Rui Jiang

Publication Activity (10 Years)

Years Active: 2006-2024
Publications (10 Years): 50

Top Topics

Convolutional Neural Network

Social Recommendation

Top Venues

Publications

Tianyu Zhang, Chengbin Hou, Rui Jiang, Xuegong Zhang, Chenghu Zhou, Ke Tang, Hairong Lv
Label Informed Contrastive Pretraining for Node Importance Estimation on Knowledge Graphs. CoRR (2024)
Yuhang Jia, Siyu Li, Rui Jiang, Shengquan Chen
Accurate Annotation for Differentiating and Imbalanced Cell Types in Single-Cell Chromatin Accessibility Data. IEEE ACM Trans. Comput. Biol. Bioinform. 21 (3) (2024)
Xuejian Cui, Xiaoyang Chen, Zhen Li, Zijing Gao, Shengquan Chen, Rui Jiang
Discrete latent embedding of single-cell chromatin accessibility sequencing data for uncovering cell heterogeneity. Nat. Comput. Sci. 4 (5) (2024)
Qijin Yin, Rui Fan, Xusheng Cao, Qiao Liu, Rui Jiang, Wanwen Zeng
DeepDrug: A general graph-based deep learning framework for drug-drug interactions and drug-target interactions prediction. Quant. Biol. 11 (3) (2023)
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
Improving artificial intelligence pipeline for liver malignancy diagnosis using ultrasound images and video frames. Briefings Bioinform. 24 (1) (2023)
Xuegong Zhang, Lei Wei, Rui Jiang, Xiaowo Wang, Jin Gu, Zhen Xie, Hairong Lv
Building digital life systems for future biology and medicine. Quant. Biol. 11 (3) (2023)
Wanwen Zeng, Qiao Liu, Qijin Yin, Rui Jiang, Wing Hung Wong
HiChIPdb: a comprehensive database of HiChIP regulatory interactions. Nucleic Acids Res. 51 (D1) (2023)
Chen Li, Xiaoyang Chen, Shengquan Chen, Rui Jiang, Xuegong Zhang
simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data. Bioinform. 39 (8) (2023)
Qiao Liu, Wanwen Zeng, Wei Zhang, Sicheng Wang, Hongyang Chen, Rui Jiang, Mu Zhou, Shaoting Zhang
Deep generative modeling and clustering of single cell Hi-C data. Briefings Bioinform. 24 (1) (2023)
Pengshuai Yang, Xiaoxu Yin, Haiming Lu, Zhongliang Hu, Xuegong Zhang, Rui Jiang, Hairong Lv
CS-CO: A Hybrid Self-Supervised Visual Representation Learning Method for H&E-stained Histopathological Images. Medical Image Anal. 81 (2022)
Qiao Liu, Kui Hua, Xuegong Zhang, Wing Hung Wong, Rui Jiang
DeepCAGE: Incorporating Transcription Factors in Genome-wide Prediction of Chromatin Accessibility. Genom. Proteom. Bioinform. 20 (3) (2022)
Xiaoyang Chen, Shengquan Chen, Shuang Song, Zijing Gao, Lin Hou, Xuegong Zhang, Hairong Lv, Rui Jiang
Cell type annotation of single-cell chromatin accessibility data via supervised Bayesian embedding. Nat. Mach. Intell. 4 (2) (2022)
Qijin Yin, Qiao Liu, Zhuoran Fu, Wanwen Zeng, Boheng Zhang, Xuegong Zhang, Rui Jiang, Hairong Lv
scGraph: a graph neural network-based approach to automatically identify cell types. Bioinform. 38 (11) (2022)
Shengquan Chen, Boheng Zhang, Xiaoyang Chen, Xuegong Zhang, Rui Jiang
stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics. Bioinform. 37 (Supplement) (2021)
Wanwen Zeng, Shengquan Chen, Xuejian Cui, Xiaoyang Chen, Zijing Gao, Rui Jiang
SilencerDB: a comprehensive database of silencers. Nucleic Acids Res. 49 (Database-Issue) (2021)
Shengquan Chen, Qiao Liu, Xuejian Cui, Zhanying Feng, Chunquan Li, Xiaowo Wang, Xuegong Zhang, Yong Wang, Rui Jiang
OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions. Nucleic Acids Res. 49 (Webserver-Issue) (2021)
Liangyong Yu, Ran Li, Xiangrui Zeng, Hongyi Wang, Jie Jin, Ge Yang, Rui Jiang, Min Xu
Few shot domain adaptation for in situ macromolecule structural classification in cryoelectron tomograms. Bioinform. 37 (2) (2021)
Pengshuai Yang, Zhiwei Hong, Xiaoxu Yin, Chengzhan Zhu, Rui Jiang
Self-supervised Visual Representation Learning for Histopathological Images. MICCAI (2) (2021)
Shengquan Chen, Mingxin Gan, Hairong Lv, Rui Jiang
DeepCAPE: A Deep Convolutional Neural Network for the Accurate Prediction of Enhancers. Genom. Proteom. Bioinform. 19 (4) (2021)
Qiao Liu, Shengquan Chen, Rui Jiang, Wing Hung Wong
Simultaneous deep generative modelling and clustering of single-cell genomic data. Nat. Mach. Intell. 3 (6) (2021)
Wanwen Zeng, Yong Wang, Rui Jiang
Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network. Bioinform. 36 (2) (2020)
Jianyu Zhou, Pan Li, Wanwen Zeng, Wenxiu Ma, Zhipeng Lu, Rui Jiang, Qiangfeng Cliff Zhang, Tao Jiang
IRIS: A method for predicting in vivo RNA secondary structures using PARIS data. Quant. Biol. 8 (4) (2020)
Xiaoyang Chen, Shengquan Chen, Rui Jiang
EnClaSC: a novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes. BMC Bioinform. (13) (2020)
Liangyong Yu, Ran Li, Xiangrui Zeng, Hongyi Wang, Jie Jin, Ge Yang, Rui Jiang, Min Xu
Few shot domain adaptation for in situ macromolecule structural classification in cryo-electron tomograms. CoRR (2020)
Qiao Liu, Jiaze Xu, Rui Jiang, Wing Hung Wong
Roundtrip: A Deep Generative Neural Density Estimator. CoRR (2020)
Pengshuai Yang, Yupeng Zhai, Lin Li, Hairong Lv, Jigang Wang, Chengzhan Zhu, Rui Jiang
Liver Histopathological Image Retrieval Based on Deep Metric Learning. BIBM (2019)
Ran Li, Xiangrui Zeng, Stephanie E. Sigmund, Ruogu Lin, Bo Zhou, Chang Liu, Kaiwen Wang, Rui Jiang, Zachary Freyberg, Hairong Lv, Min Xu
Automatic localization and identification of mitochondria in cellular electron cryo-tomography using faster-RCNN. BMC Bioinform. (3) (2019)
Qijin Yin, Mengmeng Wu, Qiao Liu, Hairong Lv, Rui Jiang
DeepHistone: a deep learning approach to predicting histone modifications. BMC Genom. 20 (S2) (2019)
Shaoming Song, Hongfei Cui, Shengquan Chen, Qiao Liu, Rui Jiang
EpiFIT: functional interpretation of transcription factors based on combination of sequence and epigenetic information. Quant. Biol. 7 (3) (2019)
Qiao Liu, Hairong Lv, Rui Jiang
hicGAN infers super resolution Hi-C data with generative adversarial networks. Bioinform. 35 (14) (2019)
Mingxin Gan, Lily Sun, Rui Jiang
GLORY: Exploration and integration of global and local correlations to improve personalized online social recommendations. Inf. Syst. Frontiers 21 (4) (2019)
Shengquan Chen, Kui Hua, Hongfei Cui, Rui Jiang
VPAC: Variational projection for accurate clustering of single-cell transcriptomic data. BMC Bioinform. (7) (2019)
Wanwen Zeng, Xu Min, Rui Jiang
EnDisease: a manually curated database for enhancer-disease associations. Database J. Biol. Databases Curation 2019 (2019)
Jie Wang, Hairong Lv, Rui Jiang, Zhen Xie
Rule-Based Method to Develop Question-Answer Dataset from Chest X-Ray Reports. CBMS (2019)
Qiao Liu, Fei Xia, Qijin Yin, Rui Jiang
Chromatin accessibility prediction via a hybrid deep convolutional neural network. Bioinform. 34 (5) (2018)
