近年来发表论文300余篇SCI期刊论文。主要开展了包括动物复杂形状多样性研究，复杂疾病的机理及前期临界状态预测等的研究，生物分子网络的因果关系构建研究，动态生物分子网络分析理论，异源数据整合及多层次网络整合、深度学习及人工智能计算的研究等。特别是   

1. 提出生物系统演化的临界状态及动态网络标记物（DNB）的崭新概念，开发早期预测的模型与方法,为这领域开创了新方向； 

2. 提出了生物分子网络的因果关系构建的全新理论和方法(PMI)； 

3. 建立了单样本网络构建方法(SSN)。 

4. 建立了生物功能注释新方法，开创网络本体论（NOA）的新概念 

5. 建立基于Embedding理论的深度学习及人工智能的计算方法 

已成功地应用DNB，PMI和SSN得到动物复杂形状多样性进化分析、肝癌、AD、糖尿病的前疾病状态及恶化前状态和关键因子群，并进一步研究了生物过程临界点前的分子及网络演变规律。该研究对进化系统生物学的核心理论体系构建、脑科学、预防性医疗和个体医疗具有重要意义。 

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. 

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, DOI: 10.1038/s41467-018-03024-2, 2018. 

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. 

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. 

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, 2018. 

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, 9(6):489-503, doi:10.1093/jmcb/mjx021, 2018. 

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. 

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, 13(7):e1005633, doi: 10.1371/journal.pcbi.1005633, 2017. 

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, 33(17):2706-2714, doi: 10.1093/bioinformatics/btx176, 2017. 

Juan Zhao, Yiwei Zhou, Xiujun Zhang,Luonan Chen*. Part mutual information for quantifying direct associations in networks.Proc Natl Acad Sci USA, 113, 5130-5135，2016. 

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. 

Pei Chen, Rui Liu*, Yongjun Li,Luonan Chen*. Detecting critical state before phase transition of complex biological systems by hidden Markov model.Bioinformatics, doi: 10.1093/bioinformatics/btw154, 2016. 

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. 

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, 17(4):576-92. doi: 10.1093/bib/bbv078, 2016. 

Xiujun Zhang, Juan Zhao, Jin-Kao Hao, Xing-Ming Zhao, andLuonan Chen*. Conditional mutual inclusive information enables accurate quantification of associations in gene regulatory networks.Nucleic Acids Research, doi: 10.1093/nar/gku1315, 2015.