Intelligent Informatics Lab

Key Laboratory of Systems Biology,

Shanghai Institutes for Biological Sciences,

Chinese Academy of Sciences

　

　

Contact

  • Present address (office): 320 YueYang Road, Shanghai 200031, China.
  • Phone (office): +86-21-5492-0100
  • Fax:+86-21-5492-0120
  • Email: lnchen@sibcb.ac.cn

　 Books

  • Combinatorial Optimization by Modern Heuristic Techniques, 1997, Nikan Publish, coauthor

  • Operation and Planning in Deregulated Power Systems, 2002, Tokyo DenKiDai Publish, coauthor

  • X.-S. Zhang, L. Chen, L.-Y. Wu, Y. Wang (eds). Optimization and System Biology (Lecture Notes in Operations Research, 7), 2007, World Publishing Corporation, Beijing.
    　
  • X.-S. Zhang, L. Chen, L.-Y. Wu, Y. Wang (eds). Optimization and System Biology (Lecture Notes in Operations Research, 8), 2008, World Publishing Corporation, Beijing.
    　
  • L. Chen, L.-Y. Wu, Y. Wang, X.-S. Zhang(eds). Optimization and System Biology (Lecture Notes in Operations Research, 9), 2009, World Publishing Corporation, Beijing.
    　
  • L. Chen, L.-Y. Wu, Y. Wang, X.-S. Zhang(eds). Optimization and System Biology (Lecture Notes in Operations Research, 10), 2010, World Publishing Corporation, Beijing.
    　
  • L. Chen, R.-S. Wang, X.-S. Zhang. Biomolecular Networks: Methods and Applications in Systems Biology, John Wiley & Sons, 2009.

  • L. Chen, R-Q. Wang, C. Li, K. Aihara, Modeling Biomolecular Networks in Cells: Structures and Dynamics, Springer-Verlag, London, 2010.

    　

Patents
  • System and method for operating power systems utilizing optimal power flow, US Patent, US 6625520 B1. September 23, 2003.
  • Decomposition method for nodal prices in power systems, Japan, JP 2000-72531. March 15, 2000.
  • Computational method of transfer capability for transmission systems, Japan, JP 2001- 143699, 2001.
　
Editorial Board at Academic Journals
  • Editorial Board Member, Journal of Molecular Cell Biology
  • Editorial Board Member, Journal of Royal Society Interface
  • Editorial Board Member, PLoS ONE
Academic Activities (Societies)
  • Chair, Technical Committee on Systems Biology, IEEE SMC Society (Systems, Man and Cybernetics Society),

  • President, Computational Systems Biology Society of ORS China.
Book Chapters
　
  • Bioinformatics Methods for Protein Identification Using Peptide Mass Fingerprinting
    Z. Song, L. Chen, D. Xu
    in Proteome bioinformatics: Informatics for mass-spectrometry based protein science
    The Human Press, Nov. 2009.
  • Inferring Gene Regulatory Networks from Genetical Genomics data
    Y. Wang, R. Wang, T. Joshi, X-S. Zhang, D. Xu, L. Chen
    in Handbook of Research on Computational Methodologies in Gene Regulatory Networks
    IGI Global, October, 2009
  • Protein Function Prediction with Data Mining Techniques.
    X-M. Zhao, L. Chen.
    in Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications
    John Wiley & Sons, June, 2010.
  • Computational Models for Condition Specific Gene and Pathway Inference
    Y-Q. Qiu, S. Zhang, X-S. Zhang, L. Chen
    in Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications
    John Wiley & Sons, 2010
　
　
　

Journal Papers

　

专著：

  1. Luonan Chen, Ruisheng Wang, Xiang-Sun Zhang, Biomolecular Networks: Methods and Applications in Systems Biology, John Wiley & Sons, 2009.
  2. Luonan Chen, Ruiqi Wang, Chunguang Li, Kazuyuki Aihara, Modelling Biomolecular Networks in Cells: Structures and Dynamics, Springer-Verlag, London, 2010.
  3. 平田祥子，陈洛南，合原一幸. 非线性时序列解析的理论基础，东京大学出版会， 2023.
  4. 陈洛南，刘锐，马欢飞，史际帆. 动力学刻画的数据科学理论与方法，科学出版社，2023.

 

