Rui Jiang 0001 - researchr alias

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Viewing Publication 1 - 32 from 32

2025

Deep multiple instance learning on heterogeneous graph for drug-disease association predictionYaowen Gu, Si Zheng, Bowen Zhang, Hongyu Kang, Rui Jiang 0001, Jiao Li 0001. cbm, 184:109403, 2025. [doi]

Prediction of mortality in intensive care unit with short-term heart rate variability: Machine learning-based analysis of the MIMIC-III databaseLexin Huang, Zixuan Dou, Fang Fang, Boda Zhou, Ping Zhang, Rui Jiang 0001. cbm, 186:109635, 2025. [doi]

A phenotype-based AI pipeline outperforms human experts in differentially diagnosing rare diseases using EHRsXiaohao 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 0001, Shuyang Zhang, Ting Chen. npjdm, 8(1), 2025. [doi]

Label Informed Contrastive Pretraining for Node Importance Estimation on Knowledge GraphsTianyu Zhang, Chengbin Hou, Rui Jiang 0001, Xuegong Zhang, Chenghu Zhou, Ke Tang 0001, Hairong Lv. tnn, 36(3):4462-4476, March 2025. [doi]

2024

A transformer-based weakly supervised computational pathology method for clinical-grade diagnosis and molecular marker discovery of gliomasRui Jiang 0001, 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. natmi, 6(8):876-891, 2024. [doi]

Discrete latent embedding of single-cell chromatin accessibility sequencing data for uncovering cell heterogeneityXuejian Cui, Xiaoyang Chen, Zhen Li, Zijing Gao, Shengquan Chen, Rui Jiang 0001. ncs, 4(5):346-359, May 2024. [doi]

Accurate Annotation for Differentiating and Imbalanced Cell Types in Single-Cell Chromatin Accessibility DataYuhang Jia, Siyu Li, Rui Jiang 0001, Shengquan Chen. tcbb, 21(3):461-471, May - June 2024. [doi]

collectNET: a web server for integrated inference of cell-cell communication networkYan Pan, Zijing Gao, Xuejian Cui, Zhen Li, Rui Jiang 0001. biodb, 2024, January 2024. [doi]

2023

Deep generative modeling and clustering of single cell Hi-C dataQiao Liu, Wanwen Zeng, Wei Zhang, Sicheng Wang, Hongyang Chen, Rui Jiang 0001, Mu Zhou, Shaoting Zhang. bib, 24(1), January 2023. [doi]

Improving artificial intelligence pipeline for liver malignancy diagnosis using ultrasound images and video framesYiming Xu, Bowen Zheng, Xiaohong Liu, Tao Wu, Jinxiu Ju, Shi-jie Wang, Yufan Lian, Hongjun Zhang, Tong Liang, Ye Sang, Rui Jiang 0001, Guangyu Wang, Jie Ren, Ting Chen 0006. bib, 24(1), January 2023. [doi]

DeepDrug: A general graph-based deep learning framework for drug-drug interactions and drug-target interactions predictionQijin Yin, Rui Fan, Xusheng Cao, Qiao Liu, Rui Jiang 0001, Wanwen Zeng. quanbio, 11(3):260-274, September 2023. [doi]

HiChIPdb: a comprehensive database of HiChIP regulatory interactionsWanwen Zeng, Qiao Liu, Qijin Yin, Rui Jiang 0001, Wing Hung Wong. nar, 51(D1):159-166, January 2023. [doi]

Building digital life systems for future biology and medicineXuegong Zhang, Lei Wei, Rui Jiang 0001, Xiaowo Wang, Jin Gu, Zhen Xie, Hairong Lv. quanbio, 11(3):207-213, September 2023. [doi]

2022

Cell type annotation of single-cell chromatin accessibility data via supervised Bayesian embeddingXiaoyang Chen, Shengquan Chen, Shuang Song 0006, Zijing Gao, Lin Hou, Xuegong Zhang, Hairong Lv, Rui Jiang 0001. natmi, 4(2):116-126, 2022. [doi]

DeepCAGE: Incorporating Transcription Factors in Genome-wide Prediction of Chromatin AccessibilityQiao Liu, Kui Hua, Xuegong Zhang, Wing Hung Wong, Rui Jiang 0001. gpb, 20(3):496-507, 2022. [doi]

