基于单样本组学数据的生物分子网络构建理论和方法
31771476
2017
C0609.生物大数据解析
陈洛南
面上项目
研究员
中国科学院分子细胞科学卓越创新中心
60万元
网络生物学;网络重构;系统生物学;人;网络分析
2018-01-01到2021-12-31
- 中英文摘要
- 结题摘要
- 结题报告
- 项目成果
- 项目参与人
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| 序号 | 标题 | 类型 | 作者 |
|---|---|---|---|
| 1 | Dynamics-based data science in biology. | 期刊论文 | Shi Jifan;Aihara Kazuyuki;Chen Luonan |
| 2 | RDAClone: Deciphering Tumor Heterozygosity through Single-Cell Genomics Data Analysis with Robust Deep Autoencoder. | 期刊论文 | Xia Jie;Wang Lequn;Zhang Guijun;Zuo Chunman;Chen Luonan |
| 3 | A Branch Point on Differentiation Trajectory is the Bifurcating Event Revealed by Dynamical Network Biomarker Analysis of Single-Cell Data | 期刊论文 | Chen Ziwei;Bai Xiangqi;Ma Liang;Wang Xiawei;Liu Xiuqin;Liu Yuting;Chen Luonan;Wan Lin |
| 4 | Deep-joint-learning analysis model of single cell transcriptome and open chromatin accessibility data. | 期刊论文 | Zuo Chunman;Chen Luonan |
| 5 | The generation mechanism of spike-and-slow wave discharges appearing on thalamic relay nuclei. | 期刊论文 | Hu Bing;Guo Yu;Shi Feng;Zou Xiaoqiang;Dong Jing;Pan Long;Yu Min;Zhou Chaowei;Cheng Zhang;Tang Wanyue;Sun Haochen;Chen Luonan |
| 6 | Revealing dynamic regulations and the related key proteins of myeloma-initiating cells by integrating experimental data into a systems biological model. | 期刊论文 | Zhang Le;Liu Guangdi;Kong Meijing;Li Tingting;Wu Dan;Zhou Xiaobo;Yang Chuanwei;Xia Lei;Yang Zhenzhou;Chen Luonan |
| 7 | Dynamic edge-based biomarker non-invasively predicts hepatocellular carcinoma with hepatitis B virus infection for individual patients based on blood testing. | 期刊论文 | Lu Yiyu;Fang Zhaoyuan;Li Meiyi;Chen Qian;Zeng Tao;Lu Lina;Chen Qilong;Zhang Hui;Zhou Qianmei;Sun Yan;Xue Xuefeng;Hu Yiyang;Chen Luonan;Su Shibing |
| 8 | Specific gut microbiome signature predicts the early-stage lung cancer | 期刊论文 | Zheng Yajuan;Fang Zhaoyuan;Xue Yun;Zhang Jian;Zhu Junjie;Gao Renyuan;Yao Shun;Ye Yi;Wang Shihui;Lin Changdong;Chen Shiyang;Huang Hsinyi;Hu Liang;Jiang Ge-Ning;Qin Huanlong;Zhang Peng;Chen Jianfeng;Ji Hongbin |
| 9 | Deep cross-omics cycle attention model for joint analysis of single-cell multi-omics data. | 期刊论文 | Zuo Chunman;Dai Hao;Chen Luonan |
| 10 | Efficient Mining Multi-Mers in a Variety of Biological Sequences | 期刊论文 | Zhang Jingsong;Guo Jianmei;Zhang Ming;Yu Xiangtian;Yu Xiaoqing;Guo Weifeng;Zeng Tao;Chen Luonan |
| 11 | Hierarchical graphical model reveals HFR1 bridging circadian rhythm and flower development in Arabidopsis thaliana. | 期刊论文 | Duren Zhana;Wang Yaling;Wang Jiguang;Zhao Xing-Ming;Lv Le;Li Xiaobo;Liu Jingdong;Zhu Xin-Guang;Chen Luonan;Wang Yong |
| 12 | Network controllability-based algorithm to target personalized driver genes for discovering combinatorial drugs of individual patients. | 期刊论文 | Guo Wei-Feng;Zhang Shao-Wu;Feng Yue-Hua;Liang Jing;Zeng Tao;Chen Luonan |
| 13 | Dynamic network biomarker indicates pulmonary metastasis at the tipping point of hepatocellular carcinoma. | 期刊论文 | Yang Biwei;Li Meiyi;Tang Wenqing;Liu Weixin;Zhang Si;Chen Luonan;Xia Jinglin |
| 14 | Different effects of fast and slow input fluctuations on output in gene regulation. | 期刊论文 | Qiu Huahai;Yuan Zhanjiang;Zhou Tianshou;Chen Luonan |
| 15 | Regulation and control roles of the basal ganglia in the development of absence epileptiform activities | 期刊论文 | Hu Bing;Wang Dingjiang;Xia Zhinan;Yang Aijun;Zhang Jingsong;Shi Qianqian;Dai Hao |