论文：

  1. Fei Li, Xudong Xing, Qiqi Jin, Xiang-Ming Wang, Pengfei Dai, Ming Han, Huili Shi, Ze Zhang, Xianlong Shao, Yunyi Peng, Yiqin Zhu, Jiayi Xu, Dan Li, Yu Chen, Wei Wu, Qiao Wang, Chen Yu*, Luonan Chen*, Fan Bai*, Dong Gao*. Sex differences orchestrated by androgens at single-cell resolution. Nature, DOI:10.1038/s41586-024-07291-6, 2024.
  2. Chunman Zuo, Luonan Chen*. Dissecting tumor microenvironment from spatially resolved transcriptomics data by heterogeneous graph learning. Nature Communications, in press, 2024.
  3. Junchao Zhu, Hao Dai, Luonan Chen*. Revealing cell-cell communication pathways with their spatially coupled gene programs. Briefings in Bioinformatics, 2024.
  4. Yun Xue, Yuting Chen, Sijia Sun, Xinyuan Tong, Yujia Chen, Shijie Tang, Xue Wang, Simin Bi, Yuqing Qiu, Qiqi Zhao, Zhen Qin, Qin Xu, Yingjie Ai, Leilei Chen, Beizhen Zhang, Zhijie Liu, Minbiao Ji, Meidong Lang, Luonan Chen*, Guoliang Xu*, liang Hu*, Dan Ye*, and Hongbin Ji*. TET2-STAT3-CXCL5 nexus promotes neutrophil lipid transfer to fuel lung adeno-to-squamous transition. Journal of Experimental Medicine, 2024.
  5. Rong Gao, Peiluan Li, Luonan Chen*. mNFE: Microbiome network flow entropy for detecting pre.disease states of type 1 diabetes. Gut Microbes, 16:1, 2327349, 2024.
  6. Yulan Deng, Liang Xia, Jian Zhang, Senyi Deng, Mengyao Wang, Shiyou Wei, Kaixiu Li, Hongjin Lai, Yunhao Yang, Yuquan Bai, Yongcheng Liu, Lanzhi Luo, Zhenyu Yang, Yaohui Chen, Ran Kang, Fanyi Gan, Qiang Pu, Jiandong Mei, Lin Ma, Feng Lin, Chenglin Guo, Hu Liao, Yunke Zhu, Zheng Liu, Chengwu Liu, Yang Hu, Yong Yuan, Zhengyu Zha, Gang Yuan, Gao Zhang, Luonan Chen, Qing Cheng, Shensi Shen, Lunxu Liu, Multicellular ecotypes shape progression of lung adenocarcinoma from ground-glass opacity toward advanced stages, Cell Reports Medicine, 101489, https://doi.org/10.1016/j.xcrm.2024.101489, 2024.
  7. Zijian Wang, Peng Tao, Luonan Chen*. Brain-inspired Chaotic Spiking Backpropagation. National Science Review, https://doi.org/10.1093/nsr/nwae0372024,2024.
  8. Chunchun Yuan, Xiang-Tian Yu, Jing Wang, Bing Shu, Xiao-Yun Wang, Chen Huang, Xia Lv, Qian-Qian Peng, Wen-Hao Qi, Jing Zhang, Yan Zheng, Si-Jia Wang, Qian-Qian Liang, Qi Shi,Ting Li, He Huang, Zhen-Dong Mei, Hai-Tao Zhang, Hong-Bin Xu, Jiarui Cui, Hongyu Wang, Hong Zhang, Bin-Hao Shi, Pan Sun, Hui Zhang, Zhao-Long Ma, Yuan Feng, Luonan Chen*, Tao Zeng*, De-Zhi Tang* and Yong-Jun Wang*. Multi-modal molecular determinants of clinically relevant osteoporosis subtypes. Cell Discovery, 10:28, 2024.
  9. Xinyuan Tong, Ayushi S. Patel, Eejung Kim, Hongjun Li, Yueqing Chen, Shuai Li, Shengwu Liu, Julien Dilly, Kevin S. Kapner, Ningxia Zhang, Yun Xue, Laura Hover, Suman Mukhopadhyay, Fiona Sherman, Khrystyna Myndzar, Priyanka Sahu, Yijun Gao, Fei Li, Fuming Li, Zhaoyuan Fang, Yujuan Jin, Juntao Gao, Minglei Shi, Satrajit Sinha, Luonan Chen, Yang Chen, Thian Kheoh, Wenjing Yang, Itai Yanai, Andre L. Moreira, Vamsidhar Velcheti, Benjamin G. Neel, Liang Hu, James G. Christensen, Peter Olson, Dong Gao, Michael Q. Zhang, Andrew J. Aguirre, Kwok-Kin Wong, Hongbin Ji. Adeno-to-squamous transition drives resistance to KRAS inhibition in LKB1 mutant lung cancer, Cancer Cell, 2024, https://doi.org/10.1016/j.ccell.2024.01.012.
  10. Peng Jin, Xiaoling Wang, Qiqi Jin, Yi Zhang, Jie Shen, Ge Jiang, Hongming Zhu, Ming Zhao,  Dan Wang, Zeyi Li, Yan Zhou, Wenzhu Li, Wei Zhang, Yabin Liu, Siyang Wang, Wen Jin, Yuncan Cao,Guangying Sheng, Fangyi Dong, Shishuang Wu, Xiaoyang Li, Zhen Jin, Mengke He, Xiaxin Liu, Luonan Chen*, Yunxiang Zhang*, Kankan Wang*, Junmin Li*. Mutant U2AF1-induced mis-splicing of mRNA translation genes confers resistance to chemotherapy in acute myeloid leukemia. Cancer Research, https://doi.org/10.1158/0008-5472.can-23-2543, 2024.
  11. Yanjing Zhu, Shijie Tang, Qiuyue Yuan, Jing Fu, Juan He, Zhuang Liu, Xiaofang Zhao, Yunguang Li, Yan Zhao, Yani Zhang, Xiaoyu Zhang, Yangqianwen Zhang, Yiqin Zhu, Wenwen Wang, Bo Zheng, Rui Wu, Tong Wu, Shuai Yang, Xinyao Qiu, Siyun Shen, Ji Hu, Luonan Chen*, Yong Wang*, Hongyang Wang*, Dong Gao*, Lei Chen*. Integrated Characterization of Hepatobiliary Tumor Organoids Provides Potential Landscape of Pharmacogenomic Interactions. Cell Reports Medicine, 5:101375, 2024.
  12. Zhen Qin, Meiting Yue, Shijie Tang, Fengying Wu, Honghua Sun, Yuan Li, Yongchang Zhang, Hiroki Izumi, Hsinyi Huang, Wanying Wang, Yun Xue, Xinyuan Tong, Shunta Mori, Tetsuro Taki, Koichi Goto, Yujuan Jin, Fei Li, Fu-Ming Li, Yijun Gao, Zhaoyuan Fang, Yisheng Fang, Liang Hu, Xiumin Yan, Guoliang Xu, Haiquan Chen, Susumu S Kobayashi, Ventura Andrea, Kwok-Kin Wong, Xueliang Zhu, Liang Chen, Shengxiang Ren, Luonan Chen*, Hongbin Ji*. EML4-ALK fusions drive lung adeno-to-squamous transdifferentiation through phase separation-mediated JAK-STAT activation. Journal of Experimental Medicine, 221(3):e20232028, 2024.
  13. Lu Wang, Luonan Chen*. NetNiche: microbe-metabolite network reconstruction and microbial niche analysis. Phenomics, 2023.
  14. Ying Li, Yuejing Lu, Chen Kang, Peiluan Li, and Luonan Chen*. Revealing Tissue Heterogeneity and Spatial Dark Genes from Spatially Resolved Transcriptomics by Multiview Graph Networks. Research, 2023;6:0228,https://doi.org/10.34133/research.0228.
  15. Chihao Zhang,Kangning Dong, Kazuyuki Aihara, Luonan Chen* and Shihua Zhang. S TAMarker: det ermining spatial domain-specific variable genes with saliency maps in deep learning. Nucleic Acids Research, 2023, 1–13, https://doi.org/10.1093/nar/gkad801.
  16. Lulu Zhang, Fang Du, Qiqi Jin, Li Sun, Boqian Wang, Ziyang Tan, Xinyu Meng, Baozhen Huang, Yifan Zhan, Luonan Chen*, Xiaoxiang Chen*, Xianting Ding*. Identification and characterization of CD8+CD27+CXCR3- T cell dysregulation and progression-associated biomarkers in systemic lupus erythematosus. DOI: 10.1002/advs.202300123, Advanced Science, 2023.
  17. Yunguang Li, Shijie Tang, Xiaohan Shi, Jingwen Lv, Xueyuan Wu, Yehan Zhang, Huan Wang, Juan He, Yiqin Zhu, Yi Ju, Yajuan Zhang, Shiwei Guo, Weiwei Yang*, Huiyong Yin*, Luonan Chen*, Dong Gao*, Gang Jin*. Metabolic classification suggests GLUT1/ALDOB/G6PD axis as a therapeutic target in chemotherapy-resistant pancreatic cancer. Cell Reports Medicine, 4:101162, 2023.
  18. Chengming Zhang, Yiwen Yang, Shijie Tang, Kazuyuki Aihara, Chuanchao Zhang and Luonan Chen*. Contrastively generative self-expression model for single-cell and spatial multimodal data. Briefings in Bioinformatics, 24(5):bbad265. doi: 10.1093/bib/bbad265, 2023.
  19. Hao Jiang,Senwen Zhan, Wai-Ki Ching, Luonan Chen*. Robust joint clustering of multi-omics single-cell data via multi-modal high-order neighborhood Laplacian Matrix optimization, Bioinformatics, https://doi.org/10.1093/bioinformatics/btad414, 2023.
  20. Lin Li, Rui Xia, Wei Chen, Luonan Chen*. Single-cell causal network inferred by cross-mapping entropy. Briefings in Bioinformatics,https://doi.org/10.1093/bib/bbad281,2023.
  21. Yuyan Tong, Renhao Hong, Ze Zhang, Kazuyuki Aihara, Pei Chen, Rui Liu, Luonan Chen*. Earthquake alerting based on spatial geodetic data by spatiotemporal information transformation learning, PNAS, Vol. 120, No. 37 e2302275120, 2023.
  22. Tao Jiang, Qiqi Jin, Jiahao Wang, fengying wu, Jiang Chen, Gongyan Chen, yunchao huang, Jianhua Chen, Ying Cheng, Qiming Wang, Yueyin Pan, Jianying Zhou, Jianhua Shi, Xingxiang Xu, Lizhu Lin, Wei Zhang, Yiping Zhang, Yunpeng Liu, Yong Fang, Jifeng Feng, Zhe-Hai Wang, Sheng Hu, Jian Fang, yongqian shu, Jiuwei Cui, Yi Hu, Wenxiu Yao, Xingya Li, Xiaoyan Lin, Rui Wang, Yongsheng Wang, Wei Shi, Gaohua Feng, Jun Ni, Beibei Mao, Dandan Ren, Huaibo Sun, Henghui Zhang, Luonan Chen*, Caicun Zhou*, and Shengxiang Ren*. HLA-I evolutionary divergence confers response to PD-1 blockade plus chemotherapy in untreated advanced non-small-cell lung cancer, Clinical Cancer Research, doi: 10.1158/1078-0432.CCR-23-0604, 2023.
  23. Zu-Qiang Liu, Hao Dai, Lu Yao, Wei-Feng Chen, Yun Wang, Li-Yun Ma, Xiao-Qing Li, Sheng-Li Lin, Meng-Jiang He, Ping-Ting Gao, Xin-Yang Liu, Jia-Xin Xu, Xiao-Yue Xu, Ke-Hao Wang, Li Wang, Luonan Chen*, Ping-Hong Zhou*, Quan-Lin Li*. A Single-Cell Transcriptional Landscape of Immune Cells in Human Achalasia. Nature Communications, 14: 4685, 2023.
  24. Xiaofei Zhang, Yi-Xuan Xiong, Meng-Guo Wang, Luonan Chen*. Cell-type Annotation with Accurate Unseen Cell-type Identification Using Multiple References, PLOS Computational Biology, https://doi.org/10.1371/journal.pcbi.1011261, 2023.
  25. Shijie Tang, Yun Xue, Zhen Qin, Zhaoyuan Fang, Yihua Sun, Chongzhe Yuan, Yunjian Pan, Yue Zhao, Xinyuan Tong, Jian Zhang, Hsinyi Huang, Yuting Chen, Liang Hu, Dasong Huang, Ruiqi Wang, Weiguo Zou, Yuan Li, Roman K Thomas, Andrea Ventura, Kwok-Kin Wong, Haiquan Chen, Luonan Chen*, Hongbin Ji. Counteracting lineage-specific transcription factor network finely tunes lung adeno-to-squamous transdifferentiation through remodeling tumor immune microenvironment. National Science Review, https://doi.org/10.1093/nsr/nwad028, 2023.
  26. Peng Tao, Jifan Shi, Luonan Chen*. Detecting dynamical causality by intersection cardinal concavity. Fundamental Research, https://doi.org/10.1016/j.fmre.2023.01.007, 2023.
  27. Peiluan Li, Luonan Chen*. Disease Prediction by Network Information Gain on a Single Sample Basis. Fundamental Research, https://doi.org/10.1016/j.fmre.2023.01.009, 2023.
  28. Yilin Xu,Jinglin Wang, Haozhen Ren, Hao Dai, Ying Zhou,Xiongzhao Ren, Yang Wang, Sisi Feng, Xiaogang Deng,Jiaying Wu, Tianlong Fu,Tengfei Nie, Haifeng He, Tongkun Wei, Bing Zhu, Lijian Hui, Bin Li, Jing Wang,Hongyan Wang, Luonan Chen*, Xiaolei Shi and Xin Cheng. Human endoderm stem cells reverse inflammation-related acute liver failure through cystatin SN-mediated inhibition of interferon signaling. Cell Research, https://doi.org/10.1038/s41422-022-00760-5, 2023.
  29. Hao Peng, Pei Chen, Rui Liu, Luonan Chen*. Spatiotemporal information conversion machine for time-series prediction. Fundamental Research, https://doi.org/10.1016/j.fmre.2022.12.009, 2023.
  30. Lin Li, Yilin Xu, Lili Yan, Xiao Li, Fei Li, Zhuang Liu, Chuanchao Zhang, Lou Yuan, Dong Gao, Xin Cheng, Luonan Chen*. Dynamic Network Biomarker Factors Orchestrate Cell Fate Determination at Tipping Points during hESC Differentiation. THE INNOVATION, https://doi.org/10.1016/j.xinn.2022.100364, 2023.
  31. Zhaoyuan Fang, Xiangkun Han, Yueqing Chen, Xinyuan Tong, Yun Xue, Shun Yao, Shijie Tang, Yunjian Pan, Yihua Sun, Xue Wang, Yujuan Jin, Haiquan Chen, Liang Hu, Lijian Hui, Lin Li, Luonan Chen*, Hongbin Ji*. Oxidative stress-triggered Wnt signaling perturbation characterizes the tipping point of lung adeno-to-squamous transdifferentiation. Signal Transduction and Targeted Therapy, DOI : 10.1038/s41392-022-01227-0, 2023.
  32. Peng Tao, Xiaohu Hao,Jie Cheng and Luonan Chen*. Predicting Time Series by Data-Driven Spatiotemporal Information Transformation. Information Sciences, https://doi.org/10.1016/j.ins.2022.11.159, 2022.
  33. Hong Yu,Li Li, Anthony Huffman, John Beverley, Junguk Hur, Eric Merrel, Hsin-hui Huang, Yang Wang, Yingtong Liu, Edison Ong, Liang Cheng, Tao Zeng, Jingsong Zhang,Pengpai Li, Zhiping Liu, Zhigang Wang,Xiangyan Zhang,Xianwei Ye,Samuel K. Handelman,Jonathan Sexton,Kathryn Eaton,Gerry Higgins,Gilbert S. Omenn,Brian Athey,Barry Smith,Luonan Chen*,Yongqun He*. A New Framework for Host-Pathogen Interaction Research. Frontiers in Immunology, 2022.
  34. Javed Akhtar,Yukun Han,Shangchen Han, Weiping Lin,Chenyu Cao,Ruowen Ge, Isaac A. Babarinde4,Qingzhao Jia,Yueyang Yuan, Guangming Chen,Yajie Zhao, Richard Ye, Guozhen Liu, Luonan Chen*, Guanyu Wang*. Bistable insulin response: the win-win solution for glycemic control. ISCIENCE,25,105561,2022.
  35. Yujie You, Le Zhang, Peng Tao, Suran Liu, and Luonan Chen*. Spatiotemporal Transformer Neural Network for Time-Series Forecasting. Entropy, 24:1651, https://doi.org/10.3390/e24111651, 2022.
  36. Chunman Zuo, Yijian Zhang, Chen Cao, Jinwang Feng, Mingqi Jiao, and Luonan Chen*. Elucidating tumor heterogeneity from spatially resolved transcriptomics data by multi-view graph collaborative learning. Nature Communications, DOI:10.1038/s41467-022-33619-9, 2022.
  37. Yiyu Lu,Meiyi Li, Qianmei Zhou, Dongdong Fang, Rong Wua, Qingya Lie, LuonanChen, Shibing Su. Dynamic network biomarker analysis and system pharmacology methods to explore the therapeutic effects and targets of Xiaoyaosan against liver cirrhosis. Journal of Ethnopharmacology, 294:115324. doi: 10.1016/j.jep.2022.115324, 2022.
  38. Peng Tao, Jie Cheng, Luonan Chen*. Brain-inspired chaotic backpropagation for MLP. Neural Networks, https://doi.org/10.1016/j.neunet.2022.08.004, 2022.
  39. Shijie Tang, Kai Yuan, Luonan Chen*. Molecular biomarkers, network biomarkers, and dynamic network biomarkers for diagnosis and prediction of rare diseases. Fundamental Research, https://doi.org/10.1016/j.fmre.2022.07.011, 2022.
  40. Huijie Miao, Yajun Geng, Yang Li, Shijie Tang, Feiling Feng, Weijian Li, Yongsheng Li, Liguo Liu, Rui Zhang, Shimei Qiu, Ying Wu, Zeyu Wang, Ziyi Wang, Ziyu Shao, Ke Liu, Lu Zou, Mao Yang, Yuhao Zhao, Chen Chen, Zhizhen Li, Dadong Zhang, Peng Peng, Xiaoyan Qiang, Frank Wu, Yongning He, Luonan Chen, Dongxi Xiang, Xiaoqing Jiang, Maolan Li, Yun Liu, Yingbin Liu. Novel Protein Kinase Inhibitor TT-00420 Inhibits Gallbladder Cancer by Inhibiting JNK/JUN-mediated Signaling Pathway. Cellular Oncology, 2022.
  41. Qiqi Jin,Chunman Zuo,Haoyue Cui,Lin Li,Yiwen Yang,Hao Dai,Luonan Chen*. Single-cell entropy network detects the activity of immune cells based on ribosomal protein genes. Computational and Structural Biotechnology Journal, 20,3556–3566, 2022.
  42. Jifan Shi, Kazuyuki Aihara, Tiejun Li, Luonan Chen*. Energy landscape decomposition for cell differentiation with proliferation effect. National Science Review, https://doi.org/10.1093/nsr/nwac116, 2022.
  43. Jining Wang, Chuan Chen, Zibin Zheng, Luonan Chen, Yuren Zhou. Predicting high-dimensional time series data with spatial, temporal and global information. Information Sciences, 607: 477-492, 2022.
  44. Yu Zhang, Xiao Chang, Jie Xia, Yanhong Huang, Shaoyan Sun, Luonan Chen*, Xiaoping Liu*. Identifying network biomarkers of cancer by sample-specific differential network. BMC Bioinformatics, https://doi.org/10.1186/s12859-022-04772-1, 2022.
  45. Chenxi Song,Zheng Qiao, Luonan Chen, Jing Ge, Sheng Yuan, Xiaohui Bian, Chunyue Wang, Qianqian Liu, Rui Fu and Kefei Dou. Identification of Key Genes as Early Warning Signals of Acute Myocardial Infarction Based on Weighted Gene Correlation Network Analysis and Dynamic Network Biomarker Algorithm. Frontiers in Immunology, doi: 10.3389/fimmu.2022.879657, 2022.
  46. Chenchen Guo, Ruijie Wan, Yayi He, Shu-Hai Lin, Jiayu Cao, Ying Qiu, Tengfei Zhang, Qiqi Zhao, Yujia Niu, Yujuan Jin, Hsin-Yi Huang, Xue Wang, Li Tan, Roman K. Thomas, Hua Zhang, Luonan Chen, Kwok-Kin Wong, Liang Hu & Hongbin Ji. Therapeutic targeting of the mevalonate–geranylgeranyl diphosphate pathway with statins overcomes chemotherapy resistance in small cell lung cancer. Nature Cancer, https://doi.org/10.1038/s43018-022-00358-1, 2022.
  47. Chenxi Song, Zheng Qiao, Luonan Chen, Jing Ge, Sheng Yuan, Xiaohui Bian, Chunyue Wang, Qianqian Liu, Rui Fu and Kefei Dou. Identification of key genes as early warning signals of acute myocardial infarction based on weighted gene correlation network analysis and dynamic network biomarker algorithm. Frontiers in Immunology, 2022.
