（1）网络生物学及生物大数据
（2）生物信息学
（3）计算系统生物学

（4）机器学习及人工智能

招收攻读博士学位的学生和留学生（或进修生），不提供住宿，需申请到奖学金后录取。

0710J3-生物信息学
085238-生物工程
085238-生物工程

计算系统生物学及网络生物学
计算生物学
生物信息学

1988-04--日本东北大学   博士
1986-04--日本东北大学   硕士
1980-09--华中科技大学   学士

-- 研究生

-- 博士

1991.4～1997.3：日本开发计算中心，主查研究员
1997.4～2000.3：日本大阪产业大学，副教授
2000.4～2002.3：美国加州大学洛山矶分校（UCLA），访问教授
2002.4～2010.3：日本大阪产业大学，教授
2009.4～现在：日本东京大学生产技术研究所，研究教授（兼）
2009.10～现在：中科院系统生物学重点实验室执行主任、研究员

2009-10~现在, 中科院上海生命科学研究院系统生物学重点实验室, 执行主任
2009-04~现在, 日本东京大学生产技术研究所, 教授（兼）
2007-01~现在, 上海大学系统生物技术研究所, 所长
2006-04~现在, 日本科学振兴机构, 复杂生命系统研究组长
2002-04~现在, 日本大阪产业大学, 教授
2000-04~现在, 美国加州大学洛杉矶分校, 访问教授
1997-04~现在, 日本大阪产业大学, 副教授

2014-09-16-今,《npj Systems Biology and Applications》, 编辑委员
2014-09-01-今,《Quantitative Biology》 , 编辑委员
2013-03-04-今,《Journal of Molecular Cell Biology》 , 编辑委员
2011-07-01-今,《 Journal of the Royal Society Interface》 , Editorial Board Member
2010-07-01-今,中国运筹学会计算系统生物学会, 理事长
2010-07-01-今,《BMC Systems Biology》 , Section Editor
2010-07-01-今,《IET Systems Biology》 , Editorial Board Member
2010-07-01-今,《Journal of Theoretical Biology》 , Editorial Board Member
2010-07-01-今,《Systems Science and Complexity》 , Editorial Board Member
2009-07-01-今,《IEEE/ACM Trans. on Computational Biology and Bioinformatics》, Associate Editor
2009-07-01-今,《Data Mining and Bioinformatics》 , Editorial Board Member
2009-01-01-今,IEEE SMC 《Systems Biology Committee》, 主席
2008-07-01-今,《Mathematical Biosciences》 , Editorial Board Member
2007-07-01-今,《Neural Processing Letters》 , Associate Editor

生物统计学
生物信息学

Books:
1. L. Chen, R-S.Wang, X-S.Zhang, Biomolecular Networks: Methods and Applications in Systems Biology, John Wiley & Sons, 2009.
2. L. Chen, R-Q.Wang, C. Li, K. Aihara, Modelling Biomolecular Networks in Cells: Structures and Dynamics, Springer-Verlag, London, 2010.