CS-CO: A Hybrid Self-Supervised Visual Representation Learning Method for H&E-stained Histopathological ImagesPengshuai Yang, Xiaoxu Yin, Haiming Lu, Zhongliang Hu, Xuegong Zhang, Rui Jiang 0001, Hairong Lv. mia, 81:102539, 2022. [doi]

scGraph: a graph neural network-based approach to automatically identify cell typesQijin Yin, Qiao Liu, Zhuoran Fu, Wanwen Zeng, Boheng Zhang, Xuegong Zhang, Rui Jiang 0001, Hairong Lv. bioinformatics, 38(11):2996-3003, 2022. [doi]

2021

DeepCAPE: A Deep Convolutional Neural Network for the Accurate Prediction of EnhancersShengquan Chen, Mingxin Gan, Hairong Lv, Rui Jiang 0001. gpb, 19(4):565-577, 2021. [doi]

OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regionsShengquan Chen, Qiao Liu, Xuejian Cui, Zhanying Feng, Chunquan Li, Xiaowo Wang, Xuegong Zhang, Yong Wang, Rui Jiang 0001. nar, 49(Webserver-Issue):483-490, 2021. [doi]

stPlus: a reference-based method for the accurate enhancement of spatial transcriptomicsShengquan Chen, Boheng Zhang, Xiaoyang Chen, Xuegong Zhang, Rui Jiang 0001. bioinformatics, 37(Supplement):299-307, 2021. [doi]

Simultaneous deep generative modelling and clustering of single-cell genomic dataQiao Liu, Shengquan Chen, Rui Jiang 0001, Wing Hung Wong. natmi, 3(6):536-544, 2021. [doi]

Self-supervised Visual Representation Learning for Histopathological ImagesPengshuai Yang, Zhiwei Hong, Xiaoxu Yin, Chengzhan Zhu, Rui Jiang 0001. miccai 2021: 47-57 [doi]

Few shot domain adaptation for in situ macromolecule structural classification in cryoelectron tomogramsLiangyong Yu, Ran Li, Xiangrui Zeng, Hongyi Wang, Jie Jin, Ge Yang, Rui Jiang 0001, Min Xu 0009. bioinformatics, 37(2):185-191, 2021. [doi]

SilencerDB: a comprehensive database of silencersWanwen Zeng, Shengquan Chen, Xuejian Cui, Xiaoyang Chen, Zijing Gao, Rui Jiang 0001. nar, 49(Database-Issue), 2021. [doi]

2020

DeepCDR: a hybrid graph convolutional network for predicting cancer drug responseQiao Liu, Zhiqiang Hu, Rui Jiang 0001, Mu Zhou. bioinformatics, 36(Supplement-2), 2020. [doi]

Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural networkWanwen Zeng, Yong Wang, Rui Jiang 0001. bioinformatics, 36(2):496-503, 2020. [doi]

2019

EpiFIT: functional interpretation of transcription factors based on combination of sequence and epigenetic informationShaoming Song, Hongfei Cui, Shengquan Chen, Qiao Liu, Rui Jiang 0001. quanbio, 7(3):233-243, 2019. [doi]

DeepHistone: a deep learning approach to predicting histone modificationsQijin Yin, Mengmeng Wu, Qiao Liu, Hairong Lv, Rui Jiang 0001. bmcgenomics, 20(S2), 2019. [doi]

2018

Prediction of enhancer-promoter interactions via natural language processingWanwen Zeng, Mengmeng Wu, Rui Jiang 0001. bmcgenomics, 19(S2), 2018. [doi]

2016

Whole genome sequencing and its applications in medical geneticsJiaxin Wu, Mengmeng Wu, Ting Chen 0006, Rui Jiang 0001. quanbio, 4(2):115-128, 2016. [doi]

2014

Constructing a Boolean implication network to study the interactions between environmental factors and OTUsCongmin Zhu, Rui Jiang 0001, Ting Chen 0002. quanbio, 2(4):127-141, 2014. [doi]

2009

Bayesian Models and Gibbs Sampling Strategies for Local Graph Alignment and Motif Identification in Stochastic Biological NetworksTing Chen 0006, Rui Jiang 0001, Fengzhu Sun. cominfsys, 9(4):347-370, 2009. [doi]

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