  48. Rong Gao, Jinling Yan, Peiluan Li and Luonan Chen*. Detecting the critical states during disease development based on temporal network flow entropy. Briefings in Bioinformatics,https://doi.org/10.1093/bib/bbac164, 2022.
  49. Jinwang Feng, Shao-Wu Zhang, Chunman Zuo, Luonan Chen*. Detection of Alzheimer's Disease Using Features of Brain Region-of-Interest-Based Individual Network Constructed with the sMRI Image. Computerized Medical Imaging and Graphics, https://doi.org/10.1016/j.compmedimag.2022.102057, 2022.
  50. Jifan Shi, Kazuyuki Aihara, Luonan Chen*. Embedding entropy: a nonlinear measure of dynamical causality. J. R. Soc. Interface. https://doi.org/10.1098/rsif.2021.0766, 2022.
  51. Runtan Cheng, Lu Wang, Shenglong Le, Yifan Yang, Can Zhao, Xiangqi Zhang, Xin Yang, Ting Xu, Leiting Xu, Petri Wiklund, Jun Ge, Dajiang Lu, Chenhong Zhang, Luonan Chen*, Sulin Cheng*. Response of microbiome network to exercise and diet intervention in nonalcoholic fatty liver disease. Nature Communications, 13, No.2555, 2022.
  52. Jifan Shi, Kenji Kirihara, Mariko Tada, Mao Fujioka, Kaori Usui, Daisuke Koshiyama, Tsuyoshi Araki, Luonan Chen, Kiyoto Kasai, Kazuyuki Aihara. Criticality in the Healthy Brain. Frontiers in Network Physiology, https://doi.org/10.3389/fnetp.2021.755685, 2022.
  53. Yiwei Meng, Yanhong Huang, Xiao Chang, Xiaoping Liu and Luonan Chen*. Transcriptome analysis method based on differential distribution evaluation. Briefings in Bioinformatics, https://doi.org/10.1093/bib/bbab608, 2022.
  54. Chengming Zhang, Yabin Chen, Tao Zeng, Chuanchao Zhang, Luonan Chen*. Deep latent space fusion for adaptive representation of heterogeneous multi-omics data. Briefings in Bioinformatics, https://doi.org/10.1093/bib/bbab600, 2022.
  55. Jason Cheok Kuan Leong, Yongxin Li, Masahiro Uesaka, Yui Uchida, Akihito Omori, Meng Hao, Wenting Wan, Yang Dong, Yandong Ren, Si Zhang, Tao Zeng, Fayou Wang, Luonan Chen, Gary Wesse, Brian T Livingston, Cynthia Bradham, Wen Wang, Naoki Irie. Derivedness Index for Estimating Degree of Phenotypic Evolution of Embryos: A Study of Comparative Transcriptomic Analyses of Chordates and Echinoderms. Front Cell Dev Biol. 2021;9:749963. doi: 10.3389/fcell.2021.749963.
  56. Junbo Jia, Luonan Chen*. Single-cell RNAsequencing data analysis based on nonuniform epsilon-neighborhood network. Bioinformatics, DOI: 10.1093/bioinformatics/btac114, 2022.
  57. Xiaohan Shi, Yunguang Li, Qiuyue Yuan, Shijie Tang, Shiwei Guo, Yehan Zhang, Juan He, Xiaoyu Zhang, Ming Han, Zhuang Liu, Yiqin Zhu, Suizhi Gao, Huan Wang, Xiongfei Xu, Kailian Zheng, Wei Jing, Luonan Chen*, Yong Wang*, Gang Jin*, and Dong Gao*. Integrated profiling of human pancreatic cancer organoids reveals chromatin accessibility to drug sensitivity networks. Nature Communications. 2022
  58. Cara L Green, Sharon E Mitchell, Davina Derous, Libia A García-Flores, Yingchun Wang, Luonan Chen, Jing-Dong J Han, Daniel E L Promislow, David Lusseau, Alex Douglas, John R Speakman. The Effects of Graded Levels of Calorie Restriction: XVI. Metabolomic Changes in the Cerebellum Indicate Activation of Hypothalamocerebellar Connections Driven by Hunger Responses. J Gerontol A Biol Sci Med Sci. 2021;76(4):601-610. doi: 10.1093/gerona/glaa261.
  59. Zemin Hou, Tao Yang, Zejie Mei, Si Zhang, Yuanyuan Gao, Xi Chen, Qilong Tan, Xuyou Zhu, Chengdang Xu, Jianpo Lian, Cuidong Bian, Ying Liu, Wei Le, Nazarov Hydyr, Denglong Wu, Luonan Chen, Shengsong Huang, Zhenfei Li. Tracing steroidogenesis in prostate biopsy samples to unveil prostate tissue androgen metabolism characteristics and potential clinical application. J Steroid Biochem Mol Biol. 2021 Jun;210:105859. doi: 10.1016/j.jsbmb.2021.105859.
  60. Jie Xia, Lequn Wang, Guijun Zhang, Chunman Zuo and Luonan Chen*. RDAClone: Deciphering Tumor Heterozygosity through Single-Cell Genomics Data Analysis with Robust Deep Autoencoder. Genes, 12(12), 2021.
  61. Lin Li, Hui Tang, Rui Xia, Hao Dai, Rui Liu and Luonan Chen*. Intrinsic entropy model for feature selection of scRNA-seq data, Journal of Molecular Cell Biology, 2021.
  62. Luonan Chen*, Rong Fan, Ruchou Tang. Advanced single-cell omics technologies and informatics tools for genomics, proteomics and bioinformatics analysis. Genomics, Proteomics and Bioinformatics, 2021.
  63. Kazuyuki Aihara, Rui Liu, Keiichi Koizumi, Xiaoping Liu, and Luonan Chen*. Dynamical Network Biomarkers: Theory and Applications. https://doi.org/10.1016/j.gene.2021.145997, GENE, 2021.
  64. Yabin Chen, Zhaoyuan Fang, Ying Tang, Yujuan Jin, Chenchen Guo, Liang Hu, Yang Xu, Xidong Ma, Jie Gao, Mei Xie, Xuelei Zang, Sanhong Liu, Haiquan Chen, Roman K Thomas, Xinying Xue, Hongbin Ji, Luonan Chen*. Integrative analysis of multi-omics data reveals the heterogeneity and signatures of immune therapy for small cell lung cancer. Clinical and Translational Medicine, https://doi.org/10.1002/ctm2.620, 2021.
  65. Chengming Zhang, Hong Zhang, Jing Ge, Tingyan Mi, Xiao Cui, Fengjuan Tu, Xuelan Gu, Tao Zeng and Luonan Chen*. Landscape dynamic network biomarker analysis reveals the tipping point of transcriptome reprogramming to prevent skin photodamage. https://doi.org/10.1093/jmcb/mjab060, Journal of Molecular Cell Biology, 2021.
  66. Shutao He,Hongxia Wang,Xiaomeng Hao,Yinliang Wu,Xiaofeng Bian,Minhao Yin,Yandi Zhang,Weijuan Fan,Hao Dai,Ling Yuan,Peng Zhang, Luonan Chen*. Dynamic network biomarker analysis discovers IbNAC083 in the initiation and regulation of sweet potato root tuberization.  https://doi.org/10.1111/tpj.15478, The Plant Journal, 2021.
  67. Caicun Zhou, Tao Jiang, pingyang wang, Jie Zhang, Yanqiu Zhao, Jianying Zhou, Yun Fan, Yongqian Shu, Xiaoqing Liu, Helong Zhang, Jianxing He, Guanghui Gao, Xiaoqian Mu, Zhang Bao, Yanjun Xu, Renhua Guo, Hong Wang, Lin Deng, Ningqiang Ma, Yalei Zhang, Chunxia Su, Sheng Yao, Jiarui Wu, Luonan Chen*, and Shengxiang Ren*. Toripalimab plus chemotherapy as second-line treatment in previously EGFR-TKIs treated patients with EGFR-mutant advanced NSCLC: a multi-center phase II trial. Signal Transduction and Targeted Therapy, 2021.
  68. Huanfei Ma, Siyang Leng, Luonan Chen*. Detecting High-Dimensional Causal Networks Using Randomly Conditioned Granger Causality. CSIAM Trans. Appl. Math., 2:680-696. 2021.
  69. Yijian Zhang, Chunman Zuo, Liguo Liu, Yunping Hu, Bo Yang, Shimei Qiu, Yang Li, Dongyan Cao, Zheng Ju, Jing Ge, Qiu Wang, Ting Wang, Lu Bai, Yang Yang, Guoqiang Li, Ziyu Shao, Yuan Gao, Yongsheng Li, Rui Bian, Huijie Miao, Lin Li, Xuechuan Li, Chengkai Jiang, Siyuan Yan, Ziyi Wang, Zeyu Wang, Xuya Cui, Wen Huang, Dongxi Xiang, Congjun Wang, Qiyun Li, Xiangsong Wu, Wei Gong, Yun Liu, Rong Shao, Fatao Liu, Maolan Li, Luonan Chen*, Yingbin Liu*. Single-cell RNA-sequencing atlas reveals an MDK-dependent immunosuppressive environment in ErbB pathway-mutated gallbladder cancer. Journal of Hepatology, https://doi.org/10.1016/j.jhep.2021.06.023, 2021.
  70. Rui Liu, Kazuyuki Aihara, Luonan Chen*. Collective fluctuation implies imminent state transition. Physics of Life Reviews, 37:103-107, 2021.
  71. Chunman Zuo, Hao Dai, Luonan Chen*. Deep cross-omics cycle attention model for joint analysis of single-cell multi-omics data. Bioinformatics, https://doi.org/10.1093/bioinformatics/btab403, 2021.
  72. Lu Wang,Yi-Ning Xu,Chung-Ching Chu,Zehua Jing,Yabin Chen,Jinsong Zhang,Mingming Pu, Tingyan Mi, Yaping Du, Zongqi Liang, Chandraprabha Doraiswamy, Tao Zeng, Jiarui Wu,Luonan Chen*. Facial skin microbiota mediated host response to pollution stress revealed by microbiome networks of individual. mSystems, 6(4):e0031921, 2021.
  73. Jinling Yan, Peiluan Li, Rong Gao, Ying Li, Luonan Chen*. Identifying critical states of complex diseases by single-sample Jensen-Shannon divergence. Frontiers in Oncology, 11:1824, 2021.
  74. Jingsong Zhang, Yang Zhang, Junyan Kang, Shuiye Chen, Yongqun He, Benhao Han, Mofang Liu, Lina Lu, Li Li, Zhigang Yi, and Luonan Chen*.Potential transmission chains of variant B.1.1.7 and co-mutations of SARS-CoV-2. Cell Discovery, 2021.
  75. Rui Liu, Jiayuan Zhong, Renhao Hong, Ely Chen, Kazuyuki Aihara, Pei Chen, Luonan Chen*. Predicting local COVID-19 outbreaks and infectious disease epidemics based on landscape network entropy. Science Bulletin,  https://doi.org/10.1016/j.scib.2021.03.022, 2021.
  76. Jifan Shi, Kazuyuki Aihara and Luonan Chen*. Dynamics-based data science in biology. doi: 10.1093/nsr/nwab029, National Science Review, 2021.
  77. Jinwang Feng, Shao-Wu Zhang, Luonan Chen*, Jie Xia. Alzheimer’s disease classification using features extracted from nonsubsampled contourlet subband-based individual networks. Neurocomputing, 421:260–272, 2021.
  78. Xue Wang, Yuetong Wang, Zhaoyuan Fang, Hua Wang，Jian Zhang，Longfu Zhang，Hsinyi Huang，Zhonglin Jiang, Yujuan Jin，Xiangkun Han, Shenda Hou, Bin Zhou, Feilong Meng, Luonan Chen, Kwok-Kin Wong, Jinfeng Liu, Zhiqi Zhang, Xin Zhang, Haiquan Chen, Yihua Sun, Liang Hu, Hongbin Ji. Targeting HSPA1A in ARID2-deficient lung adenocarcinoma. National Science Review, https://doi.org/10.1093/nsr/nwab014, 2021.
  79. Jinwang Feng, Shao-Wu Zhang, Luonan Chen*. Extracting ROI-Based Contourlet Subband Energy Feature from the sMRI Image for Alzheimer's Disease Classification. IEEE/ACM Transactions on Computational Biology and Bioinformatics, DOI: 10.1109/TCBB.2021.3051177, 2021.
  80. Yidi Sun, Chen Li, Shichao Pang, Qianlan Yao, Luonan Chen*, Yixue Li*, Rong Zeng*. Kinase-substrate Edge Biomarkers Provide A More Accurate Prognostic Prediction in ER-negative Breast Cancer. Genomics, Proteomics & Bioinformatics, https://doi.org/10.1016/j.gpb.2019.11.012, 2021.
  81. Zemin Hou, Tao Yang, Zejie Mei, Si Zhang, Yuanyuan Gao, Xi Chen, Qilong Tan, Xuyou Zhu, Chengdang Xu, Jianpo Lian, Cuidong Bian, Ying Liu, Wei Le, Nazarov Hydyr, Denglong Wu, Luonan Chen*, Shengsong Huang, Zhenfei Li. Tracing steroidogenesis in prostate biopsy samples to unveil prostate tissue androgen metabolism characteristics and potential clinical application. The Journal of Steroid Biochemistry and Molecular Biology, https://doi.org/10.1016/j.jsbmb.2021.105859, 2021.
  82. Wei-Feng Guo, Shao-Wu Zhang, Yue-Hua Feng, Jing Liang, Tao Zeng and Luonan Chen*. Network controllability-based algorithm to target personalized driver genes for discovering combinatorial drugs of individual patients. Nucleic Acids Research, doi: 10.1093/nar/gkaa1272, 2021.
  83. Weijun Jiang, Jiajia Shi, Jingjie Zhao, Qiu Wang, Dan Cong, Fenghua Chen, Yu Zhang, Yuhan Liu, Junzheng Zhao, Qian Chen, Linhao Gu, Wenjia Zhou, Chenhang Wang, Zhaoyuan Fang, Shuhui Geng, Wei Xie, Luo-Nan Chen, Yang Yang,Yun Bai, Haodong Lin, Xiajun Li. ZFP57 dictates allelic expression switch of target imprinted genes. PNAS, 118 (5) e2005377118, 2021.
  84. Jinwang Feng, Shao-Wu Zhang, Luonan Chen*. Identification of Alzheimer’s disease based on wavelet transformation energy feature of the structural MRI image and NN classifier. Artificial Intelligence In Medicine. 108:101940, 2020.
  85. Cara L Green, Sharon E Mitchell, Davina Derous, Libia A García-Flores, Yingchun Wang, Luonan Chen, Jing-Dong J Han, Daniel E L Promislow, David Lusseau, Alex Douglas, John R Speakman. The Effects of Graded Levels of Calorie Restriction: XVI. Metabolomic Changes in the Cerebellum Indicate Activation of Hypothalamocerebellar Connections Driven by Hunger Responses. The Journals of Gerontology: Series A, https://doi.org/10.1093/gerona/glaa261, 2020.
  86. Tao Jiang; Zhaoyuan Fang; Shijie Tang; Ruirui Cheng; Yanan Li; Shengxiang Ren; Chunxia Su; Weijie Min; Xianchao Guo; Wei Zhu; Henghui Zhang; Likun Hou; Yuanwei Pan; Zhigang Zhou; Jun Zhang; Guojun Zhang; Zhijian Yue; Luonan Chen*; Caicun Zhou*. Mutational landscape and evolutionary pattern of liver and brain metastasis in lung adenocarcinoma. Journal of Thoracic Oncology, https://doi.org/10.1016/j.jtho.2020.10.128, 2020.
  87. Sisi Feng, Jiaying Wu, Wei-Lin Qiu, Li Yang, Xiaogang Deng, Ying Zhou, Yabin Chen, Xiao Li, Lei Yu, Hongsheng Li, Zi-Ran Xu, Yini Xiao, Xiongzhao Ren, Ludi Zhang, Chenhua Wang, Zhen Sun, Jinglin Wang, Xiaoyan Ding, Yuelei Chen, Paul Gadue, Guoyu Pan, Mina Ogawa, Shinichiro Ogawa, Jie Na, Peilin Zhang, Lijian Hui, Hao Yin, Luonan Chen*, Cheng-Ran Xu*, and Xin Cheng*. Large-scale Generation of Functional and Transplantable Hepatocytes and Cholangiocytes from Human Endoderm Stem Cells. Cell Reports 33, 108455, 2020.
  88. Yongxin Li, Akihito Omori, Rachel L. Flores, Sheri Satterfield, Christine Nguyen, Tatsuya Ota, Toko Tsurugaya, Tetsuro Ikuta, Kazuho Ikeo, Mani Kikuchi, Jason C. K. Leong, Adrian Reich, Meng Hao, Wenting Wan, Yang Dong, Yaondong Ren, Si Zhang, Tao Zeng, Masahiro Uesaka,Yui Uchida, Xueyan Li, Tomoko F. Shibata, Takahiro Bino, Kota Ogawa, Shuji Shigenobu, Mariko Kondo, Fayou Wang, Luonan Chen, Gary Wessel, Hidetoshi Saiga, R. Andrew Cameron, Brian Livingston, Cynthia Bradham, Wen Wang and Naoki Irie. Communications Biology, 3:371, 2020.
  89. Jinsheng Guo, Weixin Liu, Zhiping Zeng, Jie Lin, Xingxin Zhang, Luonan Chen*. Tgfb3 and Mmp13 regulated the initiation of liver fibrosis progression as dynamic network biomarkers. Journal of Cellular and Molecular Medicine, http://dx.doi.org/10.1111/jcmm.16140 , 2020.
  90. Hao Dai, Qiqi Jin, Lin Li, Luonan Chen*. Reconstructing Gene Regulatory Networks in Single-cell Transcriptomic Data Analysis. Zoological Research, doi:10.24272/j.issn.2095-8137.2020.215, 2020.
  91. Yongqun He, Hong Yu, Edison Ong, Yang Wang, Yingtong Liu, Anthony Huffman, Hsin-hui Huang, John Beverley, Junguk Hur, Xiaolin Yang, Luonan Chen, Gilbert S. Omenn, Brian Athey and Barry Smith. CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis. Scientific Data volume 7: 181 (2020).
  92. Chunman Zuo, Luonan Chen*. Deep Joint-Learning Analysis Model of Single Cell Transcriptome and Open Chromatin Accessibility Data. Briefings in Bioinformatics, DOI: 10.1093/bib/bbaa287, 2020.
  93. Pei Chen, Rui Liu, Kazuyuki Aihara, Luonan Chen*. Autoreservoir computing for multistep ahead prediction based on the spatiotemporal information transformation. Nature Communications, DOI : 10.1038/s41467-020-18381-0，2020.
  94. Wangxin Guo, Lin Li, Juan He, Zhuang Liu, Ming Han, Fei Li, Xinyi Xia, Xiaoyu Zhang, Yao Zhu, Yu Wei, Yunguang Li, Rebiguli Aji, Hao Dai Hui Wei, Chunfeng Li, Yu Chen, Luonan Chen*, Dong Gao*. Single-cell transcriptomics identifies a distinct luminal progenitor cell type in the distal prostate invagination tips. Nature Genetics, Doi: 10.1038/s41588-020-0642-1, 2020.
  95. Lin Li, Hao Dai, Zhaoyuan Fang, Luonan Chen*. CCSN: Single Cell RNA Sequencing Data Analysis by Conditional Cell-specific Network. Genomics, Proteomics & Bioinformatics, DOI: 10.1101/2020.01.25.919829, 2020.
  96. Ming-Li Li, Hui Tang, Yong Shao, Ming-Shan Wang, Hai-Bo Xu, Sheng Wang, David M. Irwin, Adeniyi C. Adeola, Tao Zeng, Luonan Chen, Yan Li, Dong-Dong Wu. Evolution and transition of expression trajectory during human brain development. BMC Evolutionary Biology,  20:72, 2020.
  97. Peng Wang, Luonan Chen*. Critical transitions and tipping points in EMT. Quantitative Biology, Accepted, 2020.
  98. Siyang Leng, Huanfei Ma, J¨urgen Kurths, Ying-Cheng Lai, Wei Lin, Kazuyuki Aihara, and Luonan Chen*. Partial cross mapping eliminates indirect causal influences. Nature Communciations, 11:2632，2020.
  99. Shuo Zhang, Juan Zhao, Xiangdong Lv, Jialin Fan, Yi Lu, Tao Zeng, Hailong Wu, Luonan Chen*, Yun Zhao*. Analysis on gene modular network reveals morphogen-directed development robustness in Drosophila. Cell Discovery, 6, 43, 2020.
