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ORCIDRui Jiang 0001
Person information
- affiliation: Tsinghua University, Department of Automation, Beijing, China
Other persons with the same name
- Rui Jiang — disambiguation page
- Rui Jiang 0002
![[0000-0002-8141-5376]](https://dblp.uni-trier.de./img/orcid-mark.12x12.png "0000-0002-8141-5376")
— Xuchang University, School of Information Engineering, China (and 2 more) - Rui Jiang 0003 — Nanyang Technological University, School of Electrical and Electronic Engineering, Singapore
- Rui Jiang 0004 — Tsinghua University, Tsinghua National Laboratory for Information Science and Technology, Beijing, China
- Rui Jiang 0005 — Stanford University, Department of Energy Resources Engineering, USA
- Rui Jiang 0006 — South China University of Technology, School of Computer Science and Engineering, Guangzhou, China
- Rui Jiang 0007 — Nanjing University of Posts and Telecommunications, College of Telecommunications and Information Engineering, China (and 1 more)
- Rui Jiang 0008 — Beijing Jiaotong University, School of Systems Science, Key Laboratory of Transport Industry of Big Data Application Technologies for Comprehensive Transport, China (and 1 more)
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2020 – today
- 2024
[j71]Yan Pan, Zijing Gao, Xuejian Cui, Zhen Li, Rui Jiang:
collectNET: a web server for integrated inference of cell-cell communication network. Database J. Biol. Databases Curation 2024 (2024)- [j70]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:
A transformer-based weakly supervised computational pathology method for clinical-grade diagnosis and molecular marker discovery of gliomas. Nat. Mac. Intell. 6(8): 876-891 (2024) - [j69]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): 346-359 (2024) - [j68]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): 461-471 (2024) - [i6]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 abs/2402.17791 (2024) - 2023
- [j67]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) - [j66]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) - [j65]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) - [j64]Wanwen Zeng, Qiao Liu, Qijin Yin, Rui Jiang, Wing Hung Wong:
HiChIPdb: a comprehensive database of HiChIP regulatory interactions. Nucleic Acids Res. 51(D1): 159-166 (2023) - [j63]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): 207-213 (2023) - [j62]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): 260-274 (2023) - [c18]Yonghao Liu, Di Liang, Fang Fang, Sirui Wang, Wei Wu, Rui Jiang:
Time-Aware Multiway Adaptive Fusion Network for Temporal Knowledge Graph Question Answering. ICASSP 2023: 1-5 - [i5]Yonghao Liu, Di Liang, Fang Fang, Sirui Wang, Wei Wu, Rui Jiang:
Time-aware Multiway Adaptive Fusion Network for Temporal Knowledge Graph Question Answering. CoRR abs/2302.12529 (2023) - 2022
- [j61]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): 2996-3003 (2022) - [j60]Tianxing Ma, Qiao Liu, Haochen Li, Mu Zhou, Rui Jiang, Xuegong Zhang:
DualGCN: a dual graph convolutional network model to predict cancer drug response. BMC Bioinform. 23-S(4): 129 (2022) - [j59]Yaowen Gu, Si Zheng, Qijin Yin, Rui Jiang, Jiao Li:
REDDA: Integrating multiple biological relations to heterogeneous graph neural network for drug-disease association prediction. Comput. Biol. Medicine 150: 106127 (2022) - [j58]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): 496-507 (2022) - [j57]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: 102539 (2022) - [j56]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): 116-126 (2022) - 2021