| 16 | Facial Skin Microbiota-Mediated Host Response to Pollution Stress Revealed by Microbiome Networks of Individual. | 期刊论文 | Wang Lu;Xu Yi-Ning;Chu Chung-Ching;Jing Zehua;Chen Yabin;Zhang Jinsong;Pu Mingming;Mi Tingyan;Du Yaping;Liang Zongqi;Doraiswamy Chandraprabha;Zeng Tao;Wu Jiarui;Chen Luonan |
| 17 | Single cell clustering based on cell-pair differentiability correlation and variance analysis. | 期刊论文 | Jiang Hao;Sohn Lydia L;Huang Haiyan;Chen Luonan |
| 18 | Genome-wide dynamic network analysis reveals a critical transition state of flower development in Arabidopsis. | 期刊论文 | Zhang Fuping;Liu Xiaoping;Zhang Aidi;Jiang Zhonglin;Chen Luonan;Zhang Xiujun |
| 19 | Single-sample landscape entropy reveals the imminent phase transition during disease progression. | 期刊论文 | Liu Rui;Chen Pei;Chen Luonan |
| 20 | Collective fluctuation implies imminent state transition: Comment on "Dynamic and thermodynamic models of adaptation" by A.N. Gorban et al. | 期刊论文 | Liu Rui;Aihara Kazuyuki;Chen Luonan |
| 21 | Predicting future dynamics from short-term time series using an Anticipated Learning Machine. | 期刊论文 | Chen Chuan;Li Rui;Shu Lin;He Zhiyu;Wang Jining;Zhang Chengming;Ma Huanfei;Aihara Kazuyuki;Chen Luonan |
| 22 | Detecting early-warning signals of influenza outbreak based on dynamic network marker. | 期刊论文 | Chen Pei;Chen Ely;Chen Luonan;Zhou Xianghong Jasmine;Liu Rui |
| 23 | Identification of Key Genes for the Ultrahigh Yield of Rice Using Dynamic Cross-tissue Network Analysis. | 期刊论文 | Hu Jihong;Zeng Tao;Xia Qiongmei;Huang Liyu;Zhang Yesheng;Zhang Chuanchao;Zeng Yan;Liu Hui;Zhang Shilai;Huang Guangfu;Wan Wenting;Ding Yi;Hu Fengyi;Yang Congdang;Chen Luonan;Wang Wen |
| 24 | Detection for disease tipping points by landscape dynamic network biomarkers. | 期刊论文 | Liu Xiaoping;Chang Xiao;Leng Siyang;Tang Hui;Aihara Kazuyuki;Chen Luonan |
| 25 | Gene expression analysis reveals the tipping points during infant brain development for human and chimpanzee. | 期刊论文 | Tang Hui;Tang Ying;Zeng Tao;Chen Luonan |
| 26 | Improved Human Age Prediction by Using Gene Expression Profiles From Multiple Tissues. | 期刊论文 | Wang Fayou;Yang Jialiang;Lin Huixin;Li Qian;Ye Zixuan;Lu Qingqing;Chen Luonan;Tu Zhidong;Tian Geng |
| 27 | Tgfb3 and Mmp13 regulated the initiation of liver fibrosis progression as dynamic network biomarkers. | 期刊论文 | Guo Jinsheng;Liu Weixin;Zeng Zhiping;Lin Jie;Zhang Xingxin;Chen Luonan |
| 28 | PWCDA: Path Weighted Method for Predicting circRNA-Disease Associations. | 期刊论文 | Lei Xiujuan;Fang Zengqiang;Chen Luonan;Wu Fang-Xiang |
| 29 | Personalized Early-Warning Signals during Progression of Human Coronary Atherosclerosis by Landscape Dynamic Network Biomarker. | 期刊论文 | Ge Jing;Song Chenxi;Zhang Chengming;Liu Xiaoping;Chen Jingzhou;Dou Kefei;Chen Luonan |
| 30 | Cell-specific network constructed by single-cell RNA sequencing data. | 期刊论文 | Dai Hao;Li Lin;Zeng Tao;Chen Luonan |
| 31 | Kinase-substrate Edge Biomarkers Provide a More Accurate Prognostic Prediction in ER-negative Breast Cancer. | 期刊论文 | Sun Yidi;Li Chen;Pang Shichao;Yao Qianlan;Chen Luonan;Li Yixue;Zeng Rong |
| 32 | Identification of Alzheimer's disease based on wavelet transformation energy feature of the structural MRI image and NN classifier. | 期刊论文 | Feng Jinwang;Zhang Shao-Wu;Chen Luonan |
