Selected Publications

  1. 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, Nature Machine Intelligence, 4:116-126, 2022
  2. Qiao Liu, Shengquan Chen, Rui Jiang *, Wing Hung Wong *, Simultaneous deep generative modeling and clustering of single cell genomic data, Nature Machine Intelligence, 3:536-544, 2021
  3. 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 Research, 49(W1):W383-W490, 2021
  4. Shengquan Chen, Guanao Yan, Wenyu Zhang, Jinzhao Ji, Rui Jiang *, Zhixiang Lin *, RA3 is a reference-guided approach for epigenetic characterization of single cells, Nature Communications, 12:2177, 2021
  5. Qiao Liu, Jiaze Xu, Rui Jiang *, Wing Hung Wong, Density estimation using deep generative neural networks, Proc Natl Acad Sci USA, 118(15):e2101344118, 2021
  6. Wanwen Zeng, Shengquan Chen, Xuejian Cui, Zijing Gao, Rui Jiang *, SilencerDB: a comprehensive database of silencers, Nucleic Acids Research, 49(D1):D221-D228, 2021
  7. Wenran Li, Zhana Duren, Rui Jiang *, Wing Wong *, A method for scoring the cell-type specific impacts of non-coding variants in personal genomes, Proc Natl Acad Sci USA, 117(35):21364-21372, 2020
  8. Wanwen Zeng, Xi Chen, Zhana Duren, Yong Wang, Rui Jiang *, Wing Hung Wong *, DC3: Deconvolution and coupled clustering from bulk and single cell genomics data, Nature Communications, 10: 4613, 2019
  9. Wenran Li, Wing Hung Wong *, Rui Jiang *, DeepTACT: predicting high-resolution chromatin contacts via bootstrapping deep learning, Nucleic Acids Research, 47(10): e60, 2019
  10. Qiao Liu, Hairong Lv, Rui Jiang *, hicGAN infers super resolution Hi-C data with generative adversarial networks, ISMB 2019 & Bioinformatics, 35(14): i99-i107, 2019
  11. Qiao Liu, Fei Xia, Qijin Yin, Rui Jiang *, Chromatin accessibility prediction via a hybrid deep convolutional neural network, Bioinformatics, 34(5): 732-738, 2018
  12. Zehua Liu, Huazhe Lou, Kaikun Xie, Hao Wang, Ning Chen, Oscar M. Aparicio, Michael Q. Zhang, Rui Jiang *, Ting Chen *, Reconstructing cell cycle pseudo time-series via single-cell transcriptome data, Nature Communications, 8:22, 2017
  13. Zhana Duren, Xi Chen, Rui Jiang *, Yong Wang *, Wing Hung Wong *, Modeling gene regulation from paired expression and chromatin accessibility data, Proc Natl Acad Sci USA, 114(25): E4914-E4923, 2017
  14. Xu Min, Wanwen Zeng, Ning Chen, Ting Chen *, Rui Jiang *, Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding, ISMB 2017 & Bioinformatics, 33(14): i92-i101, 2017
  15. Shining Ma, Tao Jiang, Rui Jiang *, Differential regulation enrichment analysis via the integration of transcriptional regulatory network and gene expression data, Bioinformatics, 31(4): 563-571, 2015
  16. Jiaxin Wu, Yanda Li, Rui Jiang *, Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies, PLoS Genetics, 10(3): e1004237, 2014
  17. Feng Zeng, Rui Jiang *, Ting Chen *, PyroHMMsnp: a SNP caller for Ion Torrent and 454 sequencing data, Nucleic Acids Research, 41(13):e136, 2013
  18. Yong Chen, Tao Jiang, Rui Jiang *, Uncover disease genes by maximizing information flow in the phenome-interactome network, Bioinformatics, 27:i167-i176, 2011
  19. Wanwan Tang, Xuebing Wu, Rui Jiang *, Yanda Li *, Epistatic module detection for case-control studies: A Bayesian model with a Gibbs sampling strategy, PLoS Genetics, 5(5): e1000464, 2009
  20. Xuebing Wu, Qifang Liu, Rui Jiang *, Align human interactome with phenome to identify causative genes and networks underlying disease families, Bioinformatics, 25(1):98-104, 2009
  21. Rui Jiang, Hua Yang, Linqi Zhou, C.-C. Jay Kuo, Fengzhu Sun, Ting Chen *, Sequence-based prioritization of nonsynonymous single-nucleotide polymorphisms for the study of disease mutations, American Journal of Human Genetics, 81(2):346-360, 2007
  22. Rui Jiang, Zhidong Tu, Ting Chen *, Fengzhu Sun *, Network motif identification in stochastic networks, Proc Natl Acad Sci USA, 103(25): 9404-9409, 2006

Publications in 2021

  1. Qiao Liu, Shengquan Chen, Rui Jiang *, Wing Hung Wong *, Simultaneous deep generative modeling and clustering of single cell genomic data, Nature Machine Intelligence, 3:536-544, 2021
  2. Wanwen Zeng, Jinxue Xin, Rui Jiang *, Yong Wang *, Reusability report: Compressing regulatory networks to vectors for interpreting gene expression and genetic variants, Nature Machine Intelligence, 3:576-580, 2021
  3. Shengquan Chen, Boheng Zhang, Xiaoyang Chen, Xuegong Zhang, Rui Jiang *, stPlus: reference-based enhancement of spatial transcriptomics, Bioinformatics, 37:i299-i307, 2021
  4. 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 Research, 49(W1):W383-W490, 2021
  5. Shengquan Chen, Guanao Yan, Wenyu Zhang, Jinzhao Ji, Rui Jiang *, Zhixiang Lin *, RA3 is a reference-guided approach for epigenetic characterization of single cells, Nature Communications, 12:2177, 2021
  6. Qiao Liu, Jiaze Xu, Rui Jiang *, Wing Hung Wong, Density estimation using deep generative neural networks, Proc Natl Acad Sci USA, 118(15):e2101344118, 2021
  7. Wanwen Zeng, Shengquan Chen, Xuejian Cui, Zijing Gao, Rui Jiang *, SilencerDB: a comprehensive database of silencers, Nucleic Acids Research, 49(D1):D221-D228, 2021
  8. Honglei Liu, Zhiqiang Zhang, Yan Xu, Ni Wang, Yanqun Huang, Zhenghan Yang, Rui Jiang, Hui Chen *, Use of BERT (Bidirectional Encoder Representations from Transformers)-based deep learning method for extracting evidences in Chinese radiology reports: development of a computer-aided liver cancer diagnosis framework, Journal of Medical Internet Research, 23(1):e19689, 2021
  9. 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, Bioinformatics, 37(2):185-191, 2021
  10. Congmin Zhu, Junyi Zhang, Xin Wang, Yuqing Yang, Ning Chen, Zuhong Lu, Qinyu Ge, Rui Jiang, Xuegong Zhang, Yunfeng Yang, Ting Chen *, Responses of cyanobacterial aggregate microbial communities to algal blooms, Water Research, 196:117014, 2021