Wanwen Zeng, Mengmeng Wu, Rui Jiang
Prediction of enhancer-promoter interactions via natural language processing. BMC Genom. 19 (S2) (2018)
Mingxin Gan, Rui Jiang
FLOWER: Fusing global and local associations towards personalized social recommendation. Future Gener. Comput. Syst. 78 (2018)
Xu Min, Wanwen Zeng, Shengquan Chen, Ning Chen, Ting Chen, Rui Jiang
Predicting enhancers with deep convolutional neural networks. BMC Bioinform. 18 (S-13) (2017)
Mengmeng Wu, Wanwen Zeng, Wenqiang Liu, Yijia Zhang, Ting Chen, Rui Jiang
Integrating embeddings of multiple gene networks to prioritize complex disease-associated genes. BIBM (2017)
Qiao Liu, Mingxin Gan, Rui Jiang
A sequence-based method to predict the impact of regulatory variants using random forest. BMC Syst. Biol. 11 (S-2) (2017)
Xu Min, Wanwen Zeng, Ning Chen, Ting Chen, Rui Jiang
Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding. Bioinform. 33 (14) (2017)
Mingxin Gan, Wenran Li, Wanwen Zeng, Xiaojian Wang, Rui Jiang
Mimvec: a deep learning approach for analyzing the human phenome. BMC Syst. Biol. 11 (S-4) (2017)
Jiaxin Wu, Mengmeng Wu, Lianshuo Li, Zhuo Liu, Wanwen Zeng, Rui Jiang
dbWGFP: a database and web server of human whole-genome single nucleotide variants and their functional predictions. Database J. Biol. Databases Curation 2016 (2016)
Mengmeng Wu, Ting Chen, Rui Jiang
Global inference of disease-causing single nucleotide variants from exome sequencing data. BMC Bioinform. 17 (S-17) (2016)
Jiaxin Wu, Mengmeng Wu, Ting Chen, Rui Jiang
Whole genome sequencing and its applications in medical genetics. Quant. Biol. 4 (2) (2016)
Mingxin Gan, Lily Sun, Rui Jiang
Trinity: Walking on a User-Object-Tag Heterogeneous Network for Personalised Recommendations. J. Comput. Sci. Technol. 31 (3) (2016)
Lianshuo Li, Zicheng Wang, Peng He, Shining Ma, Jie Du, Rui Jiang
Construction and Analysis of Functional Networks in the Gut Microbiome of Type 2 Diabetes Patients. Genom. Proteom. Bioinform. 14 (5) (2016)
Xu Min, Ning Chen, Ting Chen, Rui Jiang
DeepEnhancer: Predicting enhancers by convolutional neural networks. BIBM (2016)
Shining Ma, Tao Jiang, Rui Jiang
Differential regulation enrichment analysis via the integration of transcriptional regulatory network and gene expression data. Bioinform. 31 (4) (2015)
Rui Jiang, Mengmeng Wu, Lianshuo Li
Pinpointing disease genes through phenomic and genomic data fusion. BMC Genom. 16 (S-2) (2015)
Yong Chen, Thibault Jacquemin, Shuyan Zhang, Rui Jiang
Prioritizing protein complexes implicated in human diseases by network optimization. BMC Syst. Biol. 8 (S-1) (2014)
Huiru Zheng, Rui Jiang, Zhongming Zhao
Integrated Approach in Systems Biology. Comput. Math. Methods Medicine 2014 (2014)
Congmin Zhu, Rui Jiang, Ting Chen
Constructing a Boolean implication network to study the interactions between environmental factors and OTUs. Quant. Biol. 2 (4) (2014)
Mingxin Gan, Rui Jiang
Constructing a user similarity network to remove adverse influence of popular objects for personalized recommendation. Expert Syst. Appl. 40 (10) (2013)
Mingxin Gan, Rui Jiang
Improving accuracy and diversity of personalized recommendation through power law adjustments of user similarities. Decis. Support Syst. 55 (3) (2013)
Mingxin Gan, Rui Jiang