Publications: 参照 http://sysbio.sibcb.ac.cn/sysbio/cb/chenlab/LuonanChen.htm

[1] 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.. Natl Sci Rev[J]. 2023, 10((4)): [2] 陈洛南. Earthquake alerting based on spatial geodetic data by spatiotemporal information transformation learning. Proc Natl Acad Sci U S A[J]. 2023, [3] Lin Li, Yilin Xu, Lili Yan, Xiao Li, Fei Li, Zhuang Liu, Chuanchao Zhang, Yuan Lou, Dong Gao, Xin Cheng, Luonan Chen. Dynamic network biomarker factors orchestrate cell-fate determination at tipping points during hESC differentiation. THE INNOVATION[J]. 2023, 4(1): http://dx.doi.org/10.1016/j.xinn.2022.100364.
[4] Tao, Peng, Hao, Xiaohu, Cheng, Jie, Chen, Luonan. Predicting time series by data-driven spatiotemporal information transformation. INFORMATION SCIENCES[J]. 2023, 622: 859-872, http://dx.doi.org/10.1016/j.ins.2022.11.159.
[5] Fang, Zhaoyuan, Han, Xiangkun, Chen, Yueqing, Tong, Xinyuan, Xue, Yun, Yao, Shun, Tang, Shijie, Pan, Yunjian, Sun, Yihua, Wang, Xue, Jin, Yujuan, Chen, Haiquan, Hu, Liang, Hui, Lijian, Li, Lin, Chen, Luonan, Ji, Hongbin. Oxidative stress-triggered Wnt signaling perturbation characterizes the tipping point of lung adeno-to-squamous transdifferentiation. SIGNAL TRANSDUCTION AND TARGETED THERAPY[J]. 2023, 8(1): 730-743, http://dx.doi.org/10.1038/s41392-022-01227-0.
[6] 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 shows disease-specific changes of T cell and macrophage populations in human achalasia. NATURE COMMUNICATIONS[J]. 2023, 14(1): 1-19, http://dx.doi.org/10.1038/s41467-023-39750-5.
[7] 陈洛南. http://sysbio.sibcb.ac.cn/sysbio/cb/chenlab/LuonanChen.htm. 2022, [8] Feng, Jinwang, Zhang, ShaoWu, Chen, Luonan, Zuo, Chunman, Alzheimers Dis Neuroimaging Initiative, Alzheimer s Disease Neuroimaging. 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[J]. 2022, 98: http://dx.doi.org/10.1016/j.compmedimag.2022.102057.
[9] Cheng, Runtan, Wang, Lu, Le, Shenglong, Yang, Yifan, Zhao, Can, Zhang, Xiangqi, Yang, Xin, Xu, Ting, Xu, Leiting, Wiklund, Petri, Ge, Jun, Lu, Dajiang, Zhang, Chenhong, Chen, Luonan, Cheng, Sulin. A randomized controlled trial for response of microbiome network to exercise and diet intervention in patients with nonalcoholic fatty liver disease. NATURE COMMUNICATIONS[J]. 2022, 13(1): http://dx.doi.org/10.1038/s41467-022-29968-0.
[10] Shi, Jifan, Aihara, Kazuyuki, Li, Tiejun, Chen, Luonan. Energy landscape decomposition for cell differentiation with proliferation effect. NATIONAL SCIENCE REVIEW[J]. 2022, 9(8): 135-143, http://lib.cqvip.com/Qikan/Article/Detail?id=7108215190.
[11] Shi, Xiaohan, Li, Yunguang, Yuan, Qiuyue, Tang, Shijie, Guo, Shiwei, Zhang, Yehan, He, Juan, Zhang, Xiaoyu, Han, Ming, Liu, Zhuang, Zhu, Yiqin, Gao, Suizhi, Wang, Huan, Xu, Xiongfei, Zheng, Kailian, Jing, Wei, Chen, Luonan, Wang, Yong, Jin, Gang, Gao, Dong. Integrated profiling of human pancreatic cancer organoids reveals chromatin accessibility features associated with drug sensitivity. NATURE COMMUNICATIONS[J]. 2022, 13(1): http://dx.doi.org/10.1038/s41467-022-29857-6.
[12] Yuan, Kai, Zeng, Tao, Chen, Luonan. Interpreting Functional Impact of Genetic Variations by Network QTL for Genotype-Phenotype Association Study. FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY[J]. 2022, 9: http://dx.doi.org/10.3389/fcell.2021.720321.
