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2020 – today
- 2024
- [j132]Lequn Wang, Yaofeng Hu, Kai Xiao, Chuanchao Zhang, Qianqian Shi, Luonan Chen:
Multi-modal domain adaptation for revealing spatial functional landscape from spatially resolved transcriptomics. Briefings Bioinform. 25(4) (2024) - [c51]Shangyan Cai, Weitian Huang, Weiting Yi, Bin Zhang, Yi Liao, Qiu Wang, Hongmin Cai, Luonan Chen, Weifeng Su:
Survival Analysis of Histopathological Image Based on a Pretrained Hypergraph Model of Spatial Transcriptomics Data. MICCAI (3) 2024: 455-466 - [i7]Jifan Shi, Yang Li, Juan Zhao, Siyang Leng, Kazuyuki Aihara, Luonan Chen, Wei Lin:
Deciphering interventional dynamical causality from non-intervention systems. CoRR abs/2407.01621 (2024) - [i6]Qibin Zhang, Chengshang Lyu, Lingxi Chen, Qiqi Jin, Luonan Chen:
CIDER: Counterfactual-Invariant Diffusion-based GNN Explainer for Causal Subgraph Inference. CoRR abs/2407.19376 (2024) - [i5]Jinling Yan, Shao-Wu Zhang, Chihao Zhang, Weitian Huang, Jifan Shi, Luonan Chen:
Dynamical causality under invisible confounders. CoRR abs/2408.05584 (2024) - 2023
- [j131]Lin Li, Rui Xia, Wei Chen, Qi Zhao, Peng Tao, Luonan Chen:
Single-cell causal network inferred by cross-mapping entropy. Briefings Bioinform. 24(5) (2023) - [j130]Chengming Zhang, Yiwen Yang, Shijie Tang, Kazuyuki Aihara, Chuanchao Zhang, Luonan Chen:
Contrastively generative self-expression model for single-cell and spatial multimodal data. Briefings Bioinform. 24(5) (2023) - [j129]Peng Tao, Xiaohu Hao, Jie Cheng, Luonan Chen:
Predicting time series by data-driven spatiotemporal information transformation. Inf. Sci. 622: 859-872 (2023) - [j128]Yi-Xuan Xiong, Meng-Guo Wang, Luonan Chen, Xiao-Fei Zhang:
Cell-type annotation with accurate unseen cell-type identification using multiple references. PLoS Comput. Biol. 19(6) (2023) - [j127]Yuanling Niu, Hao Kang, Pingyang Wang, Chenchen Guo, Fan Nie, Hongbin Ji, Jiarui Wu, Luonan Chen:
Why Increase of Heterogeneity Signals Pre-Deterioration During Tumor Progression: A Unified Mathematical Model. SIAM J. Appl. Math. 83(2): 791-815 (2023) - 2022
- [j126]Yiwei Meng, Yanhong Huang, Xiao Chang, Xiaoping Liu, Luonan Chen:
Transcriptome analysis method based on differential distribution evaluation. Briefings Bioinform. 23(2) (2022) - [j125]Chengming Zhang, Yabin Chen, Tao Zeng, Chuanchao Zhang, Luonan Chen:
Deep latent space fusion for adaptive representation of heterogeneous multi-omics data. Briefings Bioinform. 23(2) (2022) - [j124]Rong Gao, Jinling Yan, Peiluan Li, Luonan Chen:
Detecting the critical states during disease development based on temporal network flow entropy. Briefings Bioinform. 23(5) (2022) - [j123]Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-Hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi, Lynn M. Schriml, Jie Zheng, Anna Maria Masci, Liwei Wang, Hongfang Liu, Fatima Zohra Smaili, Robert Hoehndorf, Zoë May Pendlington, Paola Roncaglia, Xianwei Ye, Jiangan Xie, Yi-Wei Tang, Xiaolin Yang, Suyuan Peng, Luxia Zhang, Luonan Chen, Junguk Hur, Gilbert S. Omenn, Brian D. Athey, Barry Smith:
A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology. J. Biomed. Semant. 13(1): 25 (2022) - [j122]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 Bioinform. 23(1): 230 (2022) - [j121]Jinwang Feng, ShaoWu Zhang, Luonan Chen, Chunman Zuo, Alzheimer's Disease Neuroimaging Initiative:
Detection of Alzheimer's disease using features of brain region-of-interest-based individual network constructed with the sMRI image. Comput. Medical Imaging Graph. 98: 102057 (2022) - [j120]Yujie You, Le Zhang, Peng Tao, Suran Liu, Luonan Chen:
Spatiotemporal Transformer Neural Network for Time-Series Forecasting. Entropy 24(11): 1651 (2022) - [j119]Jining Wang, Chuan Chen, Zibin Zheng, Luonan Chen, Yuren Zhou:
Predicting high-dimensional time series data with spatial, temporal and global information. Inf. Sci. 607: 477-492 (2022) - [j118]Peng Tao, Jie Cheng, Luonan Chen:
Brain-inspired chaotic backpropagation for MLP. Neural Networks 155: 1-13 (2022) - [j117]Jinwang Feng, Shaowu Zhang, Luonan Chen:
Extracting ROI-Based Contourlet Subband Energy Feature From the sMRI Image for Alzheimer's Disease Classification. IEEE ACM Trans. Comput. Biol. Bioinform. 19(3): 1627-1639 (2022) - [i4]Peng Tao, Xiaohu Hao, Jie Cheng, Luonan Chen:
Time Series Prediction by Multi-task GPR with Spatiotemporal Information Transformation. CoRR abs/2204.12085 (2022) - 2021
- [j116]Yanhong Huang, Xiao Chang, Yu Zhang, Luonan Chen, Xiaoping Liu:
Disease characterization using a partial correlation-based sample-specific network. Briefings Bioinform. 22(3) (2021) - [j115]Chunman Zuo, Luonan Chen:
Deep-joint-learning analysis model of single cell transcriptome and open chromatin accessibility data. Briefings Bioinform. 22(4) (2021) - [j114]Le Zhang, Guangdi Liu, Meijing Kong, Tingting Li, Dan Wu, Xiaobo Zhou, Chuanwei Yang, Lei Xia, Zhenzhou Yang, Luonan Chen:
Revealing dynamic regulations and the related key proteins of myeloma-initiating cells by integrating experimental data into a systems biological model. Bioinform. 37(11): 1554-1561 (2021) - [j113]Chunman Zuo, Hao Dai, Luonan Chen:
Deep cross-omics cycle attention model for joint analysis of single-cell multi-omics data. Bioinform. 37(22): 4091-4099 (2021) - [j112]Lin Li, Hao Dai, Zhaoyuan Fang, Luonan Chen:
c-CSN: Single-cell RNA Sequencing Data Analysis by Conditional Cell-specific Network. Genom. Proteom. Bioinform. 19(2): 319-329 (2021) - [j111]Luonan Chen, Rong Fan, Fuchou Tang:
Advanced Single-cell Omics Technologies and Informatics Tools for Genomics, Proteomics, and Bioinformatics Analysis. Genom. Proteom. Bioinform. 19(3): 343-345 (2021) - [j110]Jinwang Feng, Shaowu Zhang, Luonan Chen, Jie Xia:
Alzheimer's disease classification using features extracted from nonsubsampled contourlet subband-based individual networks. Neurocomputing 421: 260-272 (2021) - [i3]Hao Peng, Pei Chen, Rui Liu, Luonan Chen:
Spatiotemporal convolutional network for time-series prediction and causal inference. CoRR abs/2107.01353 (2021) - 2020
- [j109]Jinwang Feng, Shao-Wu Zhang, Luonan Chen, Alzheimer's Disease Neuroimaging Initiative:
Identification of Alzheimer's disease based on wavelet transformation energy feature of the structural MRI image and NN classifier. Artif. Intell. Medicine 108: 101940 (2020) - [j108]Jifan Shi, Andrew E. Teschendorff, Weiyan Chen, Luonan Chen, Tiejun Li:
Quantifying Waddington's epigenetic landscape: a comparison of single-cell potency measures. Briefings Bioinform. 21(1): 248-261 (2020) - [j107]Weifeng Guo, Shaowu Zhang, Tao Zeng, Tatsuya Akutsu, Luonan Chen:
Network control principles for identifying personalized driver genes in cancer. Briefings Bioinform. 21(5): 1641-1662 (2020) - [j106]Rui Liu, Pei Chen, Luonan Chen:
Single-sample landscape entropy reveals the imminent phase transition during disease progression. Bioinform. 36(5): 1522-1532 (2020) - [j105]Rui Liu, Pei Chen, Luonan Chen:
Corrigendum to: Single-sample landscape entropy reveals the imminent phase transition during disease progression. Bioinform. 36(8): 2644 (2020) - [j104]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. Genom. Proteom. Bioinform. 18(3): 256-270 (2020) - [j103]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. Genom. Proteom. Bioinform. 18(5): 525-538 (2020) - [j102]Hanah Goetz, Juan Ramon Melendez-Alvarez, Luonan Chen, Xiao-Jun Tian:
A plausible accelerating function of intermediate states in cancer metastasis. PLoS Comput. Biol. 16(3) (2020) - [j101]Jingxue Xin, Junjun Hao, Lang Chen, Tao Zhang, Lei Li, Luonan Chen, Wenmin Zhao, Xuemei Lu, Peng Shi, Yong Wang:
ZokorDB: tissue specific regulatory network annotation for non-coding elements of plateau zokor. Quant. Biol. 8(1): 43-50 (2020) - [j100]Peng Wang, Luonan Chen:
Critical transitions and tipping points in EMT. Quant. Biol. 8(3): 195-202 (2020) - [j99]Ziwei Chen, Xiangqi Bai, Liang Ma, Xiawei Wang, Xiuqin Liu, Yuting Liu, Luonan Chen, Lin Wan:
A Branch Point on Differentiation Trajectory is the Bifurcating Event Revealed by Dynamical Network Biomarker Analysis of Single-Cell Data. IEEE ACM Trans. Comput. Biol. Bioinform. 17(2): 366-375 (2020) - [j98]Jifan Shi, Juan Zhao, Xiaoping Liu, Luonan Chen, Tiejun Li:
Quantifying Direct Dependencies in Biological Networks by Multiscale Association Analysis. IEEE ACM Trans. Comput. Biol. Bioinform. 17(2): 449-458 (2020) - [j97]Jingsong Zhang, Jianmei Guo, Ming Zhang, Xiangtian Yu, Xiaoqing Yu, Weifeng Guo, Tao Zeng, Luonan Chen:
Efficient Mining Multi-Mers in a Variety of Biological Sequences. IEEE ACM Trans. Comput. Biol. Bioinform. 17(3): 949-958 (2020) - [c50]Luonan Chen:
Network biomarker for quantifying regular state of a biological system, and dynamic network biomarker for quantifying critical state of a biological system. BIBM 2020: 4 - [c49]Jingsong Zhang, Cheng Bi, Yinglin Wang, Tao Zeng, Bo Liao, Luonan Chen:
Efficient Mining Closed k-Mers from DNA and Protein Sequences. BigComp 2020: 342-349 - [c48]Yongqun He, Hong Yu, Edison Ong, Yang Wang, Yingtong Liu, Anthony Huffman, Hsin-Hui Huang, John Beverley, Asiyah Yu Lin, William D. Duncan, Sivaram Arabandi, Jiangan Xie, Junguk Hur, Xiaolin Yang, Luonan Chen, Gilbert S. Omenn, Brian D. Athey, Barry Smith:
CIDO: The Community-Based Coronavirus Infectious Disease Ontology. ICBO/ODLS 2020: 1-10 - [e3]Wookey Lee, Luonan Chen, Yang-Sae Moon, Julien Bourgeois, Mehdi Bennis, Yu-Feng Li, Young-Guk Ha, Hyuk-Yoon Kwon, Alfredo Cuzzocrea:
2020 IEEE International Conference on Big Data and Smart Computing, BigComp 2020, Busan, Korea (South), February 19-22, 2020. IEEE 2020, ISBN 978-1-7281-6034-4 [contents]
2010 – 2019
- 2019
- [j96]Yong Wang, Xiang-Sun Zhang, Luonan Chen:
Systems biology intertwines with single cell and AI. BMC Bioinform. 20-S(7): 204:1-204:3 (2019) - [j95]Samantha Sayers, Li Li, Edison Ong, Shunzhou Deng, Guanghua Fu, Yu Lin, Brian Yang, Shelley Zhang, Zhenzong Fa, Bin Zhao, Zuoshuang Xiang, Yongqing Li, Xing-Ming Zhao, Michal Olszewski, Luonan Chen, Yongqun He:
Victors: a web-based knowledge base of virulence factors in human and animal pathogens. Nucleic Acids Res. 47(Database-Issue): D693-D700 (2019) - [j94]Weifeng 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 Comput. Biol. 15(11) (2019) - [j93]Jifan Shi, Tiejun Li, Luonan Chen, Kazuyuki Aihara:
Quantifying pluripotency landscape of cell differentiation from scRNA-seq data by continuous birth-death process. PLoS Comput. Biol. 15(11) (2019) - [j92]Yongcui Wang, Shilong Chen, Luonan Chen, Yong Wang:
Associating lncRNAs with small molecules via bilevel optimization reveals cancer-related lncRNAs. PLoS Comput. Biol. 15(12) (2019) - [j91]Chuan Chen, Jingxue Xin, Yong Wang, Luonan Chen, Michael K. Ng:
A Semisupervised Classification Approach for Multidomain Networks With Domain Selection. IEEE Trans. Neural Networks Learn. Syst. 30(1): 269-283 (2019) - 2018
- [j90]Weifeng Guo, Shao-Wu Zhang, Li-Li Liu, Fei Liu, Qianqian Shi, Lei Zhang, Ying Tang, Tao Zeng, Luonan Chen:
Discovering personalized driver mutation profiles of single samples in cancer by network control strategy. Bioinform. 34(11): 1893-1903 (2018) - [j89]Hao Jiang, Lydia L. Sohn, Haiyan Huang, Luonan Chen:
Single cell clustering based on cell-pair differentiability correlation and variance analysis. Bioinform. 34(21): 3684-3694 (2018) - [j88]Yong Wang, Xiang-Sun Zhang, Luonan Chen:
Integrating data- and model-driven strategies in systems biology. BMC Syst. Biol. 12(4): 38:1-38:3 (2018) - [j87]Xiujuan Lei, Ming Fang, Fang-Xiang Wu, Luonan Chen:
Improved flower pollination algorithm for identifying essential proteins. BMC Syst. Biol. 12(4): 129-140 (2018) - 2017
- [j86]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. Bioinform. 33(17): 2706-2714 (2017) - [j85]Chuanchao Zhang, Juan Liu, Qianqian Shi, Tao Zeng, Luonan Chen:
Comparative network stratification analysis for identifying functional interpretable network biomarkers. BMC Bioinform. 18(S-3): 1-12 (2017) - [j84]Yong Wang, Xiang-Sun Zhang, Luonan Chen:
Understanding biological systems through the lens of data. BMC Syst. Biol. 11(S-4): 77:1-77:2 (2017) - [j83]Ben-gong Zhang, Weibo Li, Yazhou Shi, Xiaoping Liu, Luonan Chen:
Detecting causality from short time-series data based on prediction of topologically equivalent attractors. BMC Syst. Biol. 11(S-7): 141-150 (2017) - [j82]Chuanchao Zhang, Juan Liu, Qianqian Shi, Tao Zeng, Luonan Chen:
Differential function analysis: identifying structure and activation variations in dysregulated pathways. Sci. China Inf. Sci. 60(1): 12108 (2017) - [j81]Xiaoping Liu, Xiao Chang, Rui Liu, Xiangtian Yu, Luonan Chen, Kazuyuki Aihara:
Quantifying critical states of complex diseases using single-sample dynamic network biomarkers. PLoS Comput. Biol. 13(7) (2017) - [c47]Jingsong Zhang, Jianmei Guo, Xiaoqing Yu, Xiangtian Yu, Weifeng Guo, Tao Zeng, Luonan Chen:
Mining K-mers of Various Lengths in Biological Sequences. ISBRA 2017: 186-195 - 2016
- [j80]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 Bioinform. 17(4): 576-592 (2016) - [j79]Pei Chen, Rui Liu, Yongjun Li, Luonan Chen:
Detecting critical state before phase transition of complex biological systems by hidden Markov model. Bioinform. 32(14): 2143-2150 (2016) - [j78]Guangyong Zheng, Yaochen Xu, Xiujun Zhang, Zhi-Ping Liu, Zhuo Wang, Luonan Chen, Xin-Guang Zhu:
CMIP: a software package capable of reconstructing genome-wide regulatory networks using gene expression data. BMC Bioinform. 17(S-17): 137-144 (2016) - [j77]Fei Liu, Shao-Wu Zhang, Weifeng Guo, Ze-Gang Wei, Luonan