioinform., 2020

Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network.

Wanwen Zeng, Yong Wang, Rui Jiang

Bioinform., 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, Yanjun Hu, Zhenghan Yang, Rui Jiang, Hui Chen

IEEE Access, 2020

2019

EpiFIT: functional interpretation of transcription factors based on combination of sequence and epigenetic information.

Shaoming Song, Hongfei Cui, Shengquan Chen, Qiao Liu, Rui Jiang

Quant. Biol., 2019

GLORY: Exploration and integration of global and local correlations to improve personalized online social recommendations.

Mingxin Gan, Lily Sun, Rui Jiang

Inf. Syst. Frontiers, 2019

DeepHistone: a deep learning approach to predicting histone modifications.

Qijin Yin, Mengmeng Wu, Qiao Liu, Hairong Lv, Rui Jiang

BMC Genom., 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, Chang Liu, Kaiwen Wang, Rui Jiang, Zachary Freyberg, Hairong Lv, Min Xu

BMC Bioinform., 2019

VPAC: Variational projection for accurate clustering of single-cell transcriptomic data.

Shengquan Chen, Kui Hua, Hongfei Cui, Rui Jiang

BMC Bioinform., 2019

hicGAN infers super resolution Hi-C data with generative adversarial networks.

Qiao Liu, Hairong Lv, Rui Jiang

Bioinform., 2019

EnDisease: a manually curated database for enhancer-disease associations.

Wanwen Zeng, Xu Min, Rui Jiang

Database J. Biol. Databases Curation, 2019

Instance Segmentation of Anatomical Structures in Chest Radiographs.

Jie Wang, Zhigang Li, Rui Jiang, Zhen Xie

Proceedings of the 32nd IEEE International Symposium on Computer-Based Medical Systems, 2019

Rule-Based Method to Develop Question-Answer Dataset from Chest X-Ray Reports.

Jie Wang, Hairong Lv, Rui Jiang, Zhen Xie

Proceedings of the 32nd IEEE International Symposium on Computer-Based Medical Systems, 2019

Liver Histopathological Image Retrieval Based on Deep Metric Learning.

Pengshuai Yang, Yupeng Zhai, Lin Li, Hairong Lv, Jigang Wang, Chengzhan Zhu, Rui Jiang

Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019

2018

Guest Editorial for Special Section on the Sixth National Conference on Bioinformatics and System Biology of China.

Xiaodan Fan, Xinglai Ji, Rui Jiang

IEEE ACM Trans. Comput. Biol. Bioinform., 2018

FLOWER: Fusing global and local associations towards personalized social recommendation.

Mingxin Gan, Rui Jiang

Future Gener. Comput. Syst., 2018

Prediction of enhancer-promoter interactions via natural language processing.

Wanwen Zeng, Mengmeng Wu, Rui Jiang

BMC Genom., 2018

Chromatin accessibility prediction via a hybrid deep convolutional neural network.

Qiao Liu, Fei Xia, Qijin Yin, Rui Jiang

Bioinform., 2018

Respond-CAM: Analyzing Deep Models for 3D Imaging Data by Visualizations.

Guannan Zhao, Bo Zhou, Kaiwen Wang, Rui Jiang, Min Xu

Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2018, 2018

2017

A sequence-based method to predict the impact of regulatory variants using random forest.

Qiao Liu, Mingxin Gan, Rui Jiang

BMC Syst. Biol., 2017

Mimvec: a deep learning approach for analyzing the human phenome.

Mingxin Gan, Wenran Li, Wanwen Zeng, Xiaojian Wang, Rui Jiang

BMC Syst. Biol., 2017

Predicting enhancers with deep convolutional neural networks.

Xu Min, Wanwen Zeng, Shengquan Chen, Ning Chen, Ting Chen, Rui Jiang

BMC Bioinform., 2017

Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding.

Xu Min, Wanwen Zeng, Ning Chen, Ting Chen, Rui Jiang

Bioinform., 2017

PPIM: A protein-protein interaction database for Maize.

Guanghui Zhu, Rui Jiang, Xing-Ming Zhao

Proceedings of the 13th IEEE Conference on Automation Science and Engineering, 2017

Exploring functional variant using a deep learning framework.

Tianyi Sun, Zhuo Liu, Xing-Ming Zhao, Rui Jiang

Proceedings of the 13th IEEE Conference on Automation Science and Engineering, 2017

Integrating embeddings of multiple gene networks to prioritize complex disease-associated genes.

Mengmeng Wu, Wanwen Zeng, Wenqiang Liu, Yijia Zhang, Ting Chen, Rui Jiang

Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017

2016

Whole genome sequencing and its applications in medical genetics.

Jiaxin Wu, Mengmeng Wu, Ting Chen, Rui Jiang

Quant. Biol., 2016

Trinity: Walking on a User-Object-Tag Heterogeneous Network for Personalised Recommendations.

Mingxin Gan, Lily Sun, Rui Jiang

J. Comput. Sci. Technol., 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

Genom. Proteom. Bioinform., 2016

Global inference of disease-causing single nucleotide variants from exome sequencing data.

Mengmeng Wu, Ting Chen, Rui Jiang

BMC Bioinform., 2016

dbWGFP: a database and web server of human whole-genome single nucleotide variants and their functional predictions.

Jiaxin Wu, Mengmeng Wu, Lianshuo Li, Zhuo Liu, Wanwen Zeng, Rui Jiang

Database J. Biol. Databases Curation, 2016

DeepEnhancer: Predicting enhancers by convolutional neural networks.