Publications in 2020

  1. Wenran Li, Zhana Duren, Rui Jiang *, Wing Hung Wong *, A method for scoring the cell-type specific impacts of non-coding variants in personal genomes, Proc Natl Acad Sci USA, 117(35):21364-21372, 2020
  2. Wanwen Zeng, Yong Wang *, Rui Jiang *, Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network, Bioinformatics, 36(2):496-503, 2020
  3. Qiao Liu, Zhiqiang Hu, Rui Jiang *, Mu Zhou *, DeepCDR: a hybrid graph convolutional network for predicting cancer drug response, Bioinformatics, 36(Suppl 2):i911-i918, 2020
  4. Pengshuai Yang, Yupeng Zhai, Lin Li, Hairong Lv, Jigang Wang, Chengzhan Zhu, Rui Jiang *, A deep metric learning approach for histopathological image retrieval, Methods, 179(1):14-25, 2020
  5. 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 Computational Biology, 16(11):e1008227, 2020
  6. Xiaoyang Chen, Shengquan Chen, Rui Jiang *, EnClaSC: A novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes, BMC Bioinformatics, 21(Suppl 13):392, 2020
  7. 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
  8. Xiao-Jian Wang, Xi-Qi Xu, Kai Sun, Ke-Qiang Liu, Su-Qi Li, Xin Jiang, Qin-Hua Zhao, Lan Wang, Fu-Hua Peng, Jue Ye, Yan Wu, Rui Jiang, Jin Zhang, Wei Huang, Wen-Bin Wei, Yi Yan, Jing-Hui Li, Qian-Qian Liu, Sheng Li, Yong Wang, Shu-Yang Zhang, Xue Zhang *, Zhi-Cheng Jing *, Association of rare PTGIS variants with susceptibility and pulmonary vascular response in patients with idiopathic pulmonary arterial hypertension, JAMA Cardiology, 5(6):677-684, 2020

Publications in 2019

  1. Wanwen Zeng, Xi Chen, Zhana Duren, Yong Wang, Rui Jiang *, Wing Hung Wong *, DC3: Deconvolution and coupled clustering from bulk and single cell genomics data, Nature Communications, 10: 4613, 2019
  2. Wenran Li, Wing Hung Wong *, Rui Jiang *, DeepTACT: predicting high-resolution chromatin contacts via bootstrapping deep learning, Nucleic Acids Research, 47(10): e60, 2019
  3. Qiao Liu, Hairong Lv, Rui Jiang *, hicGAN infers super resolution Hi-C data with generative adversarial networks, Bioinformatics, 35(14): i99-i107, 2019
  4. Mingxin Gan, Wenran Li, Rui Jiang *, EnContact: predicting enhancer-enhancer contacts using sequence-based deep learning model, PEERJ, 7: e7657, 2019
  5. Shengquan Chen, Kui Hua, Hongfei Cui, Rui Jiang *, VPAC: Variational projection for accurate clustering of single-cell transcriptomic data, BMC Systems Biology, 20(Suppl 7):0, 2019
  6. Wanwen Zeng, Xu Min, Rui Jiang *, EnDisease: a manually curated database for enhancer-disease associations, Database, 2019:baz020, 2019
  7. Dacheng Ma, Zhimeng Xu, Zhaoyu Zhang, Xi Chen, Xiangzhi Zeng, Yiyang Zhang, Tingyue Deng, Mengfei Ren, Zheng Sun,Rui Jiang *, Zhen Xie *, Engineer chimeric Cas9 to expand PAM recognition based on evolutionary information, Nature Communications, 10: 560, 2019
  8. Qijin Yin, Mengmeng Wu, Hairong Lv *, Rui Jiang *, DeepHistone: a deep learning approach to predicting histone modifications, BMC Genomics, 20(Suppl 2):193, 2019
  9. Ran Li, Xiangrui Zhang, Rui Jiang, Zachary Freyberg, Hairong Lv *, Min Xu *, Automatic identification and localization of mitochondria in Cellular Electron Cryo-Tomography using Faster RCNN, BMC Bioinformatics, 20(suppl3): 132, 2019
  10. Shaoming Song, Hongfei Cui, Shengquan Chen, Qiao Liu, Rui Jiang *, EpiFIT: functional interpretation of transcription factors based on combination of sequence and epigenetic information, Quantitative Biology, 7:233-243, 2019

Publications in 2017

  1. Zehua Liu, Huazhe Lou, Kaikun Xie, Hao Wang, Ning Chen, Oscar M. Aparicio, Michael Q. Zhang, Rui Jiang *, Ting Chen *, Reconstructing cell cycle pseudo time-series via single-cell transcriptome data, Nature Communications, 8:22, 2017
  2. Zhana Duren, Xi Chen, Rui Jiang *, Yong Wang *, Wing Wong *, Modeling gene regulation from paired expression and chromatin accessibility data, Proc Natl Acad Sci USA, 114(25): E4914-E4923, 2017
  3. Xu Min, Wanwen Zeng, Ning Chen, Ting Chen *, Rui Jiang *, Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding, Bioinformatics, 33(14): i92-i101, 2017
  4. Mengmeng Wu, Zhidong Lin, Shining Ma, Ting Chen, Rui Jiang *, Wing Wong *, Simultaneous inference of phenotype-associated genes and relevant tissues from GWAS data via Bayesian integration of multiple tissue-specific gene networks, Journal of Molecular Cell Biology, 9(6): 436-452, 2017
  5. Xu Min, Wanwen Zeng, Shengquan Chen, Ning Chen, Ting Chen, Rui Jiang *, Predicting enhancers with deep convolutional neural networks, BMC Bioinformatics, 18 (Suppl 13): 478, 2017
  6. Wenran Li, Meng Wang, Jinghao Sun, Yong Wang, Rui Jiang *, Gene co-opening network deciphers gene functional relationships, Molecular BioSystems, 13:2428-2439, 2017
  7. Mingxin Gan, Wenran Li, Wanwen Zeng, Rui Jiang *, Mimvec: A deep learning approach for analyzing the human phenome, BMC Systems Biology, 11 (Suppl 4): 76, 2017
  8. Mahdi Zamanighomi, Zhixiang Lin, Yong Wang, Rui Jiang, Wing Wong *, Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility and gene expression data, Nucleic Acids Research, 45(10): 5666-5677, 2017
  9. Mengmeng Wu, Ting Chen, Rui Jiang *, Leveraging multiple genomic data to prioritize disease-causing indels from exome sequencing data, Scientific Reports, 7:1804, 2017
  10. Qiao Liu, Mingxin Gan, Rui Jiang *, A sequence-based method to predict the impact of regulatory variants using random forest, BMC Systems Biology, 11 (Suppl 2): 7, 2017
  11. Mingxin Gan, Rui Jiang *, FLOWER: Fusing global and local associations towards personalized social recommendation, Future Generation Computer Systems - the International Journal of Escience, 78:462-473, 2017