  100. Chaoyuan Fang, Luonan Chen*. Personalized prediction of human diseases with single-sample dynamic network biomarkers. Biomarkers in Medicine, accepted, 2020.
  101. Yanhong Huan, Xiao Chang, Yu Zhang, Luonan Chen*, Xiaoping Liu*. Disease characterization using a partial correlation-based sample-specific network. Briefings in Bioinformatics, DOI: 10.1093/bib/bbaa062,2020.
  102. Yichong Wu, Tiejun Li, Xiaoping Liu, Luonan Chen*. Differential network inference via the fused D-trace loss with cross variables. Electronic Journal of Statistics, 14:1269–1301, 2020.
  103. Zhonglin Jiang, Lina Lu, Yuwei Liu, Si Zhang, Shuxian Li, Guanyu Wang, Peng Wang, Luonan Chen*. SMAD7 and SERPINE1 as novel dynamic network biomarkers detect and regulate the tipping point of TGF-beta induced EMT. Science Bulletin, DOI:10.1016/j.scib.2020.01.013, 2020.
  104. Tianlong Liu, Hongyan Wen, Hao Li, Haochen Xu, Ning Xiao, Rui Liu, Luonan Chen, Yingying Sun, Li Song, Congxia Bai, Jing Ge, Yinhui Zhang, Jingzhou Chen. Oleic Acid Attenuates Ang II (Angiotensin II)-Induced Cardiac Remodeling by Inhibiting FGF23 (Fibroblast Growth Factor 23) Expression in Mice. Hypertension, DOI: 10.1161/hypertensionaha.119.14167, 2020.
  105. Hanah Goetz, Juan R. Melendez-Alvarez1, Luonan Chen, Xiao-Jun Tian. A plausible accelerating function of intermediate states in cancer metastasis. PLoS Computational Biology, accepted, 2020.
  106. Hui Tang, Ying Tang, Tao Zeng, Luonan Chen*. Gene expression analysis reveals the tipping points during infant brain development for human and chimpanzee. BMC Genomics, 21:74 2020.
  107. Chuan Chen, Rui Li, Lin Shu, Zhiyu He, Jining Wang, Chengming Zhang, Huanfei Ma, Kazuyuki Aihara, Luonan Chen*. Predicting Future Dynamics from Short-term Time Series by Anticipated Learning Machine. National Science Review, https://doi.org/10.1093/nsr/nwaa025, 2020.
  108. Deshun Sun, Fei Liu, Sharon E. Mitchell, Huanfei Ma, Davina Derous, Yingchun Wang, Jackie J.D. Han, Daniel E.L. Promislow, David Lusseau, Alex Douglas, John R. Speakman and Luonan Chen*. The effects of graded levels of calorie restriction XV: phase space attractors reveal distinct bahavioral phenotypes. Journal of Gerontology: Biological Sciences, accepted, 2020.
  109. Jihong Hu, Tao Zeng, Qiongmei Xia, Liyu Huang, Yesheng Zhang, Chuanchao Zhang, Yan Zeng, Hui Liu, Shilai Zhang, Guangfu Huang, Wenting Wan, Yi Ding, Fengyi Hu, Congdang Yang, Luonan Chen*, Wen Wang*. Identification of key genes for the ultrahigh yield of rice using dynamic cross-tissue network analysis. Genomics, Proteomics & Bioinformatics, 2020.
  110. Yongcui Wang, Shilong Chen, Luonan Chen, Yong Wang. Associating lncRNAs with small molecules via bilevel optimization reveals cancer-related lncRNAs. PLoS Computational Biology, accepted, 2020.
  111. Yidi Sun, Chen Li, Shichao Pang, Qianlan Yao, Luonan Chen*, Yixue Li*, Rong Zeng*. Kinase-substrate Edge Biomarkers Provide A More Accurate Prognostic Prediction in ER-negative Breast Cancer. Genomics, Proteomics & Bioinformatics, accepted, 2020.
  112. Meiyi Li, Zhiyuan Liu, Bangguo Qian, Weixin Liu, Katsuhisa Horimoto, Huarong Zhou, and Luonan Chen*. “Dysfunctions” induced by Roux-en-Y gastric bypass surgery are concomitant with metabolic improvement independent of weight loss. Cell Discovery, accepted, 2020.
  113. Huahai Qiu, Zhanjiang Yuan, Tianshou Zhou, Luonan Chen*. Different effects of fast and slow input fluctuations on output in gene regulation. Chaos, https://doi.org/10.1063/1.5133148, 2020.
  114. Rui Liu, Pei Chen, Luonan Chen*. Single-sample landscape entropy reveals the imminent phase transition during disease progression. Bioinformatics, doi.10.1093/bioinformatics/btz758, 36(5),1522–1532，2020.
  115. Meizhu Bai, Yujiao Han, Yuxuan Wu, Jiaoyang Liao, Lin Li, Lijun Wang, Qing Li, Wenhui Xing, Luonan Chen, Weiguo Zou, Jinsong Li. (2019) Targeted genetic screening in mice through haploid embryonic stem cells identifies critical genes in bone development. PLoS Biol 17(7): e3000350. https://doi.org/10.1371/journal.pbio.3000350.
  116. Wei-Feng Guo, Shao-Wu Zhang,Tao Zeng, Yan Li, Jianxi Gao, Luonan Chen*. A novel network control model for identifying personalized driver genes in cancer. PLoS Computational Biology, 15(11): e1007520. https://doi.org/10.1371/journal.pcbi.1007520, 2019.
  117. Wei-Feng Guo, Shao-Wu Zhang,Tao Zeng, Tatsuya Akutsu, Luonan Chen*. Network control principles for identifying personalized driver genes in cancer. Briefings in Bioinformatics, doi: 10.1093/bib/bbz089, 2019.
  118. Jifan Shi, Tiejun Li, Luonan Chen*, Kazuyuki Aihara*. Quantifying pluripotency landscape of cell differentiation from scRNA-seq data by continuous birth-death process. PLOS Computational Biology, https://doi.org/10.1371/journal.pcbi.1007488, 2019.
  119. Jiayin Li, Haixiang Shi, Hui Liu, Fei Dong, Zhiping Liu, Ying-Jin Lu, Luonan Chen, Lan Bao, and Xu Zhang. Nerve Injury-Induced Neuronal PAP-I Maintains Neuropathic Pain by Activating Spinal Microglia. Journal of Neuroscience, DOI: https://doi.org/10.1523/JNEUROSCI, 2019. Rui Liu, Pei Chen, Luonan Chen*. Single-sample landscape entropy reveals the imminent phase transition during disease progression. Bioinformatics, 10.1093/bioinformatics/btz758, 2019.
  120. Zhana Duren, Yaling Wang, Jiguang Wang, Xing-Ming Zhao, Le Lv, Xiaobo Li, Jingdong Liu, Xin-Guang Zhu*, Luonan Chen*, and Yong Wang*. Hierarchical graphical model reveals HFR1 bridging circadian rhythm and flower development in Arabidopsis thaliana. npj Systems Biology and Applications, 5: 28, 2019.
  121. Le Zhang, Guangdi Liu, Meijing Kong, Tingting Li, Dan Wu, Xiaobo Zhou, Chuanwei Yang, Lei Xia, Zhenzhou Yang and Luonan Chen*. Revealing dynamic regulations and the related key proteins of myeloma-initiating cells by integrating experimental data into a systems biological model. Bioinformatics, https://doi.org/10.1093/bioinformatics/btz542, 2019.
  122. Dalang Yu, Lili Dong, Fangqi Yan, Hailong Mu, Bixia Tang, Xiao Yang, Qing Zhou, Feng Gao, Zhonghuang Wang, Ziqian Hao, Hongen Kang, Yi Zheng, Hongwei Huang, Li Lan, Yuzhang Wei, Wei Pan, Yaochen Xu, Shilei Zhao, Ciran Wang, Hua Chen, Mushan Li, Zhen Shao, Yi-Xue Li, Pengyu Wang, Long Dai, Yun-Xin Fu, Yiming Bao, Luonan Chen, Fang-Qing Zhao, Guo-Qing Zhang, Wenming Zhao, Haipeng Li. eGPS 1.0 for integrating multi-omic and evolutionary analyses. National Science Review, https://doi.org/10.1093/nsr/nwz079, 2019.
  123. Jian-Huang Xue,Guo-Dong Chen,Fuhua Hao,Hui Chen,Zhaoyuan Fang,Fang-Fang Chen,Bo Pang,Qing-Lin Yang,Xinben Wei,Qiang-Qiang Fan,Changpeng Xin,Jiaohong Zhao,Xuan Deng,Bang-An Wang,Xiao-Jie Zhang,Yueying Chu,Hui Tang,Huiyong Yin,Weimin Ma,Luonan Chen, Jianping Ding,Elmar Weinhold,Rahul M. Kohli,Wen Liu,Zheng-Jiang Zhu,Kaiyao Huang,Huiru Tang,Guo-Liang Xu. A vitamin-C-derived DNA modification catalysed by an algal TET homologue. Nature, https://doi.org/10.1038/s41586-019-1160-0DO, 2019.
  124. Li Li, Ching Chiek Koh, Daniel Reker J.B. Brown, Haishuai Wang, Nicholas Keone Lee, Hien-haw Liow, Hao Dai, Huai-Meng Fan, Luonan Chen*, and Dong-Qing Wei*. Predicting protein-ligand interactions based on bow-pharmacological space and Bayesian additive regression trees. Scientific Reports, DOI: 10.1038/s41598-019-43125-6, 2019.
  125. Yong Wang, Xiang-Sun Zhang,and Luonan Chen*. Systems biology intertwines with single cell and AI. BMC Bioinformatics 2019, 20:204, https://doi.org/10.1186/s12859-019-2731-7, 2019.
  126. Yuwei Liu, Mengzhu Xue, Shaowei Du, Wanwan Feng, Ke Zhang, Liwen Zhang, Haiyue Liu, Guoyi Jia, Lingshuang Wu, Xin Hu, Luonan Chen*, and Peng Wang*. Competitive endogenous RNA is an intrinsic component of EMT regulatory circuits and modulates EMT. Nature Communications, 10:1637.  https://doi.org/10.1038/s41467-019-09649-1, 2019.
  127. Hao Dai, Lin Li, Tao Zeng, Luonan Chen*. Cell-specific Network Constructed by Single-cell RNA Sequencing Data. Nucleic Acids Research, doi:10.1093/nar/gkz172, 2019.
  128. Xiaoping Liu, Xiao Chang, Siyang Leng, Hui Tang, Kazuyuki Aihara, Luonan Chen*. Detection for disease tipping points by landscape dynamic network biomarkers. Natl Sci Rev, 2019, https://doi.org/10.1093/nsr/nwy162.
  129. Wei Gao, Yan-Bo Sun, Wei-Wei Zhou, Zi-Jun Xiong, Luonan Chen, Hong Li, Ting-Ting Fu, Kai Xu, Wei Xu, Li Ma, Yi-Jing Chen, Xue-Yan Xiang, Long Zhou, Tao Zeng, Si Zhang, Jie-Qiong Jin, Hong-Man Chen, Guojie Zhang, David M. Hillis, Xiang Ji, Ya-Ping Zhang, and Jing Che. Evolution of viviparity: Genomic and transcriptomic investigations of the transition from egg-laying to live birth. Proc Natl Acad Sci USA, https://doi.org/10.1073/pnas.1816086116, 2019.
  130. Fuping Zhang, Xiaoping Liu, Aidi Zhang, Zhonglin Jiang, Luonan Chen*, Xiujun Zhang*. Genome-wide dynamic network analysis reveals a critical transition state of flower development in Arabidopsis. BMC Plant Biology, 2019.
  131. Xiujuan Lei, Zengqiang Fang, Fangxiang Wu, Luonan Chen*. PWCDA: Path Weighted Method for Predicting circRNA-disease Associations. International Journal of Molecular Sciences, 2018.
  132. Rui Liu, Haiyun Wang, Kazuyuki Aihara, Mariko Okada, Luonan Chen*. Hunt for the tipping point during endocrine resistance process in breast cancer by dynamic network biomarkers. Journal of Molecular Cell Biology, https://doi.org/10.1093/jmcb/mjy059, 2018.
  133. Huanfei Ma, Siyang Leng, Kazuyuki Aihara, Wei Lin, Luonan Chen*. Randomly Distributed Embedding Making Short-term High-dimensional Data Predictable. Proc Natl Acad Sci USA, https://doi.org/10.1073/pnas.1802987115, 2018.
  134. Sayers, Samantha ; Li, Li,; Ong, Edison; Deng, Shunzhou ; Fu, Guanghua ; Lin, Yu; Yang, Brian; Zhang, Shelley ; Fa, Zhenzong ; Zhao, Bin; Xiang, Zuoshuang; Li, Yongqing; Zhao, Xingming; Olszewski, Michal; Chen, Luonan*; He, Yongqun*. Victors: a web-based knowledge base of virulence factors in human and animal pathogens. Nucleic Acids Research, https://doi.org/10.1093/nar/gky999, 2018.
  135. Pei Chen, Ely Chen, Luonan Chen*, Jasmine Zhou*, Rui Liu*. Detecting early-warning signals of influenza outbreak based on dynamic network marker. Journal of Cellular and Molecular Medicine. DOI:10.1111/jcmm.13943, 2018.
  136. Jifan Shi, Andrew Teschendorff, Luonan Chen*, Tiejun Li*. Quantifying Waddington's epigenetic landscape: a comparison of single-cell potency measures. Briefings in Bioinformatics, doi: 10.1093/bib/bby093, 2018.
  137. Hao Jiang, Lydia Sohn， Haiyan Huang, Luonan Chen*. Single Cell Clustering Based on Cell-Pair Differentiability Correlation and Variance Analysis. Bioinformatics, https://doi.org/10.1093/bioinformatics/bty390, 2018.
  138. Qibiao Wu, Yahui Tian, Jian Zhang, Xinyuan Tong, Hsinyi Huang, Shuai Li, Hong Zhao, Ying Tang, Chongze Yuan, Kun Wang, Zhaoyuan Fang, Lei Gao, Xin Hu, Fuming Li, Zhen Qin, Shun Yao, Ting Chen, Haiquan Chen, Gong Zhang, Wanting Liu, Yihua Sun, Luonan Chen, Kwok-Kin Wong, Kai Ge, Liang Chen, and Hongbin Ji. In vivo CRISPR screening unveils histone demethylase UTX as an important epigenetic regulator in lung tumorigenesis. PNAS, 2018, https://doi.org/10.1073/pnas.
  139. Jingsong Zhang , Jianmei Guo, Ming Zhang, Xiangtian Yu, Xiaoqing Yu, Weifeng Guo, Tao Zeng, and Luonan Chen*. Efficient Mining Multi-Mers in a Variety of Biological Sequences. IEEE/ACM Transactions on Computational Biology and Bioinformatics, VOL. 15, doi:10.1109/TCBB.2018.2828313, 2018.
  140. Jihong Hu, Tao Zeng, Qiongmei Xia, Qian Qian, Congdang Yang, Yi Ding, Luonan Chen*, Wen Wang*. Unravelling miRNA regulation in yield of rice based on diffetrential network model. Scientific Reports, 2018.
  141. Bing Hu, Qianqian Shi, Yu Guo, Heng Guo, Jinsong Zhang, Liang Yu, Dao Da, Luonan Chen*. The oscillatory boundary conditions of different frequency bands in Parkinson’s disease. Journal of Theoretical Biology, https://doi.org/10.1016/j.jtbi.2018.04.040, 2018.
  142. Ziwei Chen, Xiangqi Bai, Liang Ma, Xiawei Wang, Xiuqin Liu, Yuting Liu, Luonan Chen*, and Lin Wan*. A Branch Point on Differentiation Trajectory is the Bifurcating Event Revealed by Dynamical Network Biomarker Analysis of Single-Cell Data. IEEE/ACM Transactions on Computational Biology and Bioinformatics, DOI: 10.1109/TCBB.2018.2847690, 2018.
  143. Jifan Shi, Juan Zhao, Xiaoping Liu, Luonan Chen*, and Tiejun Li*. Quantifying Direct Dependencies in Biological Networks by Multiscale Association Analysis. IEEE/ACM Transactions on Computational Biology and Bioinformatics, DOI:10.1109/TCBB.2018.2846648, 2018.
  144. Qing-Run Li, Zi-Ming Wang, Nicolai J. Wewer Albrechtsen, Dan-Dan Wang, Zhi-Duan Su, Xian-Fu Gao, Qing-Qing Wu, Hui-Ping Zhang, Li Zhu, Rong-Xia Li, SivHesse Jacobsen, Nils Bruun J?rgensen, Carsten Dirksen, Kirstine N. Bojsen-M?ller, Jacob S. Petersen, Sten Madsbad,Trine R. Clausen, B?rge Diderichsen, Luonan Chen*, Jens J. Holst*, Rong Zeng*, Jia-Rui Wu*.  Systems Signatures Reveal Unique Remission-path of Type 2 Diabetes Following Roux-en-Y Gastric Bypass Surgery. EBioMedicine, https://doi.org/10.1016/j.ebiom.2018.01.018, 2018.
  145. Lili Jiang, Danyang Sui, Kaini Qiao, Hao-Ming Dong, Luonan Chen*, Ying Han*. Impaired Functional Criticality of Human Brain during Alzheimer’s Disease Progression. Scientific Reports, 8:1324, DOI:10.1038/s41598-018-19674-7, 2018.
  146. Chuan Chen, Jinxue Xin, Yong Wang, Luonan Chen*, Michael K. Ng*. A Semi-supervised Classification Approach for Multi-domain Networks with Domain Selection. IEEE Transactions on Neural Networks and Learning Systems, DOI:10.1109/TNNLS.2018.2837166, 2018.
  147. Bing Hu, Yu Guo, Feng Shi, Xiaoqiang Zou, Jing Dong, Long Pan, Min Yu, Chaowei Zhou, Zhang Cheng, Wanyue Tang, Haochen Sun, Luonan Chen*. The generation mechanism of spike-and-slow wave discharges appearing on thalamic relay nuclei. Scientific Reports, 8:4953, 2018.
  148. Meiyi Li, Chen Li, Wei-Xin Liu, CongHui Liu, JingRu Cui, QingRun Li, Hong Ni, Yingcheng Yang, Chaochao Wu, Chunlei Chen, Xing Zhen, Xiaoping Liu, Tao Zeng, Mujun Zhao, Lei Chen, Jiarui Wu, Rong Zeng, Luonan Chen*. Dysfunction of PLA2G6 and CYP2C44 associated network signals imminent carcinogenesis from chronic inflammation to hepatocellular carcinoma. Journal of Molecular Cell Biology, doi:10.1093/jmcb/mjx021,2018.
  149. Wei-Feng Guo, Shao-Wu Zhang, Li-Li Liu, Fei Liu, Qian-Qian Shi, Lei Zhang, Ying Tang, Tao Zeng, Luonan Chen*. Discovering personalized driver mutation profiles of single samples in cancer by network control strategy. Bioinformatics, doi.org/10.1093/bioinformatics/bty006, 2018.
  150. Biwei Yang, Meiyi Li, Wenqing Tang, Weixin Liu, Si Zhang, Luonan Chen*, Jinglin Xia*. Dynamic network biomarker indicates pulmonary metastasis at the tipping point of hepatocellular carcinoma. Nature Communications, 2018.
  151. Wei-Feng Guo, Shao-Wu Zhang, Qian-qian Shi, Cheng-Ming Zhang, Tao Zeng, Luonan Chen*. A novel algorithm for finding optimal driver nodes to target control complex networks and its applications for drug targets identification. BMC Genomics, 2018.
  152. Bengong Zhang, Luonan Chen*. Detecting Causal Gene Regulations from Short Time-series Data Based on Prediction of Topologically Equivalent Attractors. BMC Systems Biology, 2018.
  153. MA HuanFei, LENG SiYan, CHEN LuoNan. Data-based prediction and causality inference of nonlinear dynamics. SCIENCE CHINA Mathematics, doi: 10.1007/s11425-000-0000-0, 2017.
  154. Jifan Shi, Juan Zhao, Tiejun Li, Luonan Chen*. Detecting direct associations in a network by information theoretic approaches. SCIENCE CHINA Mathematics, DOI:https://doi.org/10.1007/s11425-017-9206-0, 2017.
