发表论文
[1] Wang Zijian, Tao Peng, Chen Luonan. Brain-inspired chaotic spiking backpropagation. NATIONAL SCIENCE REVIEW[J]. 2024, 第 3 作者11(6): http://sciencechina.cn/gw.jsp?action=detail.jsp&internal_id=7771558&detailType=1.[2] Zhu, Junchao, Dai, Hao, Chen, Luonan. Revealing cell-cell communication pathways with their spatially coupled gene programs. BRIEFINGS IN BIOINFORMATICS[J]. 2024, 第 3 作者 通讯作者 25(3): http://dx.doi.org/10.1093/bib/bbae202.[3] 陈洛南. Quantifying Individual Health Status from Multi‑omics Data by Health State Map. Phenomics[J]. 2024, 第 1 作者 通讯作者 null(null): https://doi.org/10.1007/s43657-024-00188-4.[4] 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. Correction to:Identification of TAZ as the essential molecular switch in orchestrating SCLC phenotypic transition and metastasis. NATIONAL SCIENCE REVIEW. 2023, 第 20 作者10(12): 222-222, http://lib.cqvip.com/Qikan/Article/Detail?id=7111569298.[5] 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, 第 22 作者 通讯作者 10((4)): [6] 陈洛南. Earthquake alerting based on spatial geodetic data by spatiotemporal information transformation learning. Proc Natl Acad Sci U S A[J]. 2023, 第 1 作者 通讯作者 [7] 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, 第 11 作者 通讯作者 4(1): http://dx.doi.org/10.1016/j.xinn.2022.100364.[8] Tao, Peng, Hao, Xiaohu, Cheng, Jie, Chen, Luonan. Predicting time series by data-driven spatiotemporal information transformation. INFORMATION SCIENCES[J]. 2023, 第 4 作者 通讯作者 622: 859-872, http://dx.doi.org/10.1016/j.ins.2022.11.159.[9] 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, 第 16 作者 通讯作者 8(1): 730-743, http://dx.doi.org/10.1038/s41392-022-01227-0.[10] 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, 第 16 作者 通讯作者 14(1): 1-19, http://dx.doi.org/10.1038/s41467-023-39750-5.[11] 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, 第 14 作者 通讯作者 13(1): http://dx.doi.org/10.1038/s41467-022-29968-0.[12] Shi, Jifan, Aihara, Kazuyuki, Li, Tiejun, Chen, Luonan. Energy landscape decomposition for cell differentiation with proliferation effect. NATIONAL SCIENCE REVIEW[J]. 2022, 第 4 作者 通讯作者 9(8): 135-143, http://lib.cqvip.com/Qikan/Article/Detail?id=7108215190.[13] 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, 第 17 作者 通讯作者 13(1): http://dx.doi.org/10.1038/s41467-022-29857-6.[14] 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, 第 3 作者 通讯作者 9: http://dx.doi.org/10.3389/fcell.2021.720321.[15] 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, 第 6 作者 通讯作者 13(1): http://dx.doi.org/10.1038/s41467-022-33619-9.[16] 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, 第 6 作者 通讯作者 14(2): 32-42, http://lib.cqvip.com/Qikan/Article/Detail?id=7107772557.[17] You, Yujie, Zhang, Le, Tao, Peng, Liu, Suran, Chen, Luonan. Spatiotemporal Transformer Neural Network for Time-Series Forecasting. ENTROPY[J]. 2022, 第 5 作者 通讯作者 24(11): http://dx.doi.org/10.3390/e24111651.[18] 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, 第 20 作者9(7): 10-24, http://lib.cqvip.com/Qikan/Article/Detail?id=7107930144.[19] 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, 第 13 作者 通讯作者 43(5): 805-812, http://sciencechina.cn/gw.jsp?action=detail.jsp&internal_id=7322195&detailType=1.[20] Meng, Yiwei, Huang, Yanhong, Chang, Xiao, Liu, Xiaoping, Chen, Luonan. Transcriptome analysis method based on differential distribution evaluation. BRIEFINGS IN BIOINFORMATICS[J]. 2022, 第 5 作者 通讯作者 23(2): http://dx.doi.org/10.1093/bib/bbab608.[21] Tao, Peng, Cheng, Jie, Chen, Luonan. Brain-inspired chaotic backpropagation for MLP. NEURAL NETWORKS[J]. 2022, 第 3 作者 通讯作者 155: 1-13, http://dx.doi.org/10.1016/j.neunet.2022.08.004.[22] 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, 第 7 作者 通讯作者 20: 3556-3566, https://doaj.org/article/cf921a70a1b743369bba38f06e7eaf62.[23] 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, 第 3 作者 通讯作者 2(6): 894-902, http://dx.doi.org/10.1016/j.fmre.2022.07.011.[24] 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, 第 4 作者 通讯作者 23(5): http://dx.doi.org/10.1093/bib/bbac164.