Publications in 2013

  1. Yong Chen, Jingjing Hao, Wei Jiang, Tong He, Xuegong Zhang, Tao Jiang, Rui Jiang *, Identifying potential cancer driver genes by genomic data integration, Scientific Reports, 3:3538, 2013
  2. Yong Chen, Xuebing Wu, Rui Jiang *, Integrating human omics data to prioritize candidate genes, BMC Medical Genomics, 6:57, 2013
  3. Thibault Jacquemin, Rui Jiang *, Walking on a tissue-specific disease-protein-complex heterogeneous network for the discovery of disease-related protein complexes, BioMed Research International, 2013:732650, 2013
  4. Feng Zeng, Rui Jiang *, Ting Chen*, PyroHMMvar: a sensitive and accurate method to call short INDELs and SNPs for Ion Torrent and 454 data, Bioinformatics, 29(22): 2859-2868, 2013
  5. Feng Zeng, Rui Jiang *, Ting Chen*, PyroHMMsnp: a SNP caller for Ion Torrent and 454 sequencing data, Nucleic Acids Research, 41(13):e136, 2013
  6. Mingxin Gan, Rui Jiang *, Improving accuracy and diversity of personalized recommendation through power law adjustments of user similarities, Decision Support Systems, 55(3):811-821, 2013
  7. Mingxin Gan, Rui Jiang *, Constructing a user similarity network to remove adverse influence of popular objects for personalized recommendation, Expert Systems with Applications, 40:4044-4053, 2013
  8. Xin-Ming Zhao, Weidong Tian, Rui Jiang, Jun Wan, Computational Systems Biology, The Scientific World Journal, 2013:350358, 2013
  9. Mingxin Gan, Xue Dou, Rui Jiang *, From ontology to semantic similarity: calculation of ontology-based semantic similarity, The Scientific World Journal, 2013:793091, 2013
  10. Jiaxin Wu, Rui Jiang *, Prediction of deleterious nonsynonymous single-nucleotide polymorphism for human diseases, The Scientific World Journal, 2013:675851, 2013
  11. Minghua Deng, Rui Jiang, Fengzhu Sun, Xuegong Zhang (Eds.), Research in Computational Molecular Biology (Proceedings of the 17th Annual International Conference, RECOMB 2013, Beijing, China, April 7-10, 2013), Series Lecture Notes in Computer Science, Vol. 7821, 2013
  12. Mingxin Gan*, Rui Jiang, Inferring semantic similarity through correlating information contents of gene ontology terms, The Integrated Data Analysis in Systems Biology Workshop at the 2013 IEEE International Conference on Bioinformatics and Biomedicine, Dec. 18-21 2013, Shanghai, 2013

Publications in 2012

  1. Bai Jiang, Xujun, Liang, Yang Chen, Tao Ma, Liyang Liu, Junfeng Li, Rui Jiang, Ting Chen, Xuegong Zhang*, Shao Li*, Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome, Scientific Reports, 2:936, 2012
  2. Yong Chen, Wangshu Zhang, Mingxin Gan, Rui Jiang *, Constructing phenome-interactome networks for the prioritization of candidate genes, Statistics and Its Interface, 5:137-148, 2012
  3. Mingxin Gan, Xue Dou, Daoping Wang, Rui Jiang *, Comprehensive weighting method for calculation of ontology-based semantic similarity, Computer Engineering and applications, 48(17):148-153, 2012 (In Chinese)
  4. Yue Huang, Mingxin Gan, Rui Jiang *, Ontology-based genes similarity calculation with TF-IDF, Lecture Notes in Computer Science, 7473:600-607, 2012
  5. Mingxin Gan, Xue Dou, Rui Jiang *, Improving recommendation performance through ontology-based semantic similarity, Lecture Notes in Computer Science, 7473:203-210, 2012
  6. Peng He, Rui Jiang *, Integrating multiple gene semantic similarity profiles to infer disease gene, in Proceedings of the 31st Chinese Control Conference, 7420-7425, 2012

Publications in 2011

  1. Yong Chen, Tao Jiang, Rui Jiang *, Uncover disease genes by maximizing information flow in the phenome-interactome network, Bioinformatics, 27:i167-i176, 2011
  2. Wangshu Zhang, Yong Chen, Fengzhu Sun, Rui Jiang *, DomainRBF: a Bayesian regression approach to the prioritization ofcandidate domains for complex diseases, BMC Systems Biology, 5:55, 2011
  3. Jianxing Feng, Rui Jiang, Tao Jiang, A max-flow basedapproach to the identification of protein complexes using protein interaction and microarray data, IEEE-ACM Transactions on Computational Biology and Bioinformatics, 8(3): 621-634, 2011
  4. Wangshu Zhang, Fengzhu Sun, Rui Jiang *, Integrating multiple protein-protein interaction networks to prioritize disease genes: A Bayesian regression approach, BMC Bioinformatics 12(Supp 1), S11, 2011
  5. Xiaolin Hao, Rui Jiang, Ting Chen, Clustering 16S rRNA for OTU prediction: A method of unsupervised Bayesian clustering, Bioinformatics, 27: 611-618, 2011
  6. Rui Jiang *, Mingxin Gan, Peng He, Constructing a gene semantic similarity network for the prioritization of candidate genes, BMC Systems Biology, 5(Suppl 2):S2, 2011
  7. Jiaxin Wu, Mingxin Gan, Wangshu Zhang, Rui Jiang *, Extraction of sequence conservation features for the prioritization of candidate single amino acid polymorphisms, InternationalJournal of Information Engineering and Electronic Business, 3(2):1-10, 2011
  8. Jiaxin Wu, Mingxin Gan, Rui Jiang *, Prioritization ofcandidate single amino acid polymorphisms using one-class learning machines, International Journal of Computational Biology and Drug Discovery, 4(4): 316-331, 2011
  9. Jiaxin Wu, Mngxin Gan, Wangshu Zhang, Rui Jiang *, Prioritizing candidate single amino acid polymorphisms using physiochemical features, International Journal of Bioscience, Biochemistry and Bioinformatics, 1(2):102-108, 2011
  10. Rui Jiang *, Jiaxin Wu, Integrating sequence conservation features and a domain-domain interaction network to detect disease-associated nsSNPs, in Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine workshops, 262-267, 2011
  11. Mingxin Gan, Xue Dou, Daoping Wang, Rui Jiang, DOPCA:A new method for calculating ontology-based semantic similarity,in Proceedings of the 10th IEEE/ACIS International Conferenceon Computer and Information Science, 334-339, 2011
  12. Jiaxin Wu, Mingxin Gan, Rui Jiang, A genetic algorithm for optimizing subnetwork markers for the study of breast cancer metastasis, in Proceedings of the 2011 Seventh International Conference on Natural Computation (ICNC 2011), 1578-1582,2011