Inferring semantic similarity through correlating information contents of gene ontology terms. BIBM (2013)
Feng Zeng, Rui Jiang, Ting Chen
PyroHMMvar: a sensitive and accurate method to call short indels and SNPs for Ion Torrent and 454 data. Bioinform. 29 (22) (2013)
Yue Huang, Mingxin Gan, Rui Jiang
Ontology-Based Genes Similarity Calculation with TF-IDF. ICICA (LNCS) (2012)
Rui Jiang, Mingxin Gan, Jiaxin Wu
Identification of disease-related nsSNPs via the integration of protein sequence features and domain-domain interaction data. Int. J. Comput. Biol. Drug Des. 5 (3/4) (2012)
Mingxin Gan, Xue Dou, Rui Jiang
Improving Recommendation Performance through Ontology-Based Semantic Similarity. ICICA (LNCS) (2012)
Mingxin Gan, Xue Dou, Daoping Wang, Rui Jiang
DOPCA: A New Method for Calculating Ontology-Based Semantic Similarity. ACIS-ICIS (2011)
Jiaxin Wu, Mingxin Gan, Rui Jiang
Prioritisation of candidate Single Amino Acid Polymorphisms using one-class learning machines. Int. J. Comput. Biol. Drug Des. 4 (4) (2011)
Jiaxin Wu, Mingxin Gan, Rui Jiang
A genetic algorithm for optimizing subnetwork markers for the study of breast cancer metastasis. ICNC (2011)
Rui Jiang, Jiaxin Wu
Integrating sequence conservation features and a domain-domain interaction network to detect disease-associated nsSNPs. BIBM Workshops (2011)
Wangshu Zhang, Yong Chen, Fengzhu Sun, Rui Jiang
DomainRBF: a Bayesian regression approach to the prioritization of candidate domains for complex diseases. BMC Syst. Biol. 5 (2011)
Xiaolin Hao, Rui Jiang, Ting Chen
Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering. Bioinform. 27 (5) (2011)
Wangshu Zhang, Fengzhu Sun, Rui Jiang
Integrating multiple protein-protein interaction networks to prioritize disease genes: a Bayesian regression approach. BMC Bioinform. 12 (S-1) (2011)
Rui Jiang, Mingxin Gan, Peng He
Constructing a gene semantic similarity network for the inference of disease genes. BMC Syst. Biol. 5 (S-2) (2011)
Jianxing Feng, Rui Jiang, Tao Jiang
A Max-Flow-Based Approach to the Identification of Protein Complexes Using Protein Interaction and Microarray Data. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (3) (2011)
Yong Chen, Tao Jiang, Rui Jiang
Uncover disease genes by maximizing information flow in the phenome-interactome network. Bioinform. 27 (13) (2011)
Ting Chen, Rui Jiang, Fengzhu Sun
Bayesian Models and Gibbs Sampling Strategies for Local Graph Alignment and Motif Identification in Stochastic Biological Networks. Commun. Inf. Syst. 9 (4) (2009)
Wangshu Zhang, Feng Zeng, Xuebing Wu, Xuegong Zhang, Rui Jiang
A Comparative Study of Ensemble Learning Approaches in the Classification of Breast Cancer Metastasis. IJCBS (2009)
Rui Jiang, Feng Zeng, Wangshu Zhang, Xuebing Wu, Zhihong Yu
Accelerating Genome-Wide Association Studies Using CUDA Compatible Graphics Processing Units. IJCBS (2009)
Xuebing Wu, Qifang Liu, Rui Jiang
Align human interactome with phenome to identify causative genes and networks underlying disease families. Bioinform. 25 (1) (2009)
Rui Jiang, Wanwan Tang, Xuebing Wu, Wenhui Fu
A random forest approach to the detection of epistatic interactions in case-control studies. BMC Bioinform. 10 (S-1) (2009)
Rui Jiang, Hua Yang, Fengzhu Sun, Ting Chen
Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy. BMC Bioinform. 7 (2006)