[25] 陈洛南. http://sysbio.sibcb.ac.cn/sysbio/cb/chenlab/LuonanChen.htm. 2022, 第 1 作者[26] 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, 第 3 作者 通讯作者 98: http://dx.doi.org/10.1016/j.compmedimag.2022.102057.[27] Zuo, Chunman, Dai, Hao, Chen, Luonan. Deep cross-omics cycle attention model for joint analysis of single-cell multi-omics data. BIOINFORMATICS[J]. 2021, 第 3 作者 通讯作者 37(22): 4091-4099, http://dx.doi.org/10.1093/bioinformatics/btab403.[28] 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, 第 12 作者 通讯作者 108(3): 793-813, http://dx.doi.org/10.1111/tpj.15478.[29] 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, 第 4 作者 通讯作者 19(2): 319-329, http://dx.doi.org/10.1016/j.gpb.2020.05.0051672-0229.[30] Lu Wang, YiNing Xu, ChungChing 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[J]. 2021, 第 14 作者 通讯作者 6(4): http://dx.doi.org/10.1128/mSystems.00319-21.[31] Zuo, Chunman, Chen, Luonan. Deep-joint-learning analysis model of single cell transcriptome and open chromatin accessibility data. BRIEFINGS IN BIOINFORMATICS[J]. 2021, 第 2 作者 通讯作者 22(4): http://dx.doi.org/10.1093/bib/bbaa287.[32] 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 REVIEWS. 2021, 第 3 作者 通讯作者 37: 103-107, http://dx.doi.org/10.1016/j.plrev.2021.04.002.[33] 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, 第 9 作者 通讯作者 13(11): 822-833, http://dx.doi.org/10.1093/jmcb/mjab060.[34] 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, 第 5 作者 通讯作者 19: 3234-3244, http://dx.doi.org/10.1016/j.csbj.2021.05.046.[35] 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, 第 5 作者 通讯作者 11: http://dx.doi.org/10.3389/fonc.2021.684781.[36] 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, 第 6 作者 通讯作者 49(7): e37-e37, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8053130/.[37] 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 MEDICINE. 2021, 第 17 作者 通讯作者 11(12): http://dx.doi.org/10.1002/ctm2.620.[38] 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, 第 11 作者 通讯作者 7(1): https://doaj.org/article/e314ef2374e84699be54f51a01b67741.[39] Shi, Jifan, Aihara, Kazuyuki, Chen, Luonan. Dynamics-based data science in biology. NATIONAL SCIENCE REVIEW[J]. 2021, 第 3 作者 通讯作者 8(5): 11-13, https://www.sciengine.com/doi/10.1093/nsr/nwab029.[40] 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, 第 6 作者25(2): [41] 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, 第 7 作者 通讯作者 11(1): http://dx.doi.org/10.1038/s41467-020-16238-0.[42] 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, 第 7 作者 通讯作者 11(6): https://doaj.org/article/11ff5effac5e425ebbc53e6ba88d9350.[43] Dai, Hao, Jin, QiQi, Li, Lin, Chen, LuoNan. Reconstructing gene regulatory networks in single-cell transcriptomic data analysis. ZOOLOGICAL RESEARCH. 2020, 第 4 作者 通讯作者 41(6): 599-604, http://sciencechina.cn/gw.jsp?action=detail.jsp&internal_id=6901578&detailType=1.[44] Goetz, Hanah, MelendezAlvarez, Juan R, Chen, Luonan, Tian, XiaoJun. A plausible accelerating function of intermediate states in cancer metastasis. PLOS COMPUTATIONAL BIOLOGY[J]. 2020, 第 3 作者16(3): https://doaj.org/article/e285b0aae0d448bd98bfbfdc92907fdb.[45] 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, 第 3 作者 通讯作者 108: http://dx.doi.org/10.1016/j.artmed.2020.101940.[46] Chen, Pei, Liu, Rui, Aihara, Kazuyuki, Chen, Luonan. Autoreservoir computing for multistep ahead prediction based on the spatiotemporal information transformation. NATURE COMMUNICATIONS[J]. 2020, 第 4 作者 通讯作者 11(1): https://www.webofscience.com/wos/woscc/full-record/WOS:000607111200029.[47] 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, 第 10 作者 通讯作者 11(8): 649-664, http://lib.cqvip.com/Qikan/Article/Detail?id=7003064455.[48] Luonan Chen. Computational systems biology for omics data analysis. 分子细胞生物学报:英文版. 2019, 第 1 作者 通讯作者 11(8): 631-632, http://lib.cqvip.com/Qikan/Article/Detail?id=7003064452.[49] 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, 第 11 作者 通讯作者 10(1): 1-12, http://dx.doi.org/10.1038/s41467-019-09649-1.[50] 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. 第 10 作者 通讯作者 http://dx.doi.org/10.1016/j.fmre.2023.01.007.[51] 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. 第 6 作者 通讯作者 http://dx.doi.org/10.1016/j.fmre.2023.01.009.