Publications in 2010-2006

  1. MAQC Consortium. The MicroArray Quality Control (MAQC)-II study of common practices forthe development and validation of microarray-based predictive models, Nature Biotechnology, 28:827-838, 2010
  2. Wenhui Wang, Wangshu Zhang, Rui Jiang *, Yihui Luan*, Prioritisation of associations between protein domains and complex diseases using domain¨Cdomain interaction networks, IET Systems Biology, 4(3):212-222, 2010
  3. Wangshu Zhang, Yong Chen, Rui Jiang *, Comparative study of network-based prioritizations of human protein domains associated with complex diseases, Frontiers in Electronic Engineering in China, 5(2), 107-118, 2010
  4. Jiaxin Wu, Wangshu Zhang, Rui Jiang, Comparative Study of Ensemble Learning Approaches in the Identification of Disease Mutations, in Proceedings of the 3rd International Conference on Biomedical Engineering and Informatics (BMEI 2010), Yantai, Shandong, China, 2306-2310, 2010
  5. Wanwan Tang, Xuebing Wu, Rui Jiang *, Yanda Li*, Epistatic module detection for case-control studies: A Bayesian module with a Gibbs sampling strategy, PLoS Genetics, 5(5): e1000464, 2009
  6. Xuebing Wu, Qifang Liu, Rui Jiang *. Align human interactome with phenome to identify causative genes and networks underlying disease families, Bioinformatics, 25(1): 98-104, 2009
  7. Rui Jiang *, Wanwan Tang, Xuebing Wu, Wenhui Fu. A random forest approach to the detection of epistatic interactions in case-control studies, BMC Bioinformatics, 10(Suppl 1):S65, 2009
  8. Rui Jiang, Ting Chen, Fengzhu Sun. Bayesian models and Gibbs sampling strategies for local graph alignment and motif finding in stochastic networks, Communications in Informationand Systems, 9(4):347-370, 2009
  9. Rui Jiang, Feng Zeng, Wangshu Zhang, Xuebing Wu, and Zhihong Yu. Accelerating genome-wide association studies using CUDA compatible graphics cards, Proceedings of the 2009 joint conference on bioinformatics, systems biology and intelligent computing (IJCBS2009), 70-76, Shanghai, August 3-5, 2009.
    [pdf]
  10. Wangshu Zhang, Feng Zeng, Xuebing Wu, Xuegong Zhang, and Rui Jiang. A comparative study of ensemble learning approaches in the classification of breast cancer metastasis, Proceedings of the 2009 joint conference on bioinformatics, systems biology and intelligent computing (IJCBS2009), 242-245, Shanghai, August 3-5, 2009.
    [pdf]
  11. Xuebing Wu, Qifang Liu, Rui Jiang, Identification of disease genes via network alignment of human interactome and phenome, Proceedings of the Seventh Asia Pacific Bioinformatics Conference (APBC 2009), Beijing, China, January 13-16, 2009
  12. Feng Zang, Xuebing Wu, Xuegong Zhang, Rui Jiang, A functional canonical correlation analysis approach to re-verse engineering of in silico gene regulatory networks, Proceedings of the Seventh Asia Pacific Bioinformatics Conference (APBC 2009), Beijing, China, January 13-16, 2009
  13. Wenhui Wang, Wangshu Zhang, Rui Jiang, Yihui Luan, Anapproach to the discovery of associations of protein domains andcomplex diseases, Proceedings of the Seventh Asia Pacific Bioinformatics Conference (APBC 2009), Beijing, China, January 13-16, 2009
  14. Rui Jiang, Wanwan Tang, Xuebing Wu, Wenhui Fu, A random forest approach to the detection of epistatic interactions incase-control studies, Proceedings of the Seventh Asia Pacific Bioinformatics Conference (APBC 2009), Beijing, China, January 13-16, 2009
  15. Feng Zang, Xuebing Wu, Xuegong Zhang, Rui Jiang, A functional canonical correlation analysis approach to re-verse engineering of in silico gene regulatory networks, Proceedings of the Seventh Asia Pacific Bioinformatics Conference (APBC 2009), Beijing, China, January 13-16,2009
  16. Xuebing Wu, Rui Jiang, Michael Q. Zhang, Shao Li. Network-based global inference of human disease genes, MolecularSystems Biology, 4:189, 2008
  17. Xuebing Wu, Zhirong Sun, Rui Jiang, Logic motif of combinatorial control in transcriptional networks, Nature Precedings, npre.2008.2227.1, 2008
  18. Xuebing Wu, Feng Zeng, Rui Jiang, Integrative inference of gene networks from expression data, Proceedings of the 2008 Joint RECOMB Satellite Conference on Regulatory Genomics-Systems biology-DREAM3, Boston, Massachusetts, USA, Oct 29-Nov3, 2008
  19. Jianxing Feng, Rui Jiang, Tao Jiang, A max-flow basedapproach to the identification of protein complexes (extended abstract), Proceedings of the 7th Annual International Conference on Computational Systems Bioinformatics (CSB2008), Stanford, California, USA, August 26-29, 2008
  20. Rui Jiang and Xuegong Zhang, A comparative study of statistical learning methods in the prioritization of nonsynonymous single nucleotide polymorphisms, Proceedings of the Sixth Asia Pacific Bioinformatics Conference (APBC 2008), Kyoto, Japan, January 14-17, 2008
  21. Rui Jiang, Hua Yang, Linqi Zhou, C.-C. Jay Kuo, Fengzhu Sun, and Ting Chen. Sequence-based prioritization of single nucleotide polymorphisms for study of human mutations, American Journal of Human Genetics, 81(2): 346-360, 2007
  22. Rui Jiang, Zhidong Tu, Ting Chen, and Fengzhu Sun. Network Identification in Stochastic Networks. Proc. Natl. Acad. Sci. USA, 103(25): 9404~9409, 2006
  23. Rui Jiang, Hua Yang, Fengzhu Sun, and Ting Chen. Searching for interpretable rules for human mutations: A simulated annealing bump hunting strategy. BMC Bioinformatics, 7:417, 2006

Publications in 2005 and earlier

  1. Rui Jiang, and K. Y. Szeto. Extraction of investment strategies based on moving averages: A genetic algorithm approach. Proceedings of the International Conference on Computational Intelligence for Financial Engineering (CIFEr'03), Hong Kong, 2003 [pdf @ IEEE Xplore]
  2. K. Y. Szeto, and Rui Jiang. A Quasi-Parallel realization of the investment frontier in computer resource allocation using simple genetic algorithm on a single computer. Lecture Notes inComputer Science, Vol.2367, 116~118, 2002 [pdf @ SpringerLink]
  3. Rui Jiang, Yupin Luo, Dongcheng Hu, and K. Y. Szeto. A multi-agent cooperating approach to quasi-parallel genetic algorithms. ACTA ELECTRONICA SINICA. Vol.30, No.10, 1490-1495, 2002 (In Chinese) [pdf @ ACTA ELECTRONICA SINICA]
  4. Rui Jiang, Yupin Luo, and Dongcheng Hu. Adaptive genetic algorithm based on population entropy estimating. Journal of Tsinghua University (Science and Technology). Vol.42, No.3, 358 ~ 361, 2002 (In Chinese) [Paper @ Journal of Tsinghua University]
  5. Rui Jiang, Yupin Luo, and Dongcheng Hu. Distributed parallelgenetic algorithms based on multi- agent cooperating. Journalof Tsinghua University (Science and Technology). Vol.42, No.9, 1209~1213, 2002 (In Chinese) [Paper @ Journal of Tsinghua University]
  6. Rui Jiang, Yupin Luo, Dongcheng Hu, and K. Y. Szeto. Coordinating exploration and exploitation to construct genetic algorithms. Tsinghua Science and Technology. Vol.7, No.5, 608~618, 2002 [Paper @ IEEE Xplore]
  7. Rui Jiang, and K. Y. Szeto. Discovering investment strategies in portfolio management: A genetic algorithm approach. Proceedings of the 9th International Conference on Neural Information Processing (ICONIP'02), Singapore, Vol.3, 2002 [pdf @ IEEE Xplore]
  8. Rui Jiang, K. Y. Szeto, Yupin Luo, and Dongcheng Hu. A genetic algorithm architecture by coordinating exploration and exploitation. Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2001), San Francisco, 383~390, 2001
  9. Rui Jiang, Yupin Luo, Dongcheng Hu, and K. Y. Szeto. A genetic algorithm by coordinating exploration and exploitation: Convergence properties and performance analyses. Chinese Journal of Computers. Vol.24, No.12, 1233-1241, 2001
  10. Dongcheng Hu, Rui Jiang, Yupin Luo, and K. Y. Szeto. An approach to cooperative genetic algorithms. Proceedings of the Sixth International Symposium on Artificial Life and Robotics (AROB 6'01), Tokyo, Japan, Vol.2, 329~332, 2001
  11. Rui Jiang, K. Y. Szeto, Yupin Luo, and Dongcheng Hu. A path-splitting algorithm for large traveling salesman problems with distributed simulated annealing implementation. Proceedings ofthe Third Asian Control Conference. Shanghai, China. CDROM, 2000
  12. Dongcheng Hu, Rui Jiang, Yupin Luo. Effects of population topology in distributed parallel genetic algorithms. Proceedings of the Fifth International Symposium on Artificial Life and Robotics (AROB 5'00), Oita, Japan. Vol.1, 108~111, 2000
  13. Dongcheng Hu, Rui Jiang, Yupin Luo. An adaptive classifier system tree for extending genetics-based machine learning in a dynamic environment. Artificial life and robotics. Vol.4, No.1, 7-11, 2000 [pdf @ the Artificial Life andRobotics web site]