- [j55]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): 185-191 (2021) - [j54]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): 299-307 (2021) - [j53]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): 565-577 (2021) - [j52]Wanwen Zeng, Shengquan Chen, Xuejian Cui, Xiaoyang Chen, Zijing Gao, Rui Jiang:
SilencerDB: a comprehensive database of silencers. Nucleic Acids Res. 49(Database-Issue): D221-D228 (2021) - [j51]Shengquan Chen, Qiao Liu, Xuejian Cui, Zhan-Ying 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): 483-490 (2021) - [j50]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): 536-544 (2021) - [c17]Pengshuai Yang, Zhiwei Hong, Xiaoxu Yin, Chengzhan Zhu, Rui Jiang:
Self-supervised Visual Representation Learning for Histopathological Images. MICCAI (2) 2021: 47-57 - 2020
- [j49]Honglei Liu, Yan Xu, Zhiqiang Zhang, Ni Wang, Yanqun Huang, Yanjun Hu, Zhenghan Yang, Rui Jiang, Hui Chen:
A Natural Language Processing Pipeline of Chinese Free-Text Radiology Reports for Liver Cancer Diagnosis. IEEE Access 8: 159110-159119 (2020) - [j48]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): 496-503 (2020) - [j47]Xiaoyang Chen, Shengquan Chen, Rui Jiang:
EnClaSC: a novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes. BMC Bioinform. 21-S(13): 392 (2020) - [j46]Ran Li, Liangyong Yu, Bo Zhou, Xiangrui Zeng, Zhenyu Wang, Xiaoyan Yang, Jing Zhang, Xin Gao, Rui Jiang, Min Xu:
Few-shot learning for classification of novel macromolecular structures in cryo-electron tomograms. PLoS Comput. Biol. 16(11) (2020) - [j45]Jie Shi, Xiangrui Zeng, Rui Jiang, Tao Jiang, Min Xu:
A simulated annealing approach for resolution guided homogeneous cryo-electron microscopy image selection. Quant. Biol. 8(1): 51-63 (2020) - [j44]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): 369-381 (2020) - [i4]Qiao Liu, Jiaze Xu, Rui Jiang, Wing Hung Wong:
Roundtrip: A Deep Generative Neural Density Estimator. CoRR abs/2004.09017 (2020) - [i3]Honglei Liu, Yan Xu, Zhiqiang Zhang, Ni Wang, Yanqun Huang, Zhenghan Yang, Rui Jiang, Hui Chen:
A Natural Language Processing Pipeline of Chinese Free-text Radiology Reports for Liver Cancer Diagnosis. CoRR abs/2004.13848 (2020) - [i2]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 abs/2007.15422 (2020)
2010 – 2019
- 2019
- [j43]Wanwen Zeng, Xu Min, Rui Jiang:
EnDisease: a manually curated database for enhancer-disease associations. Database J. Biol. Databases Curation 2019: baz020 (2019) - [j42]Qiao Liu, Hairong Lv, Rui Jiang:
hicGAN infers super resolution Hi-C data with generative adversarial networks. Bioinform. 35(14): i99-i107 (2019) - [j41]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. 20-S(3): 75-85 (2019) - [j40]Shengquan Chen, Kui Hua, Hongfei Cui, Rui Jiang:
VPAC: Variational projection for accurate clustering of single-cell transcriptomic data. BMC Bioinform. 20-S(7): 139-151 (2019) - [j39]Qijin Yin, Mengmeng Wu, Qiao Liu, Hairong Lv, Rui Jiang:
DeepHistone: a deep learning approach to predicting histone modifications. BMC Genom. 20(S2) (2019) - [j38]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): 925-939 (2019) - [j37]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): 233-243 (2019) - [c16]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: 914-919 - [c15]Jie Wang, Hairong Lv, Rui Jiang, Zhen Xie:
Rule-Based Method to Develop Question-Answer Dataset from Chest X-Ray Reports. CBMS 2019: 26-31 - [c14]Jie Wang, Zhigang Li, Rui Jiang, Zhen Xie:
Instance Segmentation of Anatomical Structures in Chest Radiographs. CBMS 2019: 441-446 - 2018
- [j36]Qiao Liu, Fei Xia, Qijin Yin, Rui Jiang:
Chromatin accessibility prediction via a hybrid deep convolutional neural network. Bioinform. 34(5): 732-738 (2018) - [j35]Wanwen Zeng, Mengmeng Wu, Rui Jiang:
Prediction of enhancer-promoter interactions via natural language processing. BMC Genom. 19(S2) (2018) - [j34]Mingxin Gan, Rui Jiang:
FLOWER: Fusing global and local associations towards personalized social recommendation. Future Gener. Comput. Syst. 78: 462-473 (2018) - [j33]Xiaodan Fan, Xinglai Ji, Rui Jiang:
Guest Editorial for Special Section on the Sixth National Conference on Bioinformatics and System Biology of China. IEEE ACM Trans. Comput. Biol. Bioinform. 15(4): 1092 (2018) - [c13]Guannan Zhao, Bo Zhou, Kaiwen Wang, Rui Jiang, Min Xu:
Respond-CAM: Analyzing Deep Models for 3D Imaging Data by Visualizations. MICCAI (1) 2018: 485-492 - [i1]Guannan Zhao, Bo Zhou, Kaiwen Wang, Rui Jiang, Min Xu:
Respond-CAM: Analyzing Deep Models for 3D Imaging Data by Visualizations. CoRR abs/1806.00102 (2018) - 2017
- [j32]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): i92-i101 (2017) - [j31]Xu Min, Wanwen Zeng, Shengquan Chen, Ning Chen, Ting Chen, Rui Jiang:
Predicting enhancers with deep convolutional neural networks. BMC Bioinform. 18(S-13): 35-46 (2017) - [j30]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): 7:1-7:9 (2017) - [j29]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): 3-16 (2017) - [c12]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: 208-215 - [c11]Guanghui Zhu, Rui Jiang, Xing-Ming Zhao:
PPIM: A protein-protein interaction database for Maize. CASE 2017: 97 - [c10]Tianyi Sun, Zhuo Liu, Xing-Ming Zhao, Rui Jiang:
Exploring functional variant using a deep learning framework. CASE 2017: 98-99 - 2016
- [j28]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) - [j27]Mengmeng Wu, Ting Chen, Rui Jiang:
Global inference of disease-causing single nucleotide variants from exome sequencing data. BMC Bioinform. 17(S-17): 145-157 (2016) - [j26]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): 314-324 (2016) - [j25]Mingxin Gan, Lily Sun, Rui Jiang:
Trinity: Walking on a User-Object-Tag Heterogeneous Network for Personalised Recommendations. J. Comput. Sci. Technol. 31(3): 577-594 (2016) - [j24]Jiaxin Wu, Mengmeng Wu, Ting Chen, Rui Jiang:
Whole genome sequencing and its applications in medical genetics. Quant. Biol. 4(2): 115-128 (2016) - [c9]Xu Min, Ning Chen, Ting Chen, Rui Jiang:
DeepEnhancer: Predicting enhancers by convolutional neural networks. BIBM 2016: 637-644 - 2015
- [j23]Shining Ma, Tao Jiang, Rui Jiang:
Differential regulation enrichment analysis via the integration of transcriptional regulatory network and gene expression data. Bioinform. 31(4): 563-571 (2015) - [j22]Rui Jiang, Mengmeng Wu, Lianshuo Li:
Pinpointing disease genes through phenomic and genomic data fusion. BMC Genom. 16(S-2): S3 (2015) - [j21]Mingxin Gan, Rui Jiang:
ROUND: Walking on an object-user heterogeneous network for personalized recommendations. Expert Syst. Appl. 42(22): 8791-8804 (2015) - 2014
- [j20]Yong Chen, Thibault Jacquemin, Shuyan Zhang, Rui Jiang:
Prioritizing protein complexes implicated in human diseases by network optimization. BMC Syst. Biol. 8(S-1): S2 (2014) - [j19]Huiru Zheng, Rui Jiang, Zhongming Zhao:
Integrated Approach in Systems Biology. Comput. Math. Methods Medicine 2014: 656473:1-656473:2 (2014) - [j18]Congmin Zhu, Rui Jiang, Ting Chen:
Constructing a Boolean implication network to study the interactions between environmental factors and OTUs. Quant. Biol. 2(4): 127-141 (2014) - 2013
- [j17]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): 2859-2868 (2013) - [j16]Mingxin Gan, Rui Jiang:
Improving accuracy and diversity of personalized recommendation through power law adjustments of user similarities. Decis. Support Syst. 55(3): 811-821 (2013) - [j15]Mingxin Gan, Rui Jiang:
Constructing a user similarity network to remove adverse influence of popular objects for personalized recommendation. Expert Syst. Appl. 40(10): 4044-4053 (2013) - [c8]Mingxin Gan, Rui Jiang:
Inferring semantic similarity through correlating information contents of gene ontology terms. BIBM 2013: 1-5 - 2012
- [j14]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): 206-221 (2012) - [c7]Mingxin Gan, Xue Dou, Rui Jiang:
Improving Recommendation Performance through Ontology-Based Semantic Similarity. ICICA (LNCS) 2012: 203-210 - [c6]Yue Huang, Mingxin Gan, Rui Jiang:
Ontology-Based Genes Similarity Calculation with TF-IDF. ICICA (LNCS) 2012: 600-607 - 2011
- [j13]Xiaolin Hao, Rui Jiang, Ting Chen:
Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering. Bioinform. 27(5): 611-618 (2011) - [j12]Yong Chen, Tao Jiang, Rui Jiang:
Uncover disease genes by maximizing information flow in the phenome-interactome network. Bioinform. 27(13): 167-176 (2011) - [j11]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): S11 (2011) - [j10]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: 55 (2011) - [j9]Rui Jiang, Mingxin Gan, Peng He:
Constructing a gene semantic similarity network for the inference of disease genes. BMC Syst. Biol. 5(S-2): S2 (2011) - [j8]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): 316-331 (2011) - [j7]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): 621-634 (2011) - [c5]Mingxin Gan, Xue Dou, Daoping Wang, Rui Jiang:
DOPCA: A New Method for Calculating Ontology-Based Semantic Similarity. ACIS-ICIS 2011: 110-115 - [c4]Rui Jiang, Jiaxin Wu:
Integrating sequence conservation features and a domain-domain interaction network to detect disease-associated nsSNPs. BIBM Workshops 2011: 262-267 - [c3]Jiaxin Wu, Mingxin Gan, Rui Jiang:
A genetic algorithm for optimizing subnetwork markers for the study of breast cancer metastasis. ICNC 2011: 1578-1582
2000 – 2009
- 2009
- [j6]Xuebing Wu, Qifang Liu, Rui Jiang:
Align human interactome with phenome to identify causative genes and networks underlying disease families. Bioinform. 25(1): 98-104 (2009) - [j5]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) - [j4]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): 347-370 (2009) - [c2]Rui Jiang, Feng Zeng, Wangshu Zhang, Xuebing Wu, Zhihong Yu:
Accelerating Genome-Wide Association Studies Using CUDA Compatible Graphics Processing Units. IJCBS 2009: 70-76 - [c1]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: 242-245 - 2007
- [j3]Rui Jiang, Kueiming Lo:
Optimal Adaptive Controller for Multidimensional Armax Model. Cybern. Syst. 38(2): 141-154 (2007) - 2006
- [j2]Rui Jiang, Hua Yang, Fengzhu Sun, Ting Chen:
Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy. BMC Bioinform. 7: 417 (2006) - 2000
- [j1]Dongcheng Hu, Rui Jiang, Yupin Luo:
An adaptive classifier system tree for extending genetics-based machine learning in a dynamic environment. Artif. Life Robotics 4(1): 7-11 (2000)
Coauthor Index
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