[13] Zuo, Chunman, Zhang, Yijian, Cao, Chen, Feng, Jinwang, Jiao, Mingqi, Chen, Luonan. Elucidating tumor heterogeneity from spatially resolved transcriptomics data by multi-view graph collaborative learning. NATURE COMMUNICATIONS[J]. 2022, 13(1): http://dx.doi.org/10.1038/s41467-022-33619-9.
[14] Li, Lin, Tang, Hui, Xia, Rui, Dai, Hao, Liu, Rui, Chen, Luonan. Intrinsic entropy model for feature selection of scRNA-seq data. JOURNAL OF MOLECULAR CELL BIOLOGY[J]. 2022, 14(2): 32-42, http://lib.cqvip.com/Qikan/Article/Detail?id=7107772557.
[15] You, Yujie, Zhang, Le, Tao, Peng, Liu, Suran, Chen, Luonan. Spatiotemporal Transformer Neural Network for Time-Series Forecasting. ENTROPY[J]. 2022, 24(11): http://dx.doi.org/10.3390/e24111651.
[16] Yujuan Jin, Qiqi Zhao, Weikang Zhu, Yan Feng, Tian Xiao, Peng Zhang, Liyan Jiang, Yingyong Hou, Chenchen Guo, Hsinyi Huang, Yabin Chen, Xinyuan Tong, Jiayu Cao, Fei Li, Xueliang Zhu, Jun Qin, Dong Gao, XinYuan Liu, Hua Zhang, Luonan Chen, Roman KThomas, KwokKin Wong, Lei Zhang, Yong Wang, Liang Hu, Hongbin Ji. Identification of TAZ as the essential molecular switch in orchestrating SCLC phenotypic transition and metastasis. 国家科学评论:英文版. 2022, 9(7): 10-24, http://lib.cqvip.com/Qikan/Article/Detail?id=7107930144.
[17] Zhang, JingSong, Wang, HaiQuan, Xia, Jie, Sha, Kun, He, ShuTao, Dai, Hao, Hao, XiaoHu, Zhou, YiWei, Wang, Qiu, Ding, KeKe, Ju, ZhangLei, Wang, Wen, Chen, LuoNan. Coevolutionary insights between promoters and transcription factors in the plant and animal kingdoms. ZOOLOGICAL RESEARCH[J]. 2022, 43(5): 805-812, http://dx.doi.org/10.24272/j.issn.2095-8137.2022.111.
[18] Meng, Yiwei, Huang, Yanhong, Chang, Xiao, Liu, Xiaoping, Chen, Luonan. Transcriptome analysis method based on differential distribution evaluation. BRIEFINGS IN BIOINFORMATICS[J]. 2022, 23(2): http://dx.doi.org/10.1093/bib/bbab608.
[19] Tao, Peng, Cheng, Jie, Chen, Luonan. Brain-inspired chaotic backpropagation for MLP. NEURAL NETWORKS[J]. 2022, 155: 1-13, http://dx.doi.org/10.1016/j.neunet.2022.08.004.
[20] Jin, Qiqi, Zuo, Chunman, Cui, Haoyue, Li, Lin, Yang, Yiwen, Dai, Hao, Chen, Luonan. Single-cell entropy network detects the activity of immune cells based on ribosomal protein genes. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL[J]. 2022, 20: 3556-3566, https://doaj.org/article/cf921a70a1b743369bba38f06e7eaf62.
[21] Shijie Tang, Kai Yuan, Luonan Chen. Molecular biomarkers, network biomarkers, and dynamic network biomarkers for diagnosis and prediction of rare diseases. FUNDAMENTAL RESEARCH[J]. 2022, 2(6): 894-902, http://dx.doi.org/10.1016/j.fmre.2022.07.011.
[22] Gao, Rong, Yan, Jinling, Li, Peiluan, Chen, Luonan. Detecting the critical states during disease development based on temporal network flow entropy. BRIEFINGS IN BIOINFORMATICS[J]. 2022, 23(5): http://dx.doi.org/10.1093/bib/bbac164.
[23] Zuo, Chunman, Dai, Hao, Chen, Luonan. Deep cross-omics cycle attention model for joint analysis of single-cell multi-omics data. BIOINFORMATICS[J]. 2021, 37(22): 4091-4099, http://dx.doi.org/10.1093/bioinformatics/btab403.