Journal Publications

  1. Wenran Li, Zhana Duren, Rui Jiang *, Wing Wong *, A method for scoring the cell-type specific impacts of non-coding variants in personal genomes, Proc Natl Acad Sci USA, In press, 2020
  2. Wanwen Zeng, Yong Wang *, Rui Jiang *, Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network, Bioinformatics, 36(2):496-503, 2020
  3. Qiao Liu, Zhiqiang Hu, Rui Jiang *, Mu Zhou *, DeepCDR: a hybrid graph convolutional network for predicting cancer drug response, Bioinformatics, In press, 2020
  4. Shengquan Chen, Mingxin Gan *, Hairong Lv, Rui Jiang *, DeepCAPE: a deep convolutional neural network for the accurate prediction of enhancers, Genomics, Proteomics & Bioinformatics, In press, 2020
  5. Pengshuai Yang, Yupeng Zhai, Lin Li, Hairong Lv, Jigang Wang, Chengzhan Zhu, Rui Jiang *, A deep metric learning approach for histopathological image retrieval, Methods, In press (https://doi.org/10.1016/j.ymeth.2020.05.015), 2020
  6. Xiao-Jian Wang, Xi-Qi Xu, Kai Sun, Ke-Qiang Liu, Su-Qi Li, Xin Jiang, Qin-Hua Zhao, Lan Wang, Fu-Hua Peng, Jue Ye, Yan Wu, Rui Jiang, Jin Zhang, Wei Huang, Wen-Bin Wei, Yi Yan, Jing-Hui Li, Qian-Qian Liu, Sheng Li, Yong Wang, Shu-Yang Zhang, Xue Zhang *, Zhi-Cheng Jing *, Association of rare PTGIS variants with susceptibility and pulmonary vascular response in patients with idiopathic pulmonary arterial hypertension, JAMA Cardiology, doi:10.1001/jamacardio.2020.0479, 2020
  7. Yongcui Wang, Shilong Chen, Wenran Li, Rui Jiang, Yong Wang, Associating divergent lncRNA with target genes by integrating genome sequence, gene expression, and chromatin accessibility data, Nucleic Acids Research, In press, 2020
  8. Xiaoyang Chen, Shengquan Chen, Rui Jiang *, EnClaSC: A novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes, BMC Bioinformatics, In press, 2020
  9. Wanwen Zeng, Xi Chen, Zhana Duren, Yong Wang, Rui Jiang *, Wing Hung Wong *, DC3: Deconvolution and coupled clustering from bulk and single cell genomics data, Nature Communications, 10: 4613, 2019
  10. Wenran Li, Wing Hung Wong *, Rui Jiang *, DeepTACT: predicting high-resolution chromatin contacts via bootstrapping deep learning, Nucleic Acids Research, 47(10): e60, 2019
  11. Qiao Liu, Hairong Lv, Rui Jiang *, hicGAN infers super resolution Hi-C data with generative adversarial networks, Bioinformatics, 35(14): i99-i107, 2019
  12. Mingxin Gan, Wenran Li, Rui Jiang *, EnContact: predicting enhancer-enhancer contacts using sequence-based deep learning model, PEERJ, 7: e7657, 2019
  13. Shengquan Chen, Kui Hua, Hongfei Cui, Rui Jiang *, VPAC: Variational projection for accurate clustering of single-cell transcriptomic data, BMC Systems Biology, 20(Suppl 7):0, 2019
  14. Wanwen Zeng, Xu Min, Rui Jiang *, EnDisease: a manually curated database for enhancer-disease associations, Database, 2019:baz020, 2019
  15. Dacheng Ma, Zhimeng Xu, Zhaoyu Zhang, Xi Chen, Xiangzhi Zeng, Yiyang Zhang, Tingyue Deng, Mengfei Ren, Zheng Sun,Rui Jiang *, Zhen Xie *, Engineer chimeric Cas9 to expand PAM recognition based on evolutionary information, Nature Communications, 10: 560, 2019
  16. Qijin Yin, Mengmeng Wu, Hairong Lv *, Rui Jiang *, DeepHistone: a deep learning approach to predicting histone modifications, BMC Genomics, 20(Suppl 2):193, 2019
  17. Ran Li, Xiangrui Zhang, Rui Jiang, Zachary Freyberg, Hairong Lv *, Min Xu *, Automatic identification and localization of mitochondria in Cellular Electron Cryo-Tomography using Faster RCNN, BMC Bioinformatics, 20(suppl3): 132, 2019
  18. Shaoming Song, Hongfei Cui, Shengquan Chen, Qiao Liu, Rui Jiang *, EpiFIT: functional interpretation of transcription factors based on combination of sequence and epigenetic information, Quantitative Biology, 7:233-243, 2019
  19. Qiao Liu, Fei Xia, Qijin Yin, Rui Jiang *, Chromatin accessibility prediction via a hybrid deep convolutional neural network, Bioinformatics34(5): 732-738, 2018
  20. Wanwen Zeng, Mengmeng Wu, Rui Jiang *, EP2vec: a deep learning approach for extracting sequence embedding features to predict enhancer-promoter interactions, BMC Genomics, 19(Suppl 2):84, 2018
  21. Shining Ma, Tao Jiang *, Rui Jiang *, Constructing tissue-specific transcriptional regulatory networks via a Markov random field, BMC Genomics, 19 (Suppl 10):884, 2018
  22. Shining Ma, Tao Jiang *, Zicheng Wang, Huazhe, Lou, Rui Jiang *, Ting Chen *, GePMI: A statistical model for personal intestinal microbiome identification, npj Biofilms and Microbiomes, 4(20), 2018
  23. Mengmeng Wu, Wanwen Zeng, Wenqiang Liu, Yijia Zhang, Hairong Lv *, Ting Chen *, Rui Jiang *, Leveraging multiple gene networks to prioritize GWAS candidate genes via network representation learning, Methods, 145:41-50, 2018
  24. Zehua Liu, Huazhe Lou, Kaikun Xie, Hao Wang, Ning Chen, Oscar M. Aparicio, Michael Q. Zhang, Rui Jiang *, Ting Chen *, Reconstructing cell cycle pseudo time-series via single-cell transcriptome data, Nature Communications, 8:22, 2017
  25. Zhana Duren, Xi Chen, Rui Jiang *, Yong Wang *, Wing Wong *, Modeling gene regulation from paired expression and chromatin accessibility data, Proc Natl Acad Sci USA, 114(25): E4914-E4923, 2017
  26. Xu Min, Wanwen Zeng, Ning Chen, Ting Chen *, Rui Jiang *, Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding, Bioinformatics, 33(14): i92-i101, 2017
  27. Mengmeng Wu, Zhidong Lin, Shining Ma, Ting Chen, Rui Jiang *, Wing Wong *, Simultaneous inference of phenotype-associated genes and relevant tissues from GWAS data via Bayesian integration of multiple tissue-specific gene networks, Journal of Molecular Cell Biology, 9(6): 436-452, 2017
  28. Xu Min, Wanwen Zeng, Shengquan Chen, Ning Chen, Ting Chen, Rui Jiang *, Predicting enhancers with deep convolutional neural networks, BMC Bioinformatics, 18 (Suppl 13): 478, 2017
  29. Wenran Li, Meng Wang, Jinghao Sun, Yong Wang, Rui Jiang *, Gene co-opening network deciphers gene functional relationships, Molecular BioSystems, 13:2428-2439, 2017