| 33 | Identifying Critical States of Complex Diseases by Single-Sample Jensen-Shannon Divergence. | 期刊论文 | Yan Jinling;Li Peiluan;Gao Rong;Li Ying;Chen Luonan |
| 34 | Network control principles for identifying personalized driver genes in cancer. | 期刊论文 | Guo Wei-Feng;Zhang Shao-Wu;Zeng Tao;Akutsu Tatsuya;Chen Luonan |
| 35 | Individual-specific edge-network analysis for disease prediction | 期刊论文 | Yu Xiangtian;Zhang Jingsong;Sun Shaoyan;Zhou Xin;Zeng Tao;Chen Luonan |
| 36 | Systems Signatures Reveal Unique Remission-path of Type 2 Diabetes Following Roux-en-Y Gastric Bypass Surgery. | 期刊论文 | Li Qing-Run;Wang Zi-Ming;Wewer Albrechtsen Nicolai J;Wang Dan-Dan;Su Zhi-Duan;Gao Xian-Fu;Wu Qing-Qing;Zhang Hui-Ping;Zhu Li;Li Rong-Xia;Jacobsen SivHesse;Jørgensen Nils Bruun;Dirksen Carsten;Bojsen-Møller Kirstine N;Petersen Jacob S;Madsbad Sten;Clausen Trine R;Diderichsen Børge;Chen Luo-Nan;Holst Jens J;Zeng Rong;Wu Jia-Rui |
| 37 | The oscillatory boundary conditions of different frequency bands in Parkinson's disease. | 期刊论文 | Hu Bing;Shi Qianqian;Guo Yu;Diao Xiyezi;Guo Heng;Zhang Jinsong;Yu Liang;Dai Hao;Chen Luonan |
| 38 | Discovering personalized driver mutation profiles of single samples in cancer by network control strategy | 期刊论文 | Guo Wei Feng;Zhang Shao Wu;Liu Li Li;Liu Fei;Shi Qian Qian;Zhang Lei;Tang Ying;Zeng Tao;Chen Luonan |
| 39 | Autoreservoir computing for multistep ahead prediction based on the spatiotemporal information transformation. | 期刊论文 | Chen Pei;Liu Rui;Aihara Kazuyuki;Chen Luonan |
| 40 | Systems biology intertwines with single cell and AI | 期刊论文 | Wang Yong;Zhang Xiang Sun;Chen Luonan |
| 41 | "Dysfunctions" induced by Roux-en-Y gastric bypass surgery are concomitant with metabolic improvement independent of weight loss. | 期刊论文 | Li Meiyi;Liu Zhiyuan;Qian Bangguo;Liu Weixin;Horimoto Katsuhisa;Xia Jie;Shi Meilong;Wang Bing;Zhou Huarong;Chen Luonan |
| 42 | Victors: a web-based knowledge base of virulence factors in human and animal pathogens. | 期刊论文 | 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 Xing-Ming;Olszewski Michal A;Chen Luonan;He Yongqun |
| 43 | A Semisupervised Classification Approach for Multidomain Networks With Domain Selection | 期刊论文 | Chen Chuan;Xin Jingxue;Wang Yong;Chen Luonan;Ng Michael K |
| 44 | The onset mechanism of Parkinson's beta oscillations: A theoretical analysis. | 期刊论文 | Hu Bing;Diao Xiyezi;Zong Liqing;Zhang Jingsong;Yu Liang;Dai Hao;Chen Luonan |
| 45 | Low-Grade Dysplastic Nodules Revealed as the Tipping Point during Multistep Hepatocarcinogenesis by Dynamic Network Biomarkers | 期刊论文 | Lu Lina;Jiang Zhonglin;Dai Yulin;Chen Luonan |
| 46 | Unravelling miRNA regulation in yield of rice (Oryza sativa) based on differential network model. | 期刊论文 | Hu Jihong;Zeng Tao;Xia Qiongmei;Qian Qian;Yang Congdang;Ding Yi;Chen Luonan;Wang Wen |
| 47 | Disease characterization using a partial correlation-based sample-specific network. | 期刊论文 | Huang Yanhong;Chang Xiao;Zhang Yu;Chen Luonan;Liu Xiaoping |
| 48 | Potential transmission chains of variant B.1.1.7 and co-mutations of SARS-CoV-2. | 期刊论文 | Zhang Jingsong;Zhang Yang;Kang Jun-Yan;Chen Shuiye;He Yongqun;Han Benhao;Liu Mo-Fang;Lu Lina;Li Li;Yi Zhigang;Chen Luonan |