[24] He, Shutao, Wang, Hongxia, Hao, Xiaomeng, Wu, Yinliang, Bian, Xiaofeng, Yin, Minhao, Zhang, Yandi, Fan, Weijuan, Dai, Hao, Yuan, Ling, Zhang, Peng, Chen, Luonan. Dynamic network biomarker analysis discovers IbNAC083 in the initiation and regulation of sweet potato root tuberization. PLANT JOURNAL[J]. 2021, 108(3): 793-813, http://dx.doi.org/10.1111/tpj.15478.
[25] Li, Lin, Dai, Hao, Fang, Zhaoyuan, Chen, Luonan. c-CSN: Single-cell RNA Sequencing Data Analysis by Conditional Cell-specific Network. GENOMICS PROTEOMICS & BIOINFORMATICS[J]. 2021, 19(2): 319-329, http://dx.doi.org/10.1016/j.gpb.2020.05.0051672-0229.
[26] Wang, Lu, Xu, YiNing, Chu, ChungChing, Jing, Zehua, Chen, Yabin, Zhang, Jinsong, Pu, Mingming, Mi, Tingyan, Du, Yaping, Liang, Zongqi, Doraiswamy, Chandraprabha, Zeng, Tao, Wu, Jiarui, Chen, Luonan. Facial Skin Microbiota-Mediated Host Response to Pollution Stress Revealed by Microbiome Networks of Individual. MSYSTEMS[J]. 2021, 6(4): http://dx.doi.org/10.1128/mSystems.00319-21.
[27] Zuo, Chunman, Chen, Luonan. Deep-joint-learning analysis model of single cell transcriptome and open chromatin accessibility data. BRIEFINGS IN BIOINFORMATICS[J]. 2021, 22(4): http://dx.doi.org/10.1093/bib/bbaa287.
[28] Liu, Rui, Aihara, Kazuyuki, Chen, Luonan. Collective fluctuation implies imminent state transition Comment on "Dynamic and thermodynamic models of adaptation" by AN Gorban et al.. PHYSICS OF LIFE REVIEWSnull. 2021, 37: 103-107, http://dx.doi.org/10.1016/j.plrev.2021.04.002.
[29] Zhang, Chengming, Zhang, Hong, Ge, Jing, Mi, Tingyan, Cui, Xiao, Tu, Fengjuan, Gu, Xuelan, Zeng, Tao, Chen, Luonan. Landscape dynamic network biomarker analysis reveals the tipping point of transcriptome reprogramming to prevent skin photodamage. JOURNAL OF MOLECULAR CELL BIOLOGY[J]. 2021, 13(11): 822-833, http://dx.doi.org/10.1093/jmcb/mjab060.
[30] Shi, Qianqian, Li, Xinxing, Peng, Qirui, Zhang, Chuanchao, Chen, Luonan. scDA: Single cell discriminant analysis for single-cell RNA sequencing data. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL[J]. 2021, 19: 3234-3244, http://dx.doi.org/10.1016/j.csbj.2021.05.046.
[31] Yan, Jinling, Li, Peiluan, Gao, Rong, Li, Ying, Chen, Luonan. Identifying Critical States of Complex Diseases by Single-Sample Jensen-Shannon Divergence. FRONTIERS IN ONCOLOGY[J]. 2021, 11: http://dx.doi.org/10.3389/fonc.2021.684781.
[32] Guo, WeiFeng, Zhang, ShaoWu, Feng, YueHua, Liang, Jing, Zeng, Tao, Chen, Luonan. Network controllability-based algorithm to target personalized driver genes for discovering combinatorial drugs of individual patients. NUCLEIC ACIDS RESEARCH[J]. 2021, 49(7): e37-e37, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8053130/.
[33] Chen, Yabin, Fang, Zhaoyuan, Tang, Ying, Jin, Yujuan, Guo, Chenchen, Hu, Liang, Xu, Yang, Ma, Xidong, Gao, Jie, Xie, Mei, Zang, Xuelei, Liu, Sanhong, Chen, Haiquan, Thomas, Roman K, Xue, Xinying, Ji, Hongbin, Chen, Luonan. Integrative analysis of multi-omics data reveals the heterogeneity and signatures of immune therapy for small cell lung cancer. CLINICAL AND TRANSLATIONAL MEDICINEnull. 2021, 11(12): http://dx.doi.org/10.1002/ctm2.620.
[34] Zhang, Jingsong, Zhang, Yang, Kang, JunYan, Chen, Shuiye, He, Yongqun, Han, Benhao, Liu, MoFang, Lu, Lina, Li, Li, Yi, Zhigang, Chen, Luonan. Potential transmission chains of variant B.1.1.7 and co-mutations of SARS-CoV-2. CELL DISCOVERY[J]. 2021, 7(1): https://doaj.org/article/e314ef2374e84699be54f51a01b67741.