  30. Mingxin Gan, Wenran Li, Wanwen Zeng, Rui Jiang *, Mimvec: A deep learning approach for analyzing the human phenome, BMC Systems Biology, 11 (Suppl 4): 76, 2017
  31. Mahdi Zamanighomi, Zhixiang Lin, Yong Wang, Rui Jiang, Wing Wong *, Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility and gene expression data, Nucleic Acids Research, 45(10): 5666-5677, 2017
  32. Mengmeng Wu, Ting Chen, Rui Jiang *, Leveraging multiple genomic data to prioritize disease-causing indels from exome sequencing data, Scientific Reports, 7:1804, 2017
  33. Qiao Liu, Mingxin Gan, Rui Jiang *, A sequence-based method to predict the impact of regulatory variants using random forest, BMC Systems Biology, 11 (Suppl 2): 7, 2017
  34. Mingxin Gan, Rui Jiang *, FLOWER: Fusing global and local associations towards personalized social recommendation, Future Generation Computer Systems - the International Journal of Escience, 78:462-473, 2017
  35. Mengmeng Wu, Ting Chen, Rui Jiang *, Global inference of disease-causing single nucleotide variants from exome sequencing data, BMC Bioinformatics, 17(17): 468, 2016
  36. XueGong Zhang *, Rui Jiang, Xiaowo Wang, Jin Gu, and Ting Chen, From big biological data to big discovery: The past decade and the future, Chinese Science Bulletin, 61(36): 3869-3877, 2016
  37. Lianshuo Li, Zicheng Wang, Peng He, Shining Ma, Jie Du, Rui Jiang *, Construction and analysis of functional networks in human gut microbiome of type 2 diabetes, Genomics, Proteomics & Bioinformatics, 14(5): 314-324, 2016
  38. Yong Wang, Rui Jiang, Wing Wong *, Modeling the causal regulatory network by integrating chromatin accessibility and transcriptome data, National Science Review, 3: 240-251, 2016
  39. 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: The Journal of Biological Databases and Curation, 2016: baw024, 2016
  40. Mingxin Gan, Lily Sun, Rui Jiang *, Trinity: Walking on a User-Object-Tag heterogeneous network for personalised recommendations, Journal of Computer Science and Technology, 31 (3): 577-594, 2016
  41. Rui Jiang *, Walking on multiple disease-gene networks to prioritize candidate genes, Journal of Molecular Cell Biology, 7(3):214-230, 2015
  42. Shining Ma, Tao Jiang *, Rui Jiang *, Differential regulation enrichment analysis via the integration of transcriptional regulatory network and gene expression data, Bioinformatics, 31(4): 563-571, 2015
  43. Rui Jiang *, Mengmeng Wu, Lianshuo Li, Pinpointing disease genes through phenomic and genomic data fusion, BMC Genomics, 16 (Suppl 2): S3, 2015
  44. Congmin Zhu, Rui Jiang *, Ting Chen *, Constructing a Boolean implication network to study the interactions between environmental factors and OTUs, Quantitative Biology, 2:127-141, 2015
  45. Yuanhua Huang, Bosen Xu, Ying Li, Ming Lu, Rui Jiang, Tingting Li*, Systematic characterization and prediction of post-translational modification cross-talk, Molecular and Cellular Proteomics, 14(3):761-770, 2015
  46. Chengli Xu, Xiangwu Ju, Dandan Song, Fengming Huang, Depei Tang, Zhen Zou, Chao Zhang, Trupti Joshi, Lijuan Jia, Weihai Xu, Kai-Feng Xu, Qian Wang, Yanlei Xiong, Zhenmin Guo, Xiangmei Chen, Fumin Huang, Jiantao Xu, Ying Zhong, Yi Zhu, Yi Peng, Li Wang, Xinyu Zhang, Rui Jiang, Dangsheng Li, Tao Jiang, Dong Xu, Chengyu Jiang, An association analysis between psychophysical characteristics and genome-wide gene expression changes in human adaptation to the extreme climate at the Antarctic Dome Argus, Molecular Psychiatry, 20:536-544, 2015
  47. Mengmeng Wu, Rui Jiang *, Detecting epistatic interactions in metagenome-wide association studies by metaBOOST, BioMed Research International, 2014:398147, 2014
  48. Jiaxin Wu, Yanda Li, Rui Jiang *, Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies, PLoS Genetics, 10(3): e1004237, 2014
  49. Jiaxin Wu, Silu Yang, Rui Jiang *, Inferring nsSNP-disease associations via integration of multiple similarity networks, IET Systems Biology, 8(2): 33-40, 2014
  50. Yong Chen, Thibault Jacquemin, Shuyan Zhang, Rui Jiang *, Prioritizing protein complexes implicated in human diseases by network optimization, BMC Systems Biology, 8(Suppl 1):S2, 2014
  51. Yong Chen, Jingjing Hao, Wei Jiang, Tong He, Xuegong Zhang, Tao Jiang, Rui Jiang *, Identifying potential cancer driver genes by genomic data integration, Scientific Reports, 3:3538, 2013
  52. Yong Chen, Xuebing Wu, Rui Jiang *, Integrating human omics data to prioritize candidate genes, BMC Medical Genomics, 6:57, 2013
  53. Thibault Jacquemin, Rui Jiang *, Walking on a tissue-specific disease-protein-complex heterogeneous network for the discovery of disease-related protein complexes, BioMed Research International, 2013:732650, 2013
  54. Feng Zeng, Rui Jiang *, Ting Chen*, PyroHMMvar: a sensitive and accurate method to call short INDELs and SNPs for Ion Torrent and 454 data, Bioinformatics, 29(22): 2859-2868, 2013
  55. Feng Zeng, Rui Jiang *, Ting Chen*, PyroHMMsnp: a SNP caller for Ion Torrent and 454 sequencing data, Nucleic Acids Research, 41(13):e136, 2013
  56. Mingxin Gan, Rui Jiang *, Improving accuracy and diversity of personalized recommendation through power law adjustments of user similarities, Decision Support Systems, 55(3):811-821, 2013
  57. Mingxin Gan, Rui Jiang *, Constructing a user similarity network to remove adverse influence of popular objects for personalized recommendation, Expert Systems with Applications, 40:4044-4053, 2013
  58. Xin-Ming Zhao, Weidong Tian, Rui Jiang, Jun Wan, Computational Systems Biology, The Scientific World Journal, 2013:350358, 2013
  59. Mingxin Gan, Xue Dou, Rui Jiang *, From ontology to semantic similarity: calculation of ontology-based semantic similarity, The Scientific World Journal, 2013:793091, 2013
  60. Jiaxin Wu, Rui Jiang *, Prediction of deleterious nonsynonymous single-nucleotide polymorphism for human diseases, The Scientific World Journal, 2013:675851, 2013
  61. Bai Jiang, Xujun, Liang, Yang Chen, Tao Ma, Liyang Liu, Junfeng Li, Rui Jiang, Ting Chen, Xuegong Zhang*, Shao Li*, Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome, Scientific Reports, 2:936, 2012