  155. Xiangtian Yu, Jingsong Zhang, Shaoyan Sun, Xin Zhou, Tao Zeng, Luonan Chen*; Individual-specific edge-network analysis for disease prediction, Nucleic Acids Research, doi: 10.1093/nar/gkx787, 2017
  156. Lina Lu, Zhonglin Jiang and Luonan Chen*. Low-Grade Dysplastic Nodules Revealed as the Tipping Point during Multistep Hepatocarcinogenesis by Dynamic Network Biomarkers. Genes, 8, 268, 2017.
  157. Pei Chen; Yongjun Li; Xiaoping Liu; Rui Liu; Luonan Chen*. Detecting the tipping points in a three-state model of complex diseases by temporal differential networks. Journal of Translational Medicine, 15:217, 2017.
  158. Chuan Chen, Jinxue Xin, Yong Wang, Luonan Chen*, Michael K. Ng*. A Semi-supervised Classification Approach for Multi-domain Networks with Domain Selection. IEEE Transactions on Neural Networks and Learning Systems, 2017.
  159. Xiaoping Liu, Xiao Chang, Rui Liu, Xiangtian Yu, Luonan Chen* and Kazuyuki Aihara*. Quantifying critical states of complex diseases using single-sample dynamic network biomarkers. PLoS Computational Biology, doi: 10.1093/bioinformatics/btx176, 2017.
  160. Wei-Feng Guo and Shao-Wu Zhang and Ze-Gang Wei and Tao Zeng and Fei Liu and Jingsong Zhang and Fang-Xiang Wu and Luonan Chen*. Constrained target controllability of complex networks. Journal of Statistical Mechanics: Theory and Experiment. 2017 {6}, 063402, 2017.
  161. Derous D, Mitchell SE, Green CL, Wang Y, Han JDJ, Chen L, Promislow DEL, Lusseau D, Douglas A, Speakman JR. The Effects of Graded Levels of Calorie Restriction: X. Transcriptomic Responses of Epididymal Adipose Tissue.J Gerontol A Biol Sci Med Sci. 2017 May 27. doi: 10.1093/gerona/glx101.
  162. Derous D, Mitchell SE, Wang L, Green CL, Wang Y, Chen L, Han JJ, Promislow DEL, Lusseau D, Douglas A, Speakman JR. The effects of graded levels of calorie restriction: XI. Evaluation of the main hypotheses underpinning the life extension effects of CR using the hepatic transcriptome. Aging. 2017 Jul 31;9(7):1770-1824.
  163. Courtney Schiffman, Christina Lin, Funan Shi, Luonan Chen, Lydia Sohn, Haiyan Huang. SIDEseq: A Cell Similarity Measure Defined by Shared Identified Differentially Expressed Genes for Single-Cell RNA sequencing Data. Statistics in Biosciences, 2017, 9 (1), 200–216.
  164. Dan Landau, Luonan Chen*. From promise to purpose: Systems biology in cancer and systemic diseases. Current Opinion in Systems Biology. https://doi.org/10.1016/j.coisb.2017.05.012, 2017.
  165. Mitchell SE, Tang Z, Kerbois C, Delville C, Derous D, Green CL, Wang Y, Han JJ, Chen L, Douglas A, Lusseau D, Promislow DE, Speakman JR. The effects of graded levels of calorie restriction: VIII. Impact of short term calorie and protein restriction on basal metabolic rate in the C57BL/6 mouse. Oncotarget. 2017 Mar 14;8(11):17453-17474.
  166. Zhang C, Liu J, Shi Q, Zeng T, Chen L*. Comparative network stratification analysis for identifying functional interpretable network biomarkers. BMC Bioinformatics. 2017 Mar 14;18:48.
  167. Zheng G, Xu Y, Zhang X, Liu ZP, Wang Z, Chen L*, Zhu XG. CMIP: a software package capable of reconstructing genome-wide regulatory networks using gene expression data. BMC Bioinformatics. 2016 Dec 23;17:535.
  168. Chinese Journal of Cancer. (2017). The 150 most important questions in cancer research and clinical oncology series: questions 50–56. Chinese Journal of Cancer, 36, 69. http://doi.org/10.1186/s40880-017-0236-1.
  169. Yuan, X., Chen, J., Lin, Y., Li, Y., Xu, L., Chen, L., … Shen, B. (2017). Network Biomarkers Constructed from Gene Expression and Protein-Protein Interaction Data for Accurate Prediction of Leukemia. Journal of Cancer, 8(2), 278–286. http://doi.org/10.7150/jca.17302.
  170. Qianqian Shi, Chuanchao Zhang, Weifeng Guo, Tao Zeng, Lina Lu, Zhonglin Jiang, Ziming Wang, Juan Liu, Luonan Chen*. Local network component analysis for quantifying transcription factor activities. Methods, 2017.
  171. Qianqian Shi, Chuanchao Zhang, Minrui Peng, Xiangtian Yu, Tao Zeng, Juan Liu, Luonan Chen*. Pattern fusion analysis by adaptive alignment of multiple heterogeneous omics data. Bioinformatics, DOI:10.1093/bioinformatics/btx170, 2017.
  172. Xiaoping Liu, Yuetong Wang, Hongbin Ji, Kazuyuki Aihara, Luonan Chen*. Personalized characterization of diseases using sample-specific networks. Nucleic Acids Research, doi: 10.1093/nar/gkw772, 2016.
  173. Guanghui Zhu, Aibo Wu, Xin-Jian Xu, Pei-Pei Xiao, Le Lu, Jingdong Liu, Yongwei Cao, Luonan Chen*, Jun Wu*, Xing-Ming Zhao*. PPIM: A protein-protein interaction database for Maize. Plant Physiology. 170: 618-626, DOI:10.1104/pp.15.01821, 2016.
  174. Fei Liu, Shaowu Zhang, Luonan Chen*. Inference of gene regulatory network based on local Bayesian networks. PLoS Computational Biology, DOI:10.1371/journal.pcbi.1005024, 2016.
  175. Yingcheng Yang, Ximeng Lin, Xinyuan Lu, Guijuan Luo, Tao Zeng, Jing Tang, Feng Jiang, Liang Li, Xiuliang Cui, Wentao Huang, Guojun Hou, Xin Chen, Qing Ouyang, Shanhua Tang, Huanlin Sun, Luonan Chen, Frank J Gonzalez, Mengchao Wu, Wenming Cong, Lei Chen, Hongyang Wang. Interferon-microRNA signalling drives liver precancerous lesion formation and hepatocarcinogenesis. Gut, DOI: 10.1136/gutjnl-2015-310318, 2016.
  176. Juan Zhao, Yiwei Zhou, Xiujun Zhang, Luonan Chen*. Part mutual information for quantifying direct associations in networks. Proc Natl Acad Sci USA, 2016, 113, 5130-5135.
  177. Yan Wang, Wen-Sheng Cai, Luonan Chen*, Guanyu Wang*. Molecular dynamics simulation reveals how phosphorylation of tyrosine 26 of phosphoglycerate mutase 1 upregulates glycolysis and promotes tumor growth. Oncotarget, 2017.
  178.  Zou, Meng, Zhang, Peng-Jun，Chen, Luonan*，Tian, Ya-Ping*，Wang, Yong*，Identifying joint biomarker panel from multiple level dataset by an optimization model，Biomarkers in Medicine，2016.6.01，10(6)：567~575.
  179. Li, Gaopeng; Liu, Liying; Li, Ping; *Chen, Luonan; *Song, Haiyun; *Zhang, Yan. Gene expression profiling of selenophosphate synthetase 2 knockdown in Drosophila melanogaster. Metallomics, 8(3), pp 354-365, 2016.
  180. Shen, Li; Lin, Yuxin; Sun, Zhandong; Yuan, Xuye; Chen, Luonan; *Shen, Bairong. Knowledge-Guided Bioinformatics Model for Identifying Autism Spectrum Disorder Diagnostic MicroRNA Biomarkers. Scientific Reports, DOI：10.1038/srep38311, 2016.
  181. Shen, Sijia ;Lin, Yuxin ;Yuan, Xuye ;Shen, Li ;Chen, Jiajia ;Chen, Luonan ;Qin, Lei ;Shen, Bairong.  Biomarker MicroRNAs for Diagnosis, Prognosis and Treatment of Hepatocellular Carcinoma: A Functional Survey and Comparison. Scientific Reports, DOI: 10.1038/srep38311, 2016.
  182. Mitchell, Sharon E and Delville, Camille and Konstantopedos, Penelope and Derous, Davina and Green, Cara L and Chen, Luonan and Han, Jing-Dong J and Wang, Yingchun and Promislow, Daniel EL and Douglas, Alex and others. The effects of graded levels of calorie restriction: IX. Global metabolomics screen reveals modulation of carnitines, sphingolipids and bile acids in the liver of C57BL/6 mice. Aging Cell, 2017.
  183. Zhen Wang, Jifeng Zhang, Hong Li, Junyi Li, Manabu Niimi, Guohui Ding, Haifeng Chen, Jie Xu, Hongjiu Zhang, Ze Xu, Yulin Dai, Tuantuan Gui, Shengdi Li, Zhi Liu, Sujuan Wu, Mushui Cao, Lu Zhou, Xingyu Lu, Junxia Wang, Jing Yang, Yunhe Fu, Dongshan Yang, Jun Song, Tianqing Zhu, Shen Li, Bo Ning, Ziyun Wang, Tomonari Koike, Masashi Shiomi, Enqi Liu, Luonan Chen, Jianglin Fan, Y. Eugene Chen, Yixue Li. Hyperlipidemia-associated gene variations and expression patterns revealed by whole-genome and transcriptome sequencing of rabbit models. Scientific Reports, 6 : 26942 (2016), doi:10.1038/srep26942.
  184. Pei Chen, Rui Liu, Yongjun Li, Luonan Chen*. Detecting critical state before phase transition of complex bio-logical systems by hidden Markov model. Bioinformatics, doi: 10.1093/bioinformatics/btw154, 2016.
  185. Davina Derous, Sharon Mitchell, Camille Delville, PenelopeKonstantopedos, Jane Hurst, Cara Green, Luonan Chen, Jackie Han,Yingchun Wang, Daniel Promislow, David Lusseau, Alex Douglas, andJohn Speakman. The Effects of Graded Levels of CalorieRestriction: VII. Topological Rearrangement of Hypothalamic AgingNetworks, Aging, 2016.
  186. Jifan Shi, Tiejun Li, and Luonan Chen*. Towards a critical transition theory under different temporal scales and noise strengths. Physical Review E, DOI: 10.1103/PhysRevE.00.002100, 2016.
  187. Sharon Mitchell, Camille Delville, Penelope Konstantopedos, Jane Hurst, Davina Derous, Cara Green, Luonan Chen, Jackie Han, Yingchun Wang, Daniel Promislow, David Lusseau, Alex Douglas, and John Speakman. The effects of graded levels of calorie restriction: V. Impact of short term calorie and protein restriction on physical activity in the C57BL/6 mouse. Oncotarget, 2016.
  188. Yuanling Niu, Kevin Burrage, Luonan Chen*. Modelling biochemical reaction systems by stochastic differential equations with reflection. Journal of Theoretical Biology, 2016.
  189. Chuanchao Zhang, Jiguang Wang, Juan Liu, Dong Xu, Luonan Chen*. Network Stratification Analysis for Identifying Function-specific Network Layers, Molecular BioSystems, DOI: 10.1039/C5MB00782H, 2016.
  190. Rui Liu, Pei Chen, Kazuyuki Aihara, Luonan Chen*. Identifying early-warning signals of critical transitions with strong noise by dynamical network markers. Sci. Rep. 5, 17501; doi: 10.1038/srep17501 (2015).
  191. Camille Delville, Sharon Mitchell, Penelope Konstantopedos, Jane Hurst, Davina Derous, Cara Green, Luonan Chen, Jackie Han, Yingchun Wang, Daniel Promislow, David Lusseau, Alex Douglas, and John Speakman. The Effects of Graded Levels of Calorie Restriction: VI. Impact of Short-term Graded Calorie Restriction on Transcriptomic Responses of the Hypothalamic Hunger and Circadian Signaling Pathways. Aging, 2016.
  192. Rina Sa, Wanwei Zhang, Jing Ge, Xinben Wei, Yunhua Zhou, David R Landzberg, Zhengzhen Wang, Xianlin Han, Luonan Chen*, Huiyong Yin*. Discovering A Critical Transition State from Nonalcoholic Hepatosteatosis to Steatohepatitis by Lipidomics and Dynamical Network Biomarkers. Journal of Molecular Cell Biology, 2015.
  193. Dongli Song, Dragos Cretoiu, Minghuan Zheng, Mengjia Qian, Miaomiao Zhang, Sanda M. Cretoiu, Luonan Chen, Hao Fang, Laurentiu M. Popescu, Xiangdong Wang. Comparison of Chromosome 4 gene expression profile between lung telocytes and other local cell types. Journal of Cellular and Molecular Medicine, 20(1):71-80. doi: 10.1111/jcmm.12746, 2016.
  194. David Lusseau, Sharon E. Mitchell, Ceres Barros, Davina Derous, Cara Green, Luonan Chen, Jing-Dong Jackie Han, Yingchun Wang, Daniel E. L. Promislow, Alex Douglas, John R. Speakman. The effects of graded levels of calorie restriction: IV. Non-linear change in behavioural phenotype of mice in response to short-term calorie restriction. Scientific Reports, 5, 13198 (2015).
  195. Zhi-Ping Liu, Luonan Chen*. Prediction and Dissection of Protein-RNA Interactions by Molecular Descriptors. Current Topics in Medicinal Chemistry, Volume 16, Number 6, March 2016, pp. 604-615(12), 2016.
  196. Tao Zeng, Wanwei Zhang, Xiangtian Yu, Xiaoping Liu, Meiyi Li, Luonan Chen*. Big-data based edge biomarkers: study on dynamical drug sensitivity and resistance in individuals. Briefings in Bioinformatics, doi: 10.1093/bib/bbv078, 2015.
  197. Tianshou Zhou, Jiajun Zhang and Luonan Chen*. Forecasting new state vectors based on a few state vectors. Physica D, 2015.
  198. Pei Chen, Rui Liu, Luonan Chen* and Kazuyuki Aihara*. Identifying critical differentiation state of MCF-7 cells for breast cancer by dynamical network biomarkers. Front. Genet., 28, http://dx.doi.org/10.3389/fgene.2015.00252, 2015.
  199. Zhiyuan Yang, Yan Zhang, Luonan Chen*. Single amino acid changes in naked mole rat may reveal new anti-cancer mechanisms in mammals. Gene, 572(1):101-7. doi: 10.1016/j.gene.2015.07.004, 2015.
  200. Sharon Mitchell, Camille Delville, Penelope Konstantopedos, Jane Hurst, Davina Derous, Cara Green, Luonan Chen, Jackie Han, Yingchun Wang, Daniel Promislow, David Lusseau, Alex Douglas, and John Speakman. The effects of graded levels of calorie restriction: III. Impact of short term calorie and protein restriction on mean daily body temperature and torpor use in the C57BL/6 mouse. Oncotarget, 2015.
  201. Xiang-tian Yu, Tao Zeng, Xiangdong Wang, Guojun Li and Luonan Chen*. Unravelling personalized dysfunctional gene network of complex diseases based on differential network model. Journal of Translational Medicine, 13:189. doi: 10.1186/s12967-015-0546-5, 2015.
  202. Dawei Yang, Jian Zhou, Tao Zeng, Zhiyuan Yang, Xun Wang, Jie Hu, Yuanlin Song, Luonan Chen, Dan Peer, Xiangdong Wang, Chunxue Bai. Serum chemokine nework correlates with chemotherapy in non-small cell lung cancer. Cancer Letters, doi:10.1016/j.canlet.2015.05.001, 2015.
  203. Sharon Mitchell, Camille Delville, Penelope Konstantopedos, Jane Hurst, Davina Derous, Cara Green, Luonan Chen, Jackie Han, Yingchun Wang, Daniel Promislow, David Lusseau, Alex Douglas, and John Speakman. The effects of graded levels of calorie restriction: II. Impact of short term calorie and protein restriction on circulating hormone levels, glucose homeostasis and oxidative stress in male C57BL/6 mice. Oncotarget, 2015.
  204. Meng Zou, Peng-Jun Zhang, Xin-Yu Wen, Luonan Chen*, Ya-Ping Tian* and Yong Wang*. A novel mixed integer programming for multi-biomarker panel identification by distinguishing malignant from benign colorectal tumors. Methods, Volume 83, Pages 3-17, 2015.
  205. Qianqian Shi, Xiaoping Liu, Tao Zeng, William Wang and Luonan Chen*. Detecting disease genes of non-small lung cancer based on consistently differential interactions. Cancer and Metastasis Review, DOI: 10.1007/s10555-015-9561-5, 2015.
  206. Jie Lin; Ting Peng; Liang Jiang; Jia-Zuan Ni; Qiong Liu; Luonan Chen*; Yan Zhang*. Comparative genomics reveals new candidate genes involved in selenium metabolism in prokaryotes. Genome Biology and Evolution, doi: 10.1093/gbe/evv022, 2015.
  207. Hao Kang, Kwang-Hyun Cho, Xiaohua Douglas Zhang,Tao Zeng and Luonan Chen*. Inferring Sequential Order of Somatic Mutations during Tumorgenesis based on Markov Chain Model. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2015.
  208. Wanwei Zhang, Tao Zeng, Xiaoping Liu, Luonan Chen*. Diagnosing phenotypes of single-sample individuals by edge biomarkers. Journal of Molecular Cell Biology, 2015.
  209. Xinan (Holly) Yang,Meiyi Li, Bin Wang, Wanqi Zhu, Aurelie Desgardin, Kenan One , Jill de Jong, Jianjun Chen, Luonan Chen*, John M. Cunningham*. Systematic computation with functional gene-1 sets among leukemic and hematopoietic stem cells reveals a favorable prognostic signature for acute myeloid leukemia. BMC Bioinformatics, 2015.
  210. Sharon E. Mitchell, Zan Hui Tang, Celine Kerbois, Camille Delville, Penelope Konstantopedos, Aurélie Bruel, Davina Derous, Cara Green, Richard M. Aspden, Luonan Chen, Jackie J.D. Han, Yingchun Wang, Daniel E.L. Promislow, David Lusseau, Alex Douglas and John R. Speakman.The effects of graded levels of calorie restriction: I. Impact of short term calorie and protein restriction on body composition in the C57BL/6 mouse. Oncotarget, 2015.
  211. Takayuki Ishizaki, Kenji Kashima, Antoine Girard, Jun-ichi Imura,Luonan Chen*, and Kazuyuki Aihara*. Clustered Model Reduction of Positive Directed Networks. Automatica, 2015.