[35] Shi, Jifan, Aihara, Kazuyuki, Chen, Luonan. Dynamics-based data science in biology. NATIONAL SCIENCE REVIEW[J]. 2021, 8(5): 11-13, https://www.sciengine.com/doi/10.1093/nsr/nwab029.
[36] Siyang Leng, Huanfei Ma, Jrgen Kurths, YingCheng Lai, Wei Lin, Kazuyuki Aihara, Luonan Chen. Partial cross mapping eliminates indirect causal influences. NATURE COMMUNICATIONS[J]. 2020, 11(1): http://dx.doi.org/10.1038/s41467-020-16238-0.
[37] 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[J]. 2020, 25(2): [38] Ge, Jing, Song, Chenxi, Zhang, Chengming, Liu, Xiaoping, Chen, Jingzhou, Dou, Kefei, Chen, Luonan, 刘小平. Personalized Early-Warning Signals during Progression of Human Coronary Atherosclerosis by Landscape Dynamic Network Biomarker. GENES[J]. 2020, 11(6): https://doaj.org/article/11ff5effac5e425ebbc53e6ba88d9350.
[39] Dai, Hao, Jin, QiQi, Li, Lin, Chen, LuoNan. Reconstructing gene regulatory networks in single-cell transcriptomic data analysis. ZOOLOGICAL RESEARCHnull. 2020, 41(6): 599-604, https://doaj.org/article/0ee801013f794fefa0de5057c0d0b33d.
[40] Goetz, Hanah, MelendezAlvarez, Juan R, Chen, Luonan, Tian, XiaoJun. A plausible accelerating function of intermediate states in cancer metastasis. PLOS COMPUTATIONAL BIOLOGY[J]. 2020, 16(3): https://doaj.org/article/e285b0aae0d448bd98bfbfdc92907fdb.
[41] Feng, Jinwang, Zhang, ShaoWu, Chen, Luonan, Alzheimers Dis Neuroimaging Initia. Identification of Alzheimer's disease based on wavelet transformation energy feature of the structural MRI image and NN classifier. ARTIFICIAL INTELLIGENCE IN MEDICINE[J]. 2020, 108: http://dx.doi.org/10.1016/j.artmed.2020.101940.
[42] Chen, Pei, Liu, Rui, Aihara, Kazuyuki, Chen, Luonan. Autoreservoir computing for multistep ahead prediction based on the spatiotemporal information transformation. NATURE COMMUNICATIONS[J]. 2020, 11(1): https://www.webofscience.com/wos/woscc/full-record/WOS:000607111200029.
[43] Liu, Rui, Wang, Jinzeng, Ukai, Masao, Sewon, Ki, Chen, Pei, Suzuki, Yutaka, Wang, Haiyun, Aihara, Kazuyuki, OkadaHatakeyama, Mariko, Chen, Luonan. Hunt for the tipping point during endocrine resistance process in breast cancer by dynamic network biomarkers. JOURNAL OF MOLECULAR CELL BIOLOGY[J]. 2019, 11(8): 649-664, http://lib.cqvip.com/Qikan/Article/Detail?id=7003064455.
[44] Luonan Chen. Computational systems biology for omics data analysis. 分子细胞生物学报：英文版. 2019, 11(8): 631-632, http://lib.cqvip.com/Qikan/Article/Detail?id=7003064452.
[45] Yuwei Liu, Mengzhu Xue, Shaowei Du, Wanwan Feng, Ke Zhang, Liwen Zhang, Haiyue Liu, Guoyi Jia, Lingshuang Wu, Xin Hu, Luonan Chen, Peng Wang. Competitive endogenous RNA is an intrinsic component of EMT regulatory circuits and modulates EMT. NATURECOMMUNICATIONS[J]. 2019, 10(1): 1-12, http://dx.doi.org/10.1038/s41467-019-09649-1.
[46] Peng Tao, Qifan Wang, Jifan Shi, Xiaohu Hao, Xiaoping Liu, Bin Min, Yiheng Zhang, Chenyang Li, He Cui, Luonan Chen. Detecting dynamical causality by intersection cardinal concavity. FUNDAMENTAL RESEARCH. http://dx.doi.org/10.1016/j.fmre.2023.01.007.
[47] Jinling Yan, Peiluan Li, Ying Li, Rong Gao, Cheng Bi, Luonan Chen. Disease Prediction by Network Information Gain on a Single Sample Basis. FUNDAMENTAL RESEARCH. http://dx.doi.org/10.1016/j.fmre.2023.01.009.