  62. Yong Chen, Wangshu Zhang, Mingxin Gan, Rui Jiang *, Constructing phenome-interactome networks for the prioritization of candidate genes, Statistics and Its Interface, 5:137-148, 2012
  63. Mingxin Gan, Xue Dou, Daoping Wang, Rui Jiang *, Comprehensive weighting method for calculation of ontology-based semantic similarity, Computer Engineering and applications, 48(17):148-153, 2012 (In Chinese)
  64. Yong Chen, Tao Jiang, Rui Jiang *, Uncover disease genes by maximizing information flow in the phenome-interactome network, Bioinformatics, 27:i167-i176, 2011
  65. Wangshu Zhang, Yong Chen, Fengzhu Sun, Rui Jiang *, DomainRBF: a Bayesian regression approach to the prioritization ofcandidate domains for complex diseases, BMC Systems Biology, 5:55, 2011
  66. Jianxing Feng, Rui Jiang, Tao Jiang, A max-flow basedapproach to the identification of protein complexes using protein interaction and microarray data, IEEE-ACM Transactions on Computational Biology and Bioinformatics, 8(3): 621-634, 2011
  67. Wangshu Zhang, Fengzhu Sun, Rui Jiang *, Integrating multiple protein-protein interaction networks to prioritize disease genes: A Bayesian regression approach, BMC Bioinformatics 12(Supp 1), S11, 2011
  68. Xiaolin Hao, Rui Jiang, Ting Chen, Clustering 16S rRNA for OTU prediction: A method of unsupervised Bayesian clustering, Bioinformatics, 27: 611-618, 2011
  69. Rui Jiang *, Mingxin Gan, Peng He, Constructing a gene semantic similarity network for the prioritization of candidate genes, BMC Systems Biology, 5(Suppl 2):S2, 2011
  70. Jiaxin Wu, Mingxin Gan, Wangshu Zhang, Rui Jiang *, Extraction of sequence conservation features for the prioritization of candidate single amino acid polymorphisms, InternationalJournal of Information Engineering and Electronic Business, 3(2):1-10, 2011
  71. Jiaxin Wu, Mingxin Gan, Rui Jiang *, Prioritization ofcandidate single amino acid polymorphisms using one-class learning machines, International Journal of Computational Biology and Drug Discovery, 4(4): 316-331, 2011
  72. Jiaxin Wu, Mngxin Gan, Wangshu Zhang, Rui Jiang *, Prioritizing candidate single amino acid polymorphisms using physiochemical features, International Journal of Bioscience, Biochemistry and Bioinformatics, 1(2):102-108, 2011
  73. MAQC Consortium. The MicroArray Quality Control (MAQC)-II study of common practices forthe development and validation of microarray-based predictive models, Nature Biotechnology, 28:827-838, 2010
  74. Wenhui Wang, Wangshu Zhang, Rui Jiang *, Yihui Luan*, Prioritisation of associations between protein domains and complex diseases using domain¨Cdomain interaction networks, IET Systems Biology, 4(3):212-222, 2010
  75. Wangshu Zhang, Yong Chen, Rui Jiang *, Comparative study of network-based prioritizations of human protein domains associated with complex diseases, Frontiers in Electronic Engineering in China, 5(2), 107-118, 2010
  76. Wanwan Tang, Xuebing Wu, Rui Jiang *, Yanda Li*, Epistatic module detection for case-control studies: A Bayesian module with a Gibbs sampling strategy, PLoS Genetics, 5(5): e1000464, 2009
  77. Xuebing Wu, Qifang Liu, Rui Jiang *. Align human interactome with phenome to identify causative genes and networks underlying disease families, Bioinformatics, 25(1): 98-104, 2009
  78. Rui Jiang *, Wanwan Tang, Xuebing Wu, Wenhui Fu. A random forest approach to the detection of epistatic interactions in case-control studies, BMC Bioinformatics, 10(Suppl 1):S65, 2009
  79. Rui Jiang, Ting Chen, Fengzhu Sun. Bayesian models and Gibbs sampling strategies for local graph alignment and motif finding in stochastic networks, Communications in Informationand Systems, 9(4):347-370, 2009
  80. Xuebing Wu, Rui Jiang, Michael Q. Zhang, Shao Li. Network-based global inference of human disease genes, MolecularSystems Biology, 4:189, 2008
  81. Xuebing Wu, Zhirong Sun, Rui Jiang, Logic motif of combinatorial control in transcriptional networks, Nature Precedings, npre.2008.2227.1, 2008
  82. Rui Jiang, Hua Yang, Linqi Zhou, C.-C. Jay Kuo, Fengzhu Sun, and Ting Chen. Sequence-based prioritization of single nucleotide polymorphisms for study of human mutations, American Journal of Human Genetics, 81(2): 346-360, 2007
  83. Rui Jiang, Zhidong Tu, Ting Chen, and Fengzhu Sun. Network Identification in Stochastic Networks. Proc. Natl. Acad. Sci. USA, 103(25): 9404~9409, 2006
  84. Rui Jiang, Hua Yang, Fengzhu Sun, and Ting Chen. Searching for interpretable rules for human mutations: A simulated annealing bump hunting strategy. BMC Bioinformatics, 7:417, 2006
  85. Rui Jiang, Yupin Luo, Dongcheng Hu, and K. Y. Szeto. A multi-agent cooperating approach to quasi-parallel genetic algorithms. ACTA ELECTRONICA SINICA. 30(10): 1490-1495, 2002 (In Chinese)
  86. Rui Jiang, Yupin Luo, and Dongcheng Hu. Adaptive genetic algorithm based on population entropy estimating. Journal of Tsinghua University (Science and Technology). 42(3): 358-361, 2002 (In Chinese)
  87. Rui Jiang, Yupin Luo, and Dongcheng Hu. Distributed parallelgenetic algorithms based on multi- agent cooperating. Journalof Tsinghua University (Science and Technology). 42(9): 1209-1213, 2002 (In Chinese)
  88. Rui Jiang, Yupin Luo, Dongcheng Hu, and K. Y. Szeto. Coordinating exploration and exploitation to construct genetic algorithms. Tsinghua Science and Technology. 7(5):608-618, 2002
  89. Rui Jiang, Yupin Luo, Dongcheng Hu, and K. Y. Szeto. A genetic algorithm by coordinating exploration and exploitation: Convergence properties and performance analyses. Chinese Journal of Computers. 24(12):1233-1241, 2001 (In Chinese)
  90. K. Y. Szeto, and Rui Jiang. A Quasi-Parallel realization of the investment frontier in computer resource allocation using simple genetic algorithm on a single computer. Lecture Notes inComputer Science, 2367:116-118, 2002
  91. Dongcheng Hu, Rui Jiang, Yupin Luo. An adaptive classifier system tree for extending genetics-based machine learning in a dynamic environment. Artificial life and robotics. 4(1):7-11, 2000