| 49 | Single-cell RNA-sequencing atlas reveals an MDK-dependent immunosuppressive environment in ErbB pathway-mutated gallbladder cancer. | 期刊论文 | Zhang Yijian;Zuo Chunman;Liu Liguo;Hu Yunping;Yang Bo;Qiu Shimei;Li Yang;Cao Dongyan;Ju Zheng;Ge Jing;Wang Qiu;Wang Ting;Bai Lu;Yang Yang;Li Guoqiang;Shao Ziyu;Gao Yuan;Li Yongsheng;Bian Rui;Miao Huijie;Li Lin;Li Xuechuan;Jiang Chengkai;Yan Siyuan;Wang Ziyi;Wang Zeyu;Cui Xuya;Huang Wen;Xiang Dongxi;Wang Congjun;Li Qiyun;Wu Xiangsong;Gong Wei;Liu Yun;Shao Rong;Liu Fatao;Li Maolan... |
| 50 | The Effects of Graded Levels of Calorie Restriction XV: Phase Space Attractors Reveal Distinct Behavioral Phenotypes | 期刊论文 | Sun Deshun;Liu Fei;Mitchell Sharon E.;Ma Huanfei;Derous Davina;Wang Yingchun;Han Jackie J. D.;Promislow Daniel E. L.;Lusseau David;Douglas Alex;Speakman John R.;Chen Luonan |
| 51 | A novel network control model for identifying personalized driver genes in cancer. | 期刊论文 | Guo Wei-Feng;Zhang Shao-Wu;Zeng Tao;Li Yan;Gao Jianxi;Chen Luonan |
| 52 | Dynamic network biomarker analysis discovers IbNAC083 in the initiation and regulation of sweet potato root tuberization. | 期刊论文 | He Shutao;Wang Hongxia;Hao Xiaomeng;Wu Yinliang;Bian Xiaofeng;Yin Minhao;Zhang Yandi;Fan Weijuan;Dai Hao;Yuan Ling;Zhang Peng;Chen Luonan |
| 53 | Reconstructing gene regulatory networks in single-cell transcriptomic data analysis. | 期刊论文 | Dai Hao;Jin Qi-Qi;Li Lin;Chen Luo-Nan |
| 54 | High-Order Correlation Integration for Single-Cell or Bulk RNA-seq Data Analysis. | 期刊论文 | Tang Hui;Zeng Tao;Chen Luonan |
| 55 | Landscape dynamic network biomarker analysis reveals the tipping point of transcriptome reprogramming to prevent skin photodamage. | 期刊论文 | Zhang Chengming;Zhang Hong;Ge Jing;Mi Tingyan;Cui Xiao;Tu Fengjuan;Gu Xuelan;Zeng Tao;Chen Luonan |
| 56 | SMAD7 and SERPINE1 as novel dynamic network biomarkers detect and regulate the tipping point of TGF-beta induced EMT | 期刊论文 | Jiang Zhonglin;Lu Lina;Liu Yuwei;Zhang Si;Li Shuxian;Wang Guanyu;Wang Peng;Chen Luonan |
| 57 | Randomly distributed embedding making short-term high-dimensional data predictable. | 期刊论文 | Ma Huanfei;Leng Siyang;Aihara Kazuyuki;Lin Wei;Chen Luonan |
| 58 | c-CSN: Single-cell RNA Sequencing Data Analysis by Conditional Cell-specific Network. | 期刊论文 | Li Lin;Dai Hao;Fang Zhaoyuan;Chen Luonan |
| 59 | Pan-cancer network disorders revealed by overall and local signaling entropy. | 期刊论文 | Feng Li;Sun Yi-Di;Li Chen;Li Yi-Xue;Chen Luo-Nan;Zeng Rong |
| 60 | Possible pathological mechanisms of absence seizures appearing in the reticular thalamic nucleus: A theoretical basis | 期刊论文 | Bing Hu;Dingjiang Wang;Zhinan Xia;Dongmei Zhang;Aijun Yang;Qianqian Shi;Jingsong Zhang;Hao Dai |
| 61 | Hunt for the tipping point during endocrine resistance process in breast cancer by dynamic network biomarkers. | 期刊论文 | Liu Rui;Wang Jinzeng;Ukai Masao;Sewon Ki;Chen Pei;Suzuki Yutaka;Wang Haiyun;Aihara Kazuyuki;Okada-Hatakeyama Mariko;Chen Luonan |
| 62 | scDA: Single cell discriminant analysis for single-cell RNA sequencing data. | 期刊论文 | Shi Qianqian;Li Xinxing;Peng Qirui;Zhang Chuanchao;Chen Luonan |
| 63 | Partial cross mapping eliminates indirect causal influences. | 期刊论文 | Leng Siyang;Ma Huanfei;Kurths Jürgen;Lai Ying-Cheng;Lin Wei;Aihara Kazuyuki;Chen Luonan |
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