International Conference on Computational Systems Biology. http://www.aporc.org/ISB/

（ 1 ） 肝脏炎癌恶性转化关键节点的动态网络标志物模型及临床应用研究, 主持, 国家级, 2016-01--2018-12
（ 2 ） 动物复杂性状的进化解析与调控, 主持, 部委级, 2014-01--2019-06
（ 3 ） 动脉粥样硬化发生发展过程中关键节点和调控网络的系统生物学研究, 主持, 国家级, 2015-01--2017-12
（ 4 ） 蛋白质机器在肺组织生理病理临界转化过程中的系统生物学研究, 主持, 国家级, 2017-01--2021-12

已指导学生

杨志远  硕士研究生  085238-生物工程  

李美仪  博士研究生  071021-生物信息学  

张万纬  博士研究生  071021-生物信息学  

林婕  博士研究生  0710J3-生物信息学  

史倩倩  博士研究生  0710J3-生物信息学  

葛静  博士研究生  0710J3-生物信息学  

李高鹏  博士研究生  0710J3-生物信息学  

仪洪洋  硕士研究生  085238-生物工程  

卢丽娜  博士研究生  0710J3-生物信息学  

赵娟  博士研究生  0710J3-生物信息学  

姜钟琳  博士研究生  0710J3-生物信息学  

周祎炜  博士研究生  0710J3-生物信息学  

王子明  硕士研究生  0710J3-生物信息学  

张蕾  硕士研究生  085238-生物工程  

樊小亚  硕士研究生  085238-生物工程  

唐莹  硕士研究生  0710J3-生物信息学  

张思  硕士研究生  0710J3-生物信息学  

现指导学生

唐慧  博士研究生  0710J3-生物信息学  

袁铠  硕士研究生  085238-生物工程  

李琳  博士研究生  0710J3-生物信息学  

唐诗婕  博士研究生  0710J3-生物信息学  

辛振国  硕士研究生  085238-生物工程  

琚张磊  硕士研究生  071009-细胞生物学  

孟祎玮  硕士研究生  071009-细胞生物学  

张城铭  博士研究生  0710J3-生物信息学  

韩本昊  硕士研究生  085238-生物工程  

王家豪  硕士研究生  071009-细胞生物学  

王乐群  硕士研究生  0710J3-生物信息学