Conference Publications

  1. Mingxin Gan*, Rui Jiang, Inferring semantic similarity through correlating information contents of gene ontology terms, The Integrated Data Analysis in Systems Biology Workshop at the 2013 IEEE International Conference on Bioinformatics and Biomedicine, Dec. 18-21 2013, Shanghai, 2013
  2. Minghua Deng, Rui Jiang, Fengzhu Sun, Xuegong Zhang (Eds.), Research in Computational Molecular Biology (Proceedings of the 17th Annual International Conference, RECOMB 2013, Beijing, China, April 7-10, 2013), Series Lecture Notes in Computer Science, Vol. 7821, 2013
  3. Yue Huang, Mingxin Gan, Rui Jiang *, Ontology-based genes similarity calculation with TF-IDF, Lecture Notes in Computer Science, 7473:600-607, 2012
  4. Mingxin Gan, Xue Dou, Rui Jiang *, Improving recommendation performance through ontology-based semantic similarity, Lecture Notes in Computer Science, 7473:203-210, 2012
  5. Peng He, Rui Jiang *, Integrating multiple gene semantic similarity profiles to infer disease gene, in Proceedings of the 31st Chinese Control Conference, 7420-7425, 2012
  6. Rui Jiang *, Jiaxin Wu, Integrating sequence conservation features and a domain-domain interaction network to detect disease-associated nsSNPs, in Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine workshops, 262-267, 2011
  7. Mingxin Gan, Xue Dou, Daoping Wang, Rui Jiang, DOPCA:A new method for calculating ontology-based semantic similarity,in Proceedings of the 10th IEEE/ACIS International Conferenceon Computer and Information Science, 334-339, 2011
  8. Jiaxin Wu, Mingxin Gan, Rui Jiang, A genetic algorithm for optimizing subnetwork markers for the study of breast cancer metastasis, in Proceedings of the 2011 Seventh International Conference on Natural Computation (ICNC 2011), 1578-1582,2011
  9. Jiaxin Wu, Wangshu Zhang, Rui Jiang, Comparative Study of Ensemble Learning Approaches in the Identification of Disease Mutations, in Proceedings of the 3rd International Conference on Biomedical Engineering and Informatics (BMEI 2010), Yantai, Shandong, China, 2306-2310, 2010
  10. Rui Jiang, Feng Zeng, Wangshu Zhang, Xuebing Wu, and Zhihong Yu. Accelerating genome-wide association studies using CUDA compatible graphics cards, Proceedings of the 2009 joint conference on bioinformatics, systems biology and intelligent computing (IJCBS2009), 70-76, Shanghai, August 3-5, 2009
  11. Wangshu Zhang, Feng Zeng, Xuebing Wu, Xuegong Zhang, and Rui Jiang. A comparative study of ensemble learning approaches in the classification of breast cancer metastasis, Proceedings of the 2009 joint conference on bioinformatics, systems biology and intelligent computing (IJCBS2009), 242-245, Shanghai, August 3-5, 2009
  12. Xuebing Wu, Qifang Liu, Rui Jiang, Identification of disease genes via network alignment of human interactome and phenome, Proceedings of the Seventh Asia Pacific Bioinformatics Conference (APBC 2009), Beijing, China, January 13-16, 2009
  13. Rui Jiang, Wanwan Tang, Xuebing Wu, Wenhui Fu, A random forest approach to the detection of epistatic interactions incase-control studies, Proceedings of the Seventh Asia Pacific Bioinformatics Conference (APBC 2009), Beijing, China, January 13-16, 2009
  14. Feng Zang, Xuebing Wu, Xuegong Zhang, Rui Jiang, A functional canonical correlation analysis approach to re-verse engineering of in silico gene regulatory networks, Proceedings of the Seventh Asia Pacific Bioinformatics Conference (APBC 2009), Beijing, China, January 13-16, 2009
  15. Wenhui Wang, Wangshu Zhang, Rui Jiang, Yihui Luan, Anapproach to the discovery of associations of protein domains andcomplex diseases, Proceedings of the Seventh Asia Pacific Bioinformatics Conference (APBC 2009), Beijing, China, January 13-16, 2009
  16. Xuebing Wu, Feng Zeng, Rui Jiang, Integrative inference of gene networks from expression data, Proceedings of the 2008 Joint RECOMB Satellite Conference on Regulatory Genomics-Systems biology-DREAM3, Boston, Massachusetts, USA, Oct 29-Nov3, 2008
  17. Jianxing Feng, Rui Jiang, Tao Jiang, A max-flow basedapproach to the identification of protein complexes (extended abstract), Proceedings of the 7th Annual International Conference on Computational Systems Bioinformatics (CSB2008), Stanford, California, USA, August 26-29, 2008
  18. Rui Jiang and Xuegong Zhang, A comparative study of statistical learning methods in the prioritization of nonsynonymous single nucleotide polymorphisms, Proceedings of the Sixth Asia Pacific Bioinformatics Conference (APBC 2008), Kyoto, Japan, January 14-17, 2008
  19. Rui Jiang, and K. Y. Szeto. Extraction of investment strategies based on moving averages: A genetic algorithm approach. Proceedings of the International Conference on Computational Intelligence for Financial Engineering (CIFEr'03), Hong Kong, 2003
  20. Rui Jiang, and K. Y. Szeto. Discovering investment strategies in portfolio management: A genetic algorithm approach. Proceedings of the 9th International Conference on Neural Information Processing (ICONIP'02), Singapore, Vol.3, 2002
  21. Rui Jiang, K. Y. Szeto, Yupin Luo, and Dongcheng Hu. A genetic algorithm architecture by coordinating exploration and exploitation. Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2001), San Francisco, 383~390, 2001
  22. Dongcheng Hu, Rui Jiang, Yupin Luo, and K. Y. Szeto. An approach to cooperative genetic algorithms. Proceedings of the Sixth International Symposium on Artificial Life and Robotics (AROB 6'01), Tokyo, Japan, Vol.2, 329~332, 2001
  23. Rui Jiang, K. Y. Szeto, Yupin Luo, and Dongcheng Hu. A path-splitting algorithm for large traveling salesman problems with distributed simulated annealing implementation. Proceedings ofthe Third Asian Control Conference. Shanghai, China. CDROM, 2000
  24. Dongcheng Hu, Rui Jiang, Yupin Luo. Effects of population topology in distributed parallel genetic algorithms. Proceedings of the Fifth International Symposium on Artificial Life and Robotics (AROB 5'00), Oita, Japan. Vol.1, 108~111, 2000