  212. Xindong Zhang, Lin Gao, Zhi-Ping Liu, Luonan Chen*. Identifying module biomarker in type 2 diabetes mellitus by discriminative area of functional activity. BMC Bioinformatics,2015.
  213. Guoyun Cao, Luonan Chen*, Kazuyuki Aihara*. Power System Voltage Stability Assessment Based on Branch Active Powers. IEEE TRANSACTIONS ON POWER SYSTEMS, DOI: 10.1109/TPWRS.2014.2329731, 2015.
  214. Jiang Xie, Wang Ding, Luonan Chen, Qiang Guo and Wu Zhang. Advances in Protein Contact Map Prediction Based on Machine Learning. Medicinal Chemistry, 2015.
  215. Xingming Zhao, Keqin Liu, Luonan Chen*. Identifying cancer-related microRNAs based on gene expression data. Bioinformatics, doi:10.1093/bioinformatics/btu811, 2014.\
  216. Xiujun Zhang, Juan Zhao, Jin-Kao Hao, Xing-Ming Zhao, and Luonan Chen*. Conditional mutual inclusive information enables accurate quantification of associations in gene regulatory networks. Nucleic Acids Research, doi: 10.1093/nar/gku1315, 2014.
  217. Huanfei Ma, Kazuyuki Aihara, Luonan Chen*. Detecting Causality from Nonlinear Dynamics with Short-term Time Series. Scientific Reports, doi:10.1038/srep07464, 2014.
  218. Yixue Li, Luonan Chen*. Big Biological Data: Challenges and Opportunities. Genomics, Proteomics & Bioinformatics, 2014.
  219. Tao Zeng, Diane Catherine Wang, Xiangdong Wang, Feng Xud, Luonan Chen*. Prediction of dynamical drug sensitivity and resistance by module network rewiring-analysis based on transcriptional profiling. Drug Resistance Updates, DOI: 10.1016/j.drup.2014.08.002, 2014.
  220. Andrew E Teschendorff, Xiaoping Liu, Helena Caren, Steve Pollard, Stephan Beck, Martin Widschwendter, Luonan Chen*. The dynamics of DNA methylation covariation patterns in carcinogenesis. PLoS Computational Biology, 10(7): e1003709. doi:10.1371/journal.pcbi.1003709, 2014.
  221. Zhenshu Wen, Luonan Chen*. MCentridFS: a tool for identifying module biomarkers for multi-phenotypes from high-throughput data. Molecular BioSystems, DOI: 10.1039/C4MB00325J, 2014.
  222. Huanfei Ma, Tianshou Zhou, Kazuyuki Aihara, Luonan Chen*. Predicting Time-series from Short-term High-dimensional Data. International Journal of Bifurcation and Chaos, 2014.
  223. Jiang Xie, Wang Ding, Luonan Chen*, Qiang Guo and Wu Zhang. Advances in Protein Contact Map Prediction Based on Machine Learning. Medicinal Chemistry, 2014.
  224. Xiaoru Sun, Minghuan Zheng, Miaomiao Zhang, Mengjia Qian, Yonghua Zheng, Meiyi Li, Dragos Cretoiu, Chengshui Chen, Luonan Chen*, Laurentiu M. Popescu* and Xiangdong Wang*. Differences in the expression of chromosome 1 genes between lung telocytes and other cells: mesenchymal stem cells, fibroblasts, alveolar type II cells, airway epithelial cells and lymphocytes. Journal of Cellular and Molecular Medicine, 2014 May;18(5):801-10. doi: 10.1111/jcmm.12302.
  225. Xiaodan Wu, Luonan Chen* and Xiangdong Wang*. Network biomarkers, interaction networks and dynamical network biomarkers in respiratory diseases. Clinical and Translational Medicine 2014, 3:16 doi:10.1186/2001-1326-3-16.
  226. Tao Zeng, Wanwei Zhang, Xiangtian Yu, Xiaoping Liu, Meiyi Li, Rui Liu, Luonan Chen*. Edge biomarkers for classification and prediction of phenotypes. SCIENCE CHINA Life Sciences, 2014.
  227. Wanwei Zhang, Tao Zeng, Luonan Chen*. EdgeMarker: identifying differentially correlated molecule pairs as edge-biomarkers. Journal of Theoretical Biology, DOI:10.1016/j.jtbi.2014.05.041, 2014.
  228. Rui Liu, Xiangtian Yu , Xiaoping Liu, Dong Xu, Kazuyuki Aihara and Luonan Chen*. Identifying critical transitions of complex diseases based on a single sample. Bioinformatics, DOI:10.1093/bioinformatics/btu084, 2014.
  229. B.Liu, Z.Yuan, K.Aihara, L.Chen*. Reinitiation enhances reliable transcriptional responses in eukaryotes. J. R. Soc. Interface, 20140326, 2014.
  230. Fang-Xiang Wu, Lin Wu, Jianxin Wang, Juan Liu, Luonan Chen*. Transittability of complex networks and its applications to regulatory biomolecular networks. Scientific Reports, DOI: 10.1038/srep04819,2014.
  231. Tao Zeng, Chuan-chao Zhang, Wanwei Zhang, Rui Liu, Juan Liu, Luonan Chen*. Deciphering early development of complex diseases by progressive module network. Methods, http://dx.doi.org/10.1016/j.ymeth.2014.01.021, 2014.
  232. Minchao Wang, Wu Zhang, Wang Ding, Dongbo Dai, Huiran Zhang, Hao Xie, Luonan Chen, Yike Guo and Jiang Xie. Parallel Clustering Algorithm for Large-scale Biological Data Sets. PLoS One, 2014.
  233. Doss C. Priya George, Chiranjib Chakraborty, SA Syed Haneef, Nagarajan NagaSundaram, Luonan Chen*, Hailong Zhu*. Evolution- and structure-based computational strategy reveals the impact of deleterious missense mutations on MODY 2 (maturity-onset diabetes of the young, type 2). Theranostics, 4(4):366-385. doi: 10.7150/thno.7473, 2014.
  234. Zhang Pengjun, Zou Meng, Wen Xinyu, Gu Feng, Li Juan, Liu Gaixia, Dong Jingxiao, Deng Xinxin, Gao Jing, Li Xiaolong, Jia Xingwang, Dong Zhennan, Chen Luonan*, Wang Yong*, and Tian Yaping*. Development of Serum Parameters Panels for Early Detection of Pancreatic Cancer. International Journal of Cancer, 134, 2646–2655, 2014.
  235. Meng Zou, Peng-Jun Zhang, Xin-Yu Wen, Luonan Chen*, Ya-Ping Tian* and Yong Wang*. Identifying multi-biomarkers to distinguish malignant from benign colorectal tumours by a mixed integer programming. Journal of the American Medical Informatics Association, 2014.
  236. Chiranjib Chakraborty, George Priya Doss. C, Luonan Chen*, Hailong Zhu*. Evaluating protein-protein interaction (PPI) networks using in silico pharmacology: to understand the diseases pathway, target discovery and drug-design. Current Protein and Peptide Science, 15, 561-571, 2014.
  237. Xiangtan Yu, Guozheng Li, Luonan Chen*. Prediction and early diagnosis of complex diseases by edge-network. Bioinformatics, doi:10.1093/bioinformatics/btt620，2013.
  238. Tao Zeng, Shao-yan Sun, Yong Wang, Hailong Zhu, Luonan Chen*. Network biomarkers reveal dysfunctional gene regulations during disease progression. FEBS Journal, doi:10.1111/febs.12536, 2013.
  239. Yong Wang, Xiang-Sun Zhang, Luonan Chen*. Computational systems biology in the big data era. BMC Systems Biology, doi:10.1186/1752-0509-7-S2-S1, 2013.
  240. Rui Liu, Xiangdong Wang, Kazuyuki Aihara, Luonan Chen*, Early diagnosis of complex diseases by molecular biomarkers, network biomarkers, and dynamical network biomarkers. Medicinal Research Reviews, DOI:10.1002/med.21293, 2013.
  241. Shao-Yan Sun, Zhi-Ping Liu, Tao Zeng, Yong Wang, and Luonan Chen*. Spatio-temporal analysis of type 2 diabetes mellitus based on differential expression networks. Scientific Reports, DOI: 10.1038/srep02268, 2013.\
  242. Jiguang Wang, Yidan Sun, Si Zheng, Xiang-Sun Zhang, Huarong Zhou, and Luonan Chen*. APG: an Active Protein-Gene Network Model to Quantify Regulatory Signals in Complex Biological Systems. Scientific Reports, DOI: 10.1038/srep01097, 2013.
  243. Chao Zhang, Jiguang Wang, Kristina Hanspers, Dong Xu, Luonan Chen, Xiang-Sun Zhang, Alexander R. Pico. NOA: A Cytoscape Plugin for Network Ontology Analysis. Bioinformatics, doi:10.1093/bioinformatics/btt334, 2013.
  244. Xiaoping Liu, Xiaodong Zhang, Wei-Hua Tang, Luonan Chen* and Xing-Ming Zhao. eFG: an electronic resource for Fusarium graminearum. Database, doi:10.1093/database/bat042, 2013.
  245. Mingzhu Zhao, Hao-Teng Chang, Zhiping Liu, Luonan Chen*, Dongqing Wei*. Predicting Protein--Ligand Interactions Based on Chemical Preference Features with its Application to New D--Amino Acid Oxidase Inhibitor Discovery. Current Pharmaceutical Design, DOI: 10.2174/1381612819666140110114902 , 2014.
  246. Jiang Xie, Zhonghua Zhou, Kai Lu, Luonan Chen*, Wu Zhang*. Visualization of Biomolecular Networks Comparison on Cytoscape. Tsinghua Science and Technology, 2013.
  247. Zikai Wu, Yong Wang, Luonan Chen*. A New Framework for Drug Repositioning by Incorporating Functional Information. IET Systems Biology, 7(5):188-94, doi: 10.1049/iet-syb.2012.0064, 2013.
  248. Meiyi Li, Tao Zeng, Yong Wang, Luonan Chen*. Detecting tissue-specific early-warning signals for complex diseases based on dynamical network biomarkers: study of type-2 diabetes by cross-tissue analysis. Briefings in Bioinformatics, DOI:10.1093/bib/bbt027, 2013.
  249. Rui Liu, Kazuyuki Aihara, Luonan Chen*. Dynamical network biomarkers for identifying critical transitions of biological processes. Quantitative Biology, DOI 10.1007/s40484-013-0008-0, 2013.
  250. Songyot Nakariyakul, Zhi-Ping Liu, Luonan Chen*. A Sequence-based Computational Approach to Predicting PDZ Domain-Peptide Interactions. BBA - Proteins and Proteomics, 2013.
  251. Zikai Wu, Yong Wang, Luonan Chen*. Network-Based Drug Repositioning. Molecular BioSystems, DOI:10.1039/C3MB25382A, 2013.
  252. Chenglei Sun, Zheng-Zheng Shi, Xiaobo Zhou, Luonan Chen*, Xing-Ming Zhao. Prediction of S-Glutathionylation Sites Based on Protein Sequences. PLoS ONE 8(2): e55512. doi:10.1371/journal.pone.0055512, 2013.
  253. George Priya Doss C, Nagasundaram N, Chiranjib Chakraborty, Luonan Chen and Hailong Zhu. Extrapolating the effect of deleterious nsSNPs in the binding adaptability of flavopiridol with CDK7 protein: A Molecular dynamics approach, Human Genomics, 7:10, http://www.humgenomics.com/content/7/1/10, 2013.
  254. Zhiyuan Yang, Yan Zhang, and Luonan Chen*. Investigation of anti-cancer mechanisms by comparative analysis of naked mole rat and rat. BMC Systems Biology, 2013.
  255. Zhi-Ping Liu, Wanwei Zhang, Katsuhisa Horimoto, and Luonan Chen*. A Gaussian Graphical Model for Identifying Significantly Responsive Regulatory Networks from Time Course High-Throughput Data. IET Systems Biology, 2013.
  256. Peipei Zhou, Shuiming Cai, Zengrong Liu, Luonan Chen, Ruiqi Wang. Coupling switches and oscillators as a means to shape cellular signals in biomolecular systems. Chaos, Solitons & Fractals, 7242, 2013.
  257. Rui Liu, Meiyi Li, Zhi-Ping Liu, Jiarui Wu, Luonan Chen*, Kazuyuki Aihara*. Identifying critical transitions and their leading networks in complex diseases. Scientific Reports, DOI: 10.1038/srep00813, 2012.
  258. Xiaoping Liu, Rui Liu, Xing-Ming Zhao, Luonan Chen*. Detecting early-warning signals of type 1 diabetes and its leading biomolecular networks by dynamical network biomarkers. BMC Medical Genomics, doi:10.1186/1755-8794-6-S2-S8, 2013.
  259. Xiaoping Liu, Jiguang Wang, Luonan Chen*. Whole-exome sequencing reveals recurrent somatic mutation networks in cancer. Cancer Letters, http://dx.doi.org/10.1016/j.canlet.2012.11.002, 2012.
  260. Xianwen Ren, Yong Wang, Luonan Chen*, Xiang-Sun Zhang* and Qi Jin*. ellipsoidFN: a tool for identifying a heterogeneous set of cancer biomarkers based on gene expressions. Nucleic Acids Research, 41, 4 e53, doi:10.1093/nar/gks1288, 2013.
  261. Xiujun Zhang, Keqin Liu, Zhi-Ping Liu, Béatrice Duval, Jean-Michel Richer, Xing-Ming Zhao, Jin-Kao Hao, and Luonan Chen*. NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference. Bioinformatics, DOI:10.1093/bioinformatics/bts619, 2012.
  262. Ying Wang, Xiaowei Chen, Zhi-Ping Liu, Qiang Huang, Yong Wang, Xiang-Sun Zhang, Runsheng Chen, Luonan Chen*. De novo prediction of RNA-protein interactions from sequence information. Molecular BioSystems, DOI: 10.1039/c2mb25292a, 2012.
  263. Bengong Zhang, Luonan Chen*, Kazuyuki Aihara*. Incremental stability analysis of stochastic hybrid systems. Nonlinear Analysis (Series B: Real World Applications), 14, 1225-1234, 2012.
  264. Hailong Zhu, R. Shyama Prasad Rao, Jiming Liu, Tao Zeng, Luonan Chen*. Reconstructing dynamic gene regulatory networks from sample-based transcriptional data. Nucleic Acids Research, doi:10.1093/nar/gks860, 2012.
  265. Zhenshu Wen, Zhi-Ping Liu, Zhengrong Liu, Yan Zhang, Luonan Chen*. An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer. Journal of the American Medical Informatics Association, doi:10.1136/amiajnl-2012-001168, 2012.
  266. Zhenshu Wen, Zhi-Ping Liu, Yiqing Yan, Guanying Piao, Zhengrong Liu, Jiarui Wu and Luonan Chen*. Identifying responsive modules by mathematical programming: an application to budding yeast cell cycle. PLoS One, 7(7), e41854, 2012.
  267. Luonan Chen*, Rui Liu, Zhiping Liu, Meiyi Li, Kazuyuki Aihara. Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers. Scientific Reports, 2, 342; DOI:10.1038/srep00342, 2012.
  268. Zhiping Liu, Luonan Chen*. Proteome-wide prediction of protein-protein interactions from high-throughput data. Protein & Cell, 2012.
  269. Hee Sook Lee, Taejeong Bae, Ji-Hyun Lee, Dae Gyu Kim, Young Sun Oh, Yeongjun Jang, Ji-Tea Kim, Jong-Jun Lee, Alessio Innocenti, Claudiu T Supuran, Luonan Chen, Kyoohyoung Rho and Sunghoon Kim. Rational drug repositioning guided by an integrated pharmacological network of protein, disease and drug. BMC Systems Biology, 2012.
  270. Ke-Qin Liu, Zhi-Ping Liu, Jin-Kao Hao, Luonan Chen*, Xing-Ming Zhao*. Identifying dysregulated pathways in cancers from pathway interaction networks. BMC Bioinformatics, 13:126 doi:10.1186/1471-2105-13-126, 2012.
  271. Wei Song, Jiguang Wang, Ying Yang, Nai-He Jing, Xiang-Sun Zhang, Luonan Chen*, Jia-Rui Wu*. Rewiring drug-activated p53-regulatory network from suppressing to promoting tumorigenesis. Journal of Molecular Cell Biology, 4(4), 197-206, 2012.
  272. Jiajun Zhang,Luonan Chen*,and Tianshou Zhou*. Analytical Distribution and Tunability of Noise in a Model of Promoter Progress. Biophysical Journal, Vol.102, 1247–1257, 2012.
  273. Luonan Chen*, Jiarui Wu. Systems biology for complex diseases. Journal of Molecular Cell Biology, doi:10.1093/jmcb/mjs022, 2012.
  274. H.J. Li, J.H. Zhang, Z.P. Liu, L. Chen*, X.S. Zhang*. Identify overlapping communities in social networks using multi-scale local information expansion. The European Physical Journal B, 85: 190, DOI: 10.1140/epjb/e2012-30015-5, 2012.
  275. Yong Wang, Xiang-Sun Zhang, and Luonan Chen*. Modelling biological systems from molecules to dynamical networks. BMC Systems Biology, doi:10.1186/1752-0509-6-S1-S1, 2012.
  276. Zhi-Ping Liu, Jiguang Wang, Yu-Qing Qiu, Ross KK Leung, Xiang-Sun Zhang, Stephen KW Tsui and Luonan Chen*. Inferring a protein interaction map of Mycobacterium tuberculosis based on sequences and interologs. doi:10.1186/1471-2105-13-S7-S6, BMC Bioinformatics, 2012.
  277. Danning He, Zhiping Liu, Masao Honda, Shuichi Kaneko, Luonan Chen*. Coexpression network analysis in chronic hepatitis B and C hepatic lesion reveals distinct patterns of disease progression to hepatocellular carcinoma. Journal of Molecular Cell Biology, 4(3), 140-152, 2012.
  278. Lin Wang, Zhi-Ping Liu, Xiang-Sun Zhang, Luonan Chen*. Prediction of hot spots in protein interfaces using a random forest model with hybrid features. Protein Engineering, Design and Selection (PEDS), doi:10.1093/protein/gzr066, 2012.
  279. Zhi-Ping Liu, Yong Wang, Xiang-Sun Zhang and Luonan Chen*: Network-based analysis of complex diseases. IET Systems Biology, doi: 10.1049/iet-syb.2010.0052, 2012.
  280. Hui-Jia Li, Yong Wang, Ling-Yun Wu, Zhi-Ping Liu, Luo-Nan Chen* and Xiang-Sun Zhang*. Community structure detection based on Potts model and network’s spectral characterization. Europhysics Letters, 97 (48005), doi:10.1209/0295-5075/97/48005, 2012.
  281. Tao Zeng and Luonan Chen*. Tracing dynamic biological processes during phase transition. BMC Systems Biology, doi:10.1186/1752-0509-6-S1-S12, 2012.
  282. Guanyin Piao, Shigeru Saito, Yidan Sun, Zhi-Ping Liu2, Yong Wang, Xiao Han, Jiarui Wu, Huarong Zhou, Luonan Chen*, Katsuhisa Horimoto*. A computational procedure for identifying master regulator candidates for diabetes progression in Goto-Kakizaki rat. BMC Systems Biology, doi:10.1186/1752-0509-6-S1-S2, 2012.