Xu Min, Ning Chen, Ting Chen, Rui Jiang

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

2015

ROUND: Walking on an object-user heterogeneous network for personalized recommendations.

Mingxin Gan, Rui Jiang

Expert Syst. Appl., 2015

Pinpointing disease genes through phenomic and genomic data fusion.

Rui Jiang, Mengmeng Wu, Lianshuo Li

BMC Genom., 2015

Differential regulation enrichment analysis via the integration of transcriptional regulatory network and gene expression data.

Shining Ma, Tao Jiang, Rui Jiang

Bioinform., 2015

2014

Constructing a Boolean implication network to study the interactions between environmental factors and OTUs.

Congmin Zhu, Rui Jiang, Ting Chen

Quant. Biol., 2014

Integrated Approach in Systems Biology.

Huiru Zheng, Rui Jiang, Zhongming Zhao

Comput. Math. Methods Medicine, 2014

Prioritizing protein complexes implicated in human diseases by network optimization.

Yong Chen, Thibault Jacquemin, Shuyan Zhang, Rui Jiang

BMC Syst. Biol., 2014

2013

Constructing a user similarity network to remove adverse influence of popular objects for personalized recommendation.

Mingxin Gan, Rui Jiang

Expert Syst. Appl., 2013

Improving accuracy and diversity of personalized recommendation through power law adjustments of user similarities.

Mingxin Gan, Rui Jiang

Decis. Support Syst., 2013

PyroHMMvar: a sensitive and accurate method to call short indels and SNPs for Ion Torrent and 454 data.

Feng Zeng, Rui Jiang, Ting Chen

Bioinform., 2013

Inferring semantic similarity through correlating information contents of gene ontology terms.

Mingxin Gan, Rui Jiang

Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013

2012

Identification of disease-related nsSNPs via the integration of protein sequence features and domain-domain interaction data.

Rui Jiang, Mingxin Gan, Jiaxin Wu

Int. J. Comput. Biol. Drug Des., 2012

Ontology-Based Genes Similarity Calculation with TF-IDF.

Yue Huang, Mingxin Gan, Rui Jiang

Proceedings of the Information Computing and Applications - Third International Conference, 2012

Improving Recommendation Performance through Ontology-Based Semantic Similarity.

Mingxin Gan, Xue Dou, Rui Jiang

Proceedings of the Information Computing and Applications - Third International Conference, 2012

2011

A Max-Flow-Based Approach to the Identification of Protein Complexes Using Protein Interaction and Microarray Data.

Jianxing Feng, Rui Jiang, Tao Jiang

IEEE ACM Trans. Comput. Biol. Bioinform., 2011

Prioritisation of candidate Single Amino Acid Polymorphisms using one-class learning machines.

Jiaxin Wu, Mingxin Gan, Rui Jiang

Int. J. Comput. Biol. Drug Des., 2011

DomainRBF: a Bayesian regression approach to the prioritization of candidate domains for complex diseases.

Wangshu Zhang, Yong Chen, Fengzhu Sun, Rui Jiang

BMC Syst. Biol., 2011

Constructing a gene semantic similarity network for the inference of disease genes.

Rui Jiang, Mingxin Gan, Peng He

BMC Syst. Biol., 2011

Integrating multiple protein-protein interaction networks to prioritize disease genes: a Bayesian regression approach.

Wangshu Zhang, Fengzhu Sun, Rui Jiang

BMC Bioinform., 2011

Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering.

Xiaolin Hao, Rui Jiang, Ting Chen

Bioinform., 2011

Uncover disease genes by maximizing information flow in the phenome-interactome network.

Yong Chen, Tao Jiang, Rui Jiang

Bioinform., 2011

A genetic algorithm for optimizing subnetwork markers for the study of breast cancer metastasis.

Jiaxin Wu, Mingxin Gan, Rui Jiang

Proceedings of the Seventh International Conference on Natural Computation, 2011

Integrating sequence conservation features and a domain-domain interaction network to detect disease-associated nsSNPs.

Rui Jiang, Jiaxin Wu

Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2011

DOPCA: A New Method for Calculating Ontology-Based Semantic Similarity.

Mingxin Gan, Xue Dou, Daoping Wang, Rui Jiang

Proceedings of the 10th IEEE/ACIS International Conference on Computer and Information Science, 2011

2009

Bayesian Models and Gibbs Sampling Strategies for Local Graph Alignment and Motif Identification in Stochastic Biological Networks.

Ting Chen, Rui Jiang, Fengzhu Sun

Commun. Inf. Syst., 2009

A random forest approach to the detection of epistatic interactions in case-control studies.

Rui Jiang, Wanwan Tang, Xuebing Wu, Wenhui Fu

BMC Bioinform., 2009

Align human interactome with phenome to identify causative genes and networks underlying disease families.

Xuebing Wu, Qifang Liu, Rui Jiang

Bioinform., 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

Proceedings of the International Joint Conferences on Bioinformatics, 2009

Accelerating Genome-Wide Association Studies Using CUDA Compatible Graphics Processing Units.

Rui Jiang, Feng Zeng, Wangshu Zhang, Xuebing Wu, Zhihong Yu

Proceedings of the International Joint Conferences on Bioinformatics, 2009

2007

Optimal Adaptive Controller for Multidimensional Armax Model.

Rui Jiang, Kueiming Lo

Cybern. Syst., 2007

2006

Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy.

Rui Jiang, Hua Yang, Fengzhu Sun, Ting Chen

BMC Bioinform., 2006

2000

An adaptive classifier system tree for extending genetics-based machine learning in a dynamic environment.

Dongcheng Hu, Rui Jiang, Yupin Luo

Artif. Life Robotics, 2000