  283. Danning He, Zhi-Ping Liu, Luonan Chen*. Identification of dysfunctional modules and disease genes in congenital heart disease by a network-based approach. BMC Genomics, 12:592, 2011.
  284. Xiaoping Liu, Zhiping Liu, Xingming Zhao, Luonan Chen*. Identifying disease genes and module biomarkers with differential interactions. Journal of the American Medical Informatics Association, doi:10.1136/amiajnl-2011-000658, 2011.
  285. Xiujun Zhang, Xingming Zhao, Kun He, Le Lu, Yongwei Cao, Jingdong Liu, Jin-Kao Hao, Zhiping Liu, Luonan Chen*. Inferring gene regulatory networks from gene expression data by PC-algorithm based on conditional mutual information. Bioinformatics, doi: 10.1093/bioinformatics/btr626, 2011.
  286. Ruiqi Wang, Kaihui Liu, Luonan Chen* and Kazuyuki Aihara*. Neural fate decisions mediated by trans-activation and cis-inhibition in Notch signaling. Bioinformatics, doi:10.1093/bioinformatics/btr551, 2011.
  287. Achyut Sapkota, Xiaoping Liu, Xingming Zhao, Yongwei Cao, Jingding Liu, Zhiping Liu, Luonan Chen*. DIPOS: Database of Interacting Proteins in Oryza Sativa. Molecular BioSystems, DOI: 10.1039/C1MB05120B, 2011.
  288. Jiguang Wang, Qiang Huang, Zhi-Ping Liu, Yong Wang, Ling-Yun Wu, Luonan Chen*, and Xiang-Sun Zhang*. NOA: a novel Network Ontology Analysis method. Nucleic Acids Research, doi: 10.1093/nar/gkr251, 2011.
  289. Zhi-Ping Liu, Yong Wang, Xiang-Sun Zhang and Luonan Chen*. Detecting and analyzing differentially activated pathways in brain regions of Alzheimer’s disease patients. Molecular BioSystems, DOI: 10.1039/C0MB00325E, 2011.
  290. Yong Wang, Xiang-Sun Zhang, Luonan Chen*. Computational systems biology: integration of sequence, structure, network, and dynamics. BMC Systems Biology, doi:10.1186/1752-0509-5-S1-S1, 2011.
  291. Graziano Chesi, Luonan Chen*. Systems Biology. Int. J. Robust. Nonlinear Control, 21:1729, 2011.
  292. D. Liu, X. Chang, Z.Liu, L.Chen, R.Wang. Bistability and oscillations in gene regulation mediated by small noncoding RNAs. PLoS ONE 6(3): e17029. doi:10.1371/journal.pone.0017029, 2011.
  293. X. Chang, D.Liu, Z.Liu, L.Chen, R.Wang. Adaptation of simple molecular networks to time dependent stimulus. Asian Journal of Control, Volume 13, Issue 5, pages 701C712, September 2011.
  294. Zhenping Li, Ruisheng Wang, Xiang-Sun Zhang, Luonan Chen*. Drug target identification based on flux balance analysis in metabolic network. BMC Systems Biology, accepted, 2011.
  295. Songyot Nakariyakul, Zhi-Ping Liu, Luonan Chen*. Detecting thermophilic proteins through selecting amino acid and dipeptide composition features. Amino Acids, DOI 10.1007/s00726-011-0923-1, 2011.
  296. Hongbo Lei, Jifeng Zhang, Luonan Chen*. Property of Multiple Equilibria for SSI Metabolic Module. BMC Systems Biology, doi:10.1186/1752-0509-5-S1-S15, 2011.
  297. Huarong Zhou, Zhiping Liu, Kazu Horimoto, Luonan Chen*. Network Screening of Goto-Kakizaki Rat Liver Microarray Data during Diabetic Progression. BMC Systems Biology, doi:10.1186/1752-0509-5-S1-S16, 2011.
  298. Hong-Bo Lei, Xin Wang, Ruiqi Wang, Xin-Guang Zhu, Luonan Chen*, Ji-Feng Zhang*. A parameter condition for ruling out multiple equilibria of the photosynthetic carbon metabolism. Asian Journal of Control, Volume 13, Issue 5, pages 611C624, September 2011.
  299. Luonan Chen*, James Lam, Zidong Wang. ANALYSIS AND CONTROL OF BIOLOGICAL NETWORKS. Asian Journal of Control, DOI: 10.1002/asjc.424, 2011.
  300. Graziano Chesi1, Luonan Chen* and Kazuyuki Aihara*. On the robust stability of time varying uncertain genetic regulatory networks. Int. J. Robust. Nonlinear Control, DOI:10.1002/rnc.1775, 2011.
  301. Vasilescu Gabriel, Luonan Chen*. Spice Simulation of Intracellular Transport: Free Diffusion. Asian Journal of Control, Volume 13, Issue 5, pages 738C748, September 2011
  302. Hongbo Lei, Jifeng Zhang, Luonan Chen*. Multi-equilibrium property of metabolic networks: Exclusion of multi-stability for SSN metabolic modules. International Journal of Robust and Nonlinear Control, DOI: 10.1002/rnc.1718, 2011.
  303. D.Liu, X.Chang, Z.Liu, L.Chen, R.Wang. The effect of coupled feedback on noise filtering in signal transduction networks. J. Syst. Sci. Complex, vol.23, 942C950, 2010.
  304. Xiaoping Liu, Wei-Hua Tang, Xingming Zhao, Luonan Chen*. A Network Approach to Predict Pathogenic Genes for Fusarium graminearum. PLoS One, 5(10): e13021, 2010.
  305. Yong Wang, Xiang-Sun Zhang, and Luonan Chen*. Optimization Meets Systems Biology. BMC Systems Biology, doi:10.1186/1752-0509-4-S2-S1, 2010.
  306. Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, Luonan Chen*. Prediction of protein-RNA binding sites by a random forest method with combined features. Bioinformatics, Vol. 26, 1616C1622, 2010.
  307. Zikai Wu, Xing-Ming Zhao, Luonan Chen*. A systems biology approach to identify effective cocktail drugs. BMC Systems Biology, doi:10.1186/1752-0509-4-S2-S7, 2010.
  308. Zhiping Liu, Weiming Xia, Xiang-Sun Zhang, Luonan Chen*. Identifying dysfunctional crosstalk of pathways in various regions of Alzheimers’ disease brains. BMC Systems Biology, doi:10.1186/1752-0509-4-S2-S11, 2010.
  309. Chenglei Sun, Xing-Ming Zhao, Weihua Tang, Luonan Chen*. FGsub: Fusarium graminearum protein subcellular localization prediction from primary structures. BMC Systems Biology, doi:10.1186/1752-0509-4-S2-S12, 2010.
  310. Lin Wang, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, Luonan Chen*. SANA: an algorithm for sequential and non-sequential protein structure alignment. Amino Acids, 39(2):417-25, 2010.
  311. Yu-Qing Qiu, Shihua Zhang, Xiang-Sun Zhang, Luonan Chen*. Detecting disease associated modules and prioritizing active genes based on high throughput data. BMC Bioinformatics, 11:26, 2010.
  312. Yi Ding, Peng Wang, L. Goel1, Luonan Chen*, Poh Chiang Loh. A Penalty Scheme for Reducing Electricity Price Volatility. IEEE Transactions on Power Systems, 25(1): 223-233, 2010.
  313. Zhao Song, Luonan Chen*, Dong Xu*, Bioinformatics Methods for Protein Identification Using Peptide Mass Fingerprinting. Proteome bioinformatics: Informatics for mass-spectrometry based protein science, Methods in Molecular Biology, 604:7-22, 2010.
  314. Xingming Zhao, Kazuyuki Aihara, Luonan Chen*. A discriminative approach to identifying domain-domain interactions from protein-protein interactions. PROTEINS: Structure, Function, and Bioinformatics, 78(5), 1243-1253, 2009.
  315. Xingming Zhao, Xiao-Wei Zhang, Weihua Tang, Luonan Chen*. FPPI: Fusarium graminearum protein-protein interaction database. Journal of Proteome Research, DOI: 10.1021/pr900415b, 2009.
  316. Jiguang Wang, Shihua Zhang, Yong Wang, Luonan Chen*, Xiang-Sun Zhang*. Disease-aging network reveals significant roles of aging genes in connecting genetic diseases. PLoS Computational Biology, PLoS Comput Biol 5(9): e1000521. doi:10.1371journal.pcbi.1000521, 2009.
  317. Zhao Song, Luonan Chen*, Dong Xu*. Confidence Assessment for Protein Identification by Using Peptide-Mass Fingerprinting Data. Proteomics, 9(11), 3090-3099, 2009.
  318. Y. Li, Z. Liu, J. Zhang, R. Wang, L.Chen*. Synchronisation mechanisms of circadian rhythms in the suprachiasmatic nucleus. IET Systems Biology, 3(2), 100-112, 2009.
  319. X. S. Zhang, R. S. Wang, Y. Wang, J. Wang, Y. Qiu, L. Wang and L.Chen*. Modularity optimization in community detection of complex networks. Europhysics Letters, 87:38002, 2009.
  320. R.Wang, G.Jin, X-S. Zhang, L.Chen*. Modelling post-transcriptional regulation of microRNAs in E.coli. BMC Bioinformatics, 10(Suppl 4):S6, 2009.
  321. Y.Wang, X-S.Zhang, L.Chen*. A network biology study on circadian rhythm by integrating various omics data. OMICS, 13(4):313-24, 2009.
  322. Y.Wang, J.Shen, B.Niu, Z.Liu, L.Chen*. Robustness of interval gene networks with multiple time-varying delays and noise. Neurocomputing, doi:10.1016/j.neucom.2009.02.012, 2009.
  323. Y.Wang, Z.Ma, J.Shen, Z.Liu, L.Chen*. Periodic oscillation in delayed gene networks with SUM regulatory logic and small perturbations. Mathematical Biosciences, doi:10.1016/j.mbs.2009.03.010, 2009.
  324. Y.Qiu, S.Zhang, X-S.Zhang, L.Chen. Identifying differentially expressed pathways via a mixed integer linear programming model. IET Systems Biology, 3, 475-486, 2009.
  325. Jianwei Shen, Zengrong Liu, Weixing Zheng, Fengdan Xu, Luonan Chen*. Oscillatory dynamics in a simple gene regulatory network mediated by small RNAs. Physica A: Statistical Mechanics and its Applications. 388(14), 2995-3000, 2009.
  326. Guangxu Jin, Xiaobo Zhou, Kemin Cui, Xiang-Sun Zhang, Luonan Chen*, and Steve T.C. Wong. Cross-platform method for identifying candidate network biomarkers for prostate cancer. IET Systems Biology, 3(6), 505-512, 2009.
  327. B.Wang, L.Chen*, K.Aihara*. Limited ability driven phase transitions in the coevolution process in Axelrod’s model. Physics Letters A, 373(17), 1519-1523, 2009.
  328. L-Y.Wu, Z.Li, R.Wang, X-S.Zhang, L.Chen*. Self-organizing map approaches for the haplotype assembly problem Mathematics and Computers in Simulation. Mathematics and Computers in Simulation,79(10), 3026-3037, 2009.
  329. Z.Li, R.Wang, X-S.Zhang, L.Chen*. Detecting drug targets in metabolic networks by integer linear programming. IET Systems Biology, Vol. 3, No.6, pp. 523-533, 2009.
  330. H. Fan, Z. Wang, L.Chen*, K. Aihara*. Feedback mechanism in network dynamics with preferential flow. Physical Review E, 79:026107, 2009.
  331. Xing-Ming Zhao, Rui-Sheng Wang, Luonan Chen*, Kazuyuki Aihara. Automatic modeling of signaling pathways by network flow model. Journal of Bioinformatics and Computational Biology, 7(2):309-22, 2009.
  332. Z.Wu, X.Zhao, L.Chen*. Detecting signal transduction pathways from high-throughput data. Mol. Cells, 27, 271-277, 2009.
  333. S.Fan, L.Chen*, W. J. Lee*. Short-term Load Forecasting Using Comprehensive Combination based on Multi- Meteorological Information. IEEE Trans. on Industry Application. Vol. 45, No. 4, pp. 1460-1466, 2009.
  334. S.Fan, Y.Yokoyama, L.Chen*. Forecasting the Wind Generation Using A Two-stage Network Based on Meteorological Information. IEEE Transactions on Energy Conversion. Vol. 24, No. 2, pp. 474-482, 2009.
  335. G. Jin, X.Zhou, H.Wang, H.Zhao, K.Cui, X. Zhang, L.Chen, S. Hazen, K. Li, S. Wong. The knowledge-integrated network biomarkers discovery for Major Adverse Cardiac Events. Journal of Proteome Research, 7 (9), 4013-4021, 10.1021/pr8002886, 2008.
  336. S.Zhang, X-S.Zhang, L.Chen*. Biomolecular network querying: a promising approach in systems biology. BMC Systems Biology, 2:5, doi:10.1186/1752-0509-2-5, 2008.
  337. X. Zhao, R.Wang, L.Chen*, K.Aihara*. Uncovering signal transduction networks from highthroughput data by integer linear programming. Nucleic Acids Research, Vol.36, No.9, e48, doi:10.1093/nar/gkn145, 2008.
  338. Z.Liu, L.Wu, Y.Wang, X-S. Zhang, L.Chen*. Bridging protein local structures and protein functions. Amino Acids, DOI 10.1007/s00726-008-0088-8, 2008.
  339. X.Zhao, K.Aihara, L.Chen*. Protein function prediction with high-throughput data. Amino Acids, Vol.35, pp.517-530, DOI 10.1007/s00726-008-0077-y, 2008.
  340. Y.Xie, L.Chen*, Y.Kang, K. Aihara. Controlling the onset of Hopf bifurcation in the Hodgkin-Huxley model. Physical Review E. 77, 061921, 2008.
  341. B. Wang, K. Aihara* and L.Chen*. Jamming in weighted scale-free gradient networks. Europhysics Letters. 83, 28006, 2008.
  342. C. Li, L.Chen*, K.Aihara*. Impulsive control of stochastic systems with applications in chaos control, chaos synchronization, and neural networks. Chaos. Vol.18, 023132, 2008.
  343. T.Zhou, J. Zhang, Z. Yuan, L.Chen*. Synchronization of Genetic Oscillators. Chaos. Vol.18, No.3, 037126, 2008.
  344. Z. Li, S.Zhang, R. Wang, X.S.Zhang, L.Chen*. Novel quantitative function for community detection. Physical Review E, 77, 036109, 2008.
  345. X.Zhao, Y.Wang, L.Chen*, K.Aihara*. Gene function prediction using labeled and unlabeled data. BMC Bioinformatics, 9:57, doi:10.1186/1471-2105-9-57, 2008.
  346. X.Zhao, Y.Wang, L.Chen*, K.Aihara*. Protein domain annotation with integration of heterogeneous information sources. Proteins: Structure, Function, and Bioinformatics, Vol.72, no.1, 461 - 473, 2008.
  347. G.He, L.Chen, K.Aihara. Associative Memory with a Controlled Chaotic Neural Network. Neurocomputing, 71, 2794-2805, 2008.
  348. Y.Wang, L-Y.Wu, J.Zhang, Z.Zhan, X-S.Zhang, L.Chen*. Evaluating Protein Similarity From Coarse Structures. IEEE/ACM Transactions on Computational Biology and Bioinformatics, doi:10.1109/TCBB.2007.70250, 2008.
  349. R.Wang, C.Li, L.Chen*, K.Aihara*. Modeling and Analyzing Biological Oscillations in Molecular Networks. Proceedings of The IEEE, Vol.96, 1361-1385, 2008.
  350. R.-S. Wang, S. Zhang, Y. Wang, X.-S. Zhang, L.Chen*. Clustering complex networks and biological networks by Nonnegative Matrix Factorization with various similarity measures. Neurocomputing, 72, 134-141, 2008.
  351. X.-M. Zhao, Y. Wang, L.Chen*, and K. Aihara*. Protein domain annotation with predicted domain-domain interaction networks. Protein & Peptide Letters, 15, 456-462, 2008.
  352. X.-M. Zhao, L.Chen*, and K. Aihara*. Protein function prediction with the shortest path in functional linkage graph and boosting. International Journal of Bioinformatics Research and Applications, 4, 375 - 384, 2008.
  353. Z.-P. Liu, L.-Y. Wu, Y. Wang, X.-S. Zhang, L.Chen*. Protein cavity clustering based on community structure of pocket similarity network. International Journal of Bioinformatics Research and Applications, 4, 445-460, 2008.
  354. Z.Liu, L-Y.Wu, X-S.Zhang, L.Chen*. Analysis of protein surface patterns by pocket similarity network in a systems biology framework. Protein & Peptide Letter, 15, 448-455, 2008.
  355. S. Fan, L.Chen*, W. J. Lee*. Machine Learning Based Switching Model for Electricity Load Forecasting. Energy Conversion and Management, Vol. 49, No. 6, pp. 1331-1344, 2008
  356. Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Luonan Chen* and Xiang-Sun Zhang. Predicting Gene Ontology Functions from Protein’s Regional Surface Structures. BMC Bioinformatics, 8:475, doi:10.1186/1471-2105-8-475, 2007.
  357. Guangxu Jin, Shihua Zhang, Xiang-Sun Zhang, Luonan Chen*. Hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast. PLoS ONE, 2(11): e1207, doi: 10.1371/journal.pone.0001207, 2007.
  358. Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen*. Inferring transcriptional interactions and regulator activities from experimental data. Molecules and Cells, vol.24, 307-315, 2007.
  359. R.Wang, Y.Wang, L-Y.Wu, X-S.Zhang, L.Chen*. Analysis on Multi-domain Cooperation for Predicting Protein-Protein Interactions. BMC Bioinformatics, 8:391, doi:10.1186/1471-2105-8-391, 2007.
  360. R. Wang, Y.Wang, X-S. Zhang, L.Chen*. Inferring Transcriptional Regulatory Networks from High-throughput Data. Bioinformatics, 23(22):3056-3064, 2007.
  361. X.Zhao, L.Chen*, K.Aihara*. Protein classification with imbalanced data. Proteins: Structure, Function, and Bioinformatics, Vol.70, 1125 - 1132, 2007.
  362. L.Chen*, Y.Wang, M.Fei, Z.Liu. Systems Biology from Theoretical and Engineering Perspective. SCIENCE & TECHNOLOGY REVIEW, Vol.25, No.10, 5-10, 2007.
  363. C. Li, L.Chen*, K. Aihara*. Stochastic Stability of Genetic Networks with Disturbance Attenuation. IEEE TCAS-II, Vol.54, No.10, 892-896, 2007.
  364. Z.Li, S. Zhang, Y.Wang, X-S.Zhang, L.Chen*. Alignment of molecular networks by integer quadratic programming. Bioinformatics, 23, 1631-1639, 2007.
  365. S. Zhang, G. Jin, X-S. Zhang, L.Chen*. Discovering functions and revealing mechanisms at molecular level from biological networks, Proteomics, Vol.7, 2856-2869, 2007.
  366. R.Wang, L.Chen*, K.Aihara*. Detection of Cellular Rhythms and Global Stability within Interlocked Feedback Systems, Mathematical Biosciences, Vol.209, 171-189, 2007.
  367. C.Li, L.Chen*, K.Aihara*. Stochastic Synchronization of Genetic Oscillator Networks. BMC Systems Biology, doi:10.1186/1752-0509-1-6, 2007.
  368. Z.Wu, Y.Wang, E.Feng, L.Chen*. A new geometric-topological method to measure protein fold similarity. Chemical Physics Letters, Vol.433,432-438, 2007.
  369. Z.Wu, E.Feng, Y.Wang, L.Chen*. Discrimination of Outer Membrane Proteins by a New Measure of Information Discrepancy. Protein & Peptide Letters, 14, 37-44, 2007.
  370. C.Li, L.Chen*, K.Aihara*. A systems biology perspective on signal processing in genetic network motifs. IEEE Signal Processing Magazine, Vol.24, No.2, 136-147, 2007.
  371. Zhao Song, Luonan Chen, Ashwin Ganapathy, Xiu-FengWan, Laurent Brechenmacher, Nengbing Tao, David Emerich, Gary Stacey, Dong Xu. Development and Assessment of Scoring Functions for Protein Identification Using Peptide Mass Fingerprinting Data. ELECTROPHORESIS, 28, 864-870, 2007.
  372. S,Fukutome, H. Azuma, N. Honjou, L.Chen*, Development of Generation-Transmission Expansion Planning Method Based on A Hierarchical Model, Transactions IEE of Japan, Vol.127-B, No.1, 130-136, 2007.
  373. S.Fan, C.Mao, L.Chen*, Next-Day Electricity Price Forecasting Using a Hybrid Network. IET Generation, Transmission & Distribution, Vol.1, No.1, 176-182, 2007.
  374. R-S. Wang, L-Y.Wu, X-S.Zhang, L.Chen*. A Markov Chain Model for Haplotype Assembly from SNP Fragments. Genome Informatics, Vol.17,No.2. 2006.
  375. Y.Wang, L-Y.Wu, X-S.Zhang and L.Chen*. Exploring the classification of protein structures on geometric patterns by neural networks. International Journal of Computational Intelligence Research, Vol. 2, No. 1, pp. 105-109, 2006.
  376. Y.Wang, X-S.Zhang, L.Chen*. Supervised Classification of Protein Structures, International Journal of Bioinformatics Research and Applications, Vol.3, No.2, 2006.
  377. L.Chen*, L-Y.Wu, Y.Wang, S.Zhang, X-S.Zhang, Revealing Divergent Evolution, Identifying Circular Permutations and Detecting Active-Sites by Protein Structure Comparison, BMC Structural Biology, doi:10.1186/1472-6807-6-18, 2006.
  378. Y.Wang, T.Joshi, D.Xu, X-S.Zhang, L.Chen*, Inferring Gene Regulatory Networks from Multiple Microarray Datasets, Bioinformatics, 22, 2413 - 2420, 2006.
  379. S.Fan, C.Mao, L.Chen*, Electricity Peak Load Forecasting with Self-Organizing Map and Support Vector Regression, Transactions IEE of Japan, Vol.1, 330-336, 2006.
  380. C.Li, L.Chen*, K.Aihara*, Transient Resetting: a novel mechanism for biological synchrony, PLoS Computational Biology, DOI:10.1371/journal.pcbi.0020103.eor, 2006.
  381. Y.Wang, L-Y.Wu, X-S.Zhang, L.Chen*, Automatic Classification of Protein Structures Based on Convex Hull Representation by Integrated Neural Network. Lecture Notes in Computer Science, Springer Berlin Heidelberg, Vol.3959, 505-514,2006.
  382. R.Wang, L.Chen*,K.Aihara*, Synchronizing a Multicellular System by External Input: An Artificial Control Strategy,Bioinformatics, 22, 1775 - 1781, 2006.
  383. R.Wang, L.Chen*, K.Aihara*, ”Construction of Genetic Oscillators with Interlocked Feedback Networks”, Journal of Theoretical Biology, Vol.242, 454-463, 2006.
  384. C.Li, L.Chen*, K.Aihara*, ”Synchronization of Coupled Nonidentical Genetic Oscillators”, Physical Biology, 3, 37-44, 2006.
  385. R.Li, L.Chen*, R.Yokoyama*, ”A Pricing Method for Transmission Loss Based on Sensitivity Analysis”, IEEE Trans. on Power Systems, Vo.21, No.3, pp.1201 - 1208, 2006.
  386. X-S.Zhang, R-S. Wang, L-Y. Wu, L.Chen*, ”Models and Algorithms for Haplotyping Problem,”Current Bioinformatics, 1, 105-114, 2006.
  387. L.Chen*, L-Y. Wu, Y.Wang, X-S. Zhang, ”Inferring Protein Interactions from Experimental Data by Association Probabilistic Method,” Proteins, 62, 833-837, 2006.
  388. T.Wachi, S.Fukutome, L.Chen*, Y.Makino, ”Decomposition of Market Clearing Price in Electricity Markets,” Transactions IEE of Japan, Vol. 126-B, No.3, pp.297-307, 2006.
  389. L.Chen*, R.Wang, ”Designing Gene Regulatory Networks with Specified Functions,” IEEE Trans. on Circuits and Systems - I: Fundamental Theory and Applications, Vol.53, No.11, 2444-2450, 2006.
  390. C.Li, L.Chen*, K.Aihara*, ”Stability of Genetic Networks with SUM Regulatory Logic,” IEEE Trans. on Circuits and Systems - I: Fundamental Theory and Applications, Vol.53, No.11, 2451-2458, 2006.
  391. Z. Jing, R. Wang, L.Chen, J.Deng, ”Attractive Regions in Power Systems by Singular Perturbation Analysis,” DOI 10.1007/3-7643-7429-28, Differential Equations with Symbolic Computation, 2006.
  392. S.Fan, L.Chen*, ”Short-Term Load Forecasting Based on an Adaptive Hybrid Method,” IEEE Trans. on Power Systems, 21, 392- 401, 2006.
  393. S.Fan, C.Mao, L.Chen*, ”Optimal coordinated PET and generator excitation control for power systems,” International Journal of Electrical Power & Energy Systems, 28, No.3, 158-165, 2006.
  394. L.Chen*, L-Y.Wu, R.Wang, Y.Wang, S.Zhang, X-S.Zhang, ”Comparison of Protein Structures by Multi-Objective Optimization,” Genome Informatics, Vol.16, No.2, pp.114-124, 2005.
  395. T. Zhou, L.Chen*, K.Aihara, ”Molecular Communication through Stochastic Synchronization Induced by Extracellular Fluctuations,” Physical Review Letter, 95, 178103, 2005.
  396. R.Li, R.Yokoyama, L.Chen*, ”Pricing for Load and Wheeling Charge Considering Transmission Paths in Deregulated Power Markets” International Journal of Electrical Power & Energy Systems, Vol.27, pp.496-505, 2005.
  397. T.Zhou, L.Chen, R.Wang, ”A mechanism of synchronization in interacting multi-cell genetic systems,” Physica D, 211, 107-127, 2005.
  398. Z.Li, W.Zhou, X.Zhang, L.Chen*, ”A Parsimonious Tree-Grow Method for Haplotype Inference,”Bioinformatics, 21, 3475-3481, 2005.
  399. T.Zhou, L.Chen*, R.Wang*, ”Excitation functions of coupling,” Physical Review E, 71, 066211, 2005.
  400. R.Wang, L.Chen*, ”Synchronizing genetic oscillators by signalling molecules,”Journal of Biological Rhythms, 20, 257-269, 2005.
  401. L.Chen*, R.Wang, T.Zhou, K.Aihara,”Noise-induced Cooperative Behavior in a Multi-Cell System,” Bioinformatics, Vol.21, 2722-2729, 2005.
  402. T.Zhou, L.Chen, Y.Tang, X.Zhang, ”Aligning Multiple Protein Structures by Deterministic Annealing,” Journal of Bioinformatics and Computational Biology, Vol.3, No.4, 837-860, 2005.
  403. X.Zhang, Y.Wang, Z. Zhan, L.Wu, L.Chen*, ”Exploring Protein’s Optimal HP Configurations by Self-Organizing Mapping,” Journal of Bioinformatics and Computational Biology, Vol.3, No.2, 385-400, 2005.
  404. P.Wei, L.Chen, H-D. Chiang, ”Bidding price analysis for competitive generators and large consumers,” International Journal of Electrical Power & Energy Systems, Vol.27, 169-176, 2005.
  405. S.Fan, C.Mao, L.Chen*, ”Peak load forecasting using the self-organizing map”, 640-647, Advances in Neural Networks, Springer, 2005.
  406. Geerli, L.Chen, I.Kurihara, K.Takahasi, ”Cooperative Game Theory Applied to Transmission Expansion Cost Allocation for Congestion Relief,” International Journal of Electrical Power & Energy Systems, Vol.27, 61-67, 2005.
  407. Z.Li, X.Zhang, L.Chen*, ”Unique Optimal Foldings of Protein on a Triangular Lattice,” Journal of Applied Bioinformatics, Vol.4, 105-116, 2005.
  408. L.Chen*, T.Zhou, Y.Tang, ”Protein Structure Alignment by Deterministic Annealing,” Bioinformatics, Vol.21, 51-62, 2005.
  409. R. Wang, Z.Jing, L.Chen*, ”Modelling Periodic Oscillation in Gene Regulatory Networks by Cyclic Feedback Systems,” Bulletin of Mathematical Biology, Vol.67, 339-367, 2005.
  410. T. Wachi, S.Fukutome, L.Chen*, Y. Makino, G. Koshimizu, ”Application for Single Price Auction Model (SPA) in AC Network,” Transactions IEE of Japan, Vol.125-B, 81-89, 2005.
  411. T.Zhou, L.Chen*, R.Wang, K.Aihara, Intercellular Communications Induced by Random Fluctuations, Genome Informatics, Vol.15, No.2, 223-233, 2004.
  412. R. Wang, Z. Jing, L.Chen*, ”Periodic oscillators in genetic networks with negative feedback loops,” WSEAS Trans. on Mathematics, Vol.3, No.1, pp.150-156, 2004.
  413. R. Wang, T. Zhou, Z. Jing, L.Chen*, ”Modelling Periodic Oscillation of Biological Systems with Multiple Time Scale Networks, ” Systems Biology, Vol.1, No.1, pp.71-84,2004.
  414. L.Chen*, R. Wang, T. Kobayashi, K.Aihara, ”Dynamics of gene regulatory networks with cell division cycle,” Physical Review E, Vol. 70, 011909, 2004.
  415. P.Charusanti, X.Hu, L.Chen, D.Neuhauser, J.Distefano, A mathematical model of BCRABL autophosphorylation, signaling through the CRKL pathway, and gleevec dynamics in chronic myeloid leukemia, Discrete and Continuous Dynamical Systems - Series B, Vol.4, No.1, pp.99-114,2004.
  416. T.Zhou, J.Lu, L.Chen*, Z.Jing, Y.Tang*, ”On the optimal solutions for power flow equations,”International Journal of Electrical Power & Energy Systems, Vol.25, pp.533-541, 2003.
  417. Z.Jing, D.Xu, Y.Chang, L.Chen*, ”Bifurcations, chaos, and system collapse in a three node power system,” International Journal of Electrical Power & Energy Systems, Vol.25, No.6, pp.443-461, 2003.
  418. T.Kobayashi, L.Chen, K.Aihara, ”Modeling Genetic Switches with Positive Feedback Loops,”Journal of Theoretical Biology, Vol.221, pp.379-399, 2003.
  419. S.Fukutome, H.Azuma, T. Saishoji, M.Yasuda, H.Saito, K.Ogimoto, L.Chen* ,”Fast power system reliability evaluation by Monte Carlo method,” Transactions IEE of Japan, Vol.122-B, No.3, pp.369-374, 2002.
  420. R. Yuan, Z.Jing, L.Chen*, ”UNIFORM ASYMPTOTIC STABILITY OF HYBRID DYNAMICAL SYSTEMS WITH DELAY,” IEEE Trans. on Automatic Control, Vol.48, No.2, pp.344-348, 2003.
  421. L.Chen*, K.Aihara, ”A Model of Periodic Oscillation for Genetic Regulatory Systems,” IEEE Trans. on Circuits and Systems - I: Fundamental Theory and Applications. Vol.49, No.10, pp.1429-1436,2002.
  422. Z.Jing, J.Wang, L.Chen*, ”Computation of Limit Cycle via Higher Order Harmonic Balance Approximation and Its Application to a 3-Bus Power System,” IEEE Trans. on Circuits and Systems - I: Fundamental Theory and Applications. Vol.49, No.9, pp.1360-1370, 2002.
  423. L.Chen*, K.Aihara, ”Stability of Genetic Regulatory Networks with Time Delay,” IEEE Trans. on Circuits and Systems - I: Fundamental Theory and Applications. Vol.49, No.5, pp.602-608, 2002.
  424. L.Chen*, H.Suzuki, K.Wachi, Y.Shimura, ”Components of Nodal Prices For Electric Power Systems,” IEEE Trans. on Power Systems. Vol.17, no.1, pp.41-49, 2002.
  425. S. Fukutome, M. Yasuda, L.Chen*, ”Fast power system reliability evaluation by Monte Carlo method,” Transactions IEE of Japan, Vol. 122-B, No.3, pp. 369-374, 2002.
  426. L.Chen*, K.Aihara, ”Chaotic dynamics of neural networks and its application to combinatorial optimization,” Journal of Dynamical Systems and Differential Equations, invited review paper, vol.9, no.3, pp.139-168, 2001.
  427. L.Chen*, K.Aihara, ”Stability and Bifurcation Analysis of Differential-Difference-Algebraic Equations,” IEEE Transactions on Circuits and Systems - I: Fundamental Theory and Applications. Vol.48, No.3, pp.308-326,2001.
  428. L.Chen*, Y.Tada, H.Okamoto, R.Tanabe, A.Ono, ”Optimal Operation Solutions of Power Systems with Transient Stability Constraints,” IEEE Transactions on Circuits and Systems - I: Fundamental Theory and Applications. Vol.48, No.3, pp.327-339,2001.
  429. Geerli, L.Chen, R.Yokoyama, ”Pricing and operation in deregulated electricity market by noncooperative game,” Electrical Power Systems Research, Vol.57, pp.133-139, 2001.
  430. J.Wang, L.Chen*, Z.Jing*, ”Chaos and asymptotical stability in discrete-time recurrent neural networks with generalized input-output function,” Science in China, vol.44, no.2, pp.193-200, 2001.
  431. L.Chen*, K.Aihara, ”Strange Attractors in Chaotic Neural Networks,” IEEE Transactions on Circuits and Systems - I: Fundamental Theory and Applications, Vol.47, No.10, pp. 1455-1468, 2000.
  432. L.Chen*, et al., ”Optimal Operation of Power Systems Constrained by Transient Stability,”Transactions IEE of Japan, Vol. 120-B, No.12, pp. 1582-1594, 2000.
  433. L.Chen*, et al., ”Analysis of Nodal Prices for Power Systems,” Transactions IEE of Japan, Vol.120-B, No.5, pp.686-693, 2000.
  434. Geerli, L.Chen, et al., ”Negotiation Models for Electric Pricing and Load Dispatch in Electricity Market,” Transactions IEE of Japan, Vol.120-B, No.2, pp.219-226, 2000.
  435. L.Chen*, H.Tanaka, K.Katou, Y.Nakamura, ”Stability analysis for digital controls of power systems,” Electric Power Systems Research, Vol. 55, pp.79-86, 2000.
  436. L.Chen*, K.Aihara, ”Global Searching Ability of Chaotic Neural Networks,” IEEE Transactions on Circuits and Systems- I: Fundamental Theory and Applications, Vol.46, No.8,pp.974-993, 1999.
  437. L.Chen*, S.Matoba, et al., ”Surrogate Constraint Method for Optimal Power Flow,” IEEE Transactions on Power Systems, Vol.13, No.3, pp.1084-1089,1998.
  438. L.Chen*, H.Susuki, et al., ”Mean Field Theory for Optimal Power Flow,” IEEE Transactions on Power Systems,Vol.12, No.4, pp.1481-1486, 1997.
  439. L.Chen, K.Aihara, ”Chaos and Asymptotical Stability in discrete-time neural networks”, Physica D, Vol.104, pp.286-325, 1997.
  440. L.Chen, et al ”A Comparison of Reliability Evaluation Techniques for Power Systems,”Transactions of IEE Japan, Vol.116-B,No.3, 1996.
  441. L.Chen, K.Aihara, ”Chaotic Simulated Annealing by a Neural Network Model with Transient Chaos,” Neural Networks, Vol.8, No.6, pp.915-930, 1995.
  442. L.Chen, K.Aihara, ”Chaotic Simulated Annealing for Combinatorial Optimization,” N.Aoki, et al (Eds.), Dynamic Systems and Chaos, World Scientific, Vol.1, pp.319-322, 1995.
  443. L.Chen, K.Aihara, ”Chaotic simulated annealing and combinatorial optimization,” Journal of Computation Technology, Vol.25, No.2, pp.20-28, 1994.
  444. L.Chen, K.Aihara, ”Transient Chaotic Neural Networks and Chaotic Simulated Annealing,”M. Yamaguti(Editor), Towards the Harnessing of Chaos, Elsevier Science B.V., pp.347-352, 1994.
  445. L. Chen, et al, ”Optimal Electric Generation Planning for Interconnected Systems by Benders Decomposition,” Transactions of IEE Japan,, Vol.B-113, No.6, pp.643-652, 1993.
  446. L. Chen, J. Toyoda, ”Optimal Generating Unit Maintenance Scheduling for Multi-Area System with Network Constraints,” IEEE Transactions on Power Systems, Vol.PWRS-6, No.3, pp.1168-1174, August 1991.
  447. L. Chen, J. Toyoda, ”Power Arrival Evaluation of Bulk System Including Network Constraints Based on Linear Programming Approach,” IEEE Transactions on Power Systems, Vol.PWRS-6, No.1, pp.37-42, February 1991.
  448. L. Chen, J. Toyoda, ”Maintenance Scheduling Based on Two Level Hierarchical Structure to Equalize Incremental Risk ,” IEEE Transactions on Power Systems, Vol.PWRS-5, No.4, pp.1510-1516, November 1990.
  449. L. Chen, J. Toyoda, ”Optimal Unit Commitment Scheduling of Thermal Power System Based on the Monte Carlo Method, ” Transactions of IEE Japan, Vol.B-109, No.3, pp.73-80, 1989.
  450. L. Chen, J.Toyoda, ”A New Approach to Maintenance Scheduling Based on Incremental Reliability Index,” Transactions of IEE Japan, Vol.B-108, No.5, pp.205-212, 1988.

 

Conference Papers

•More than 300 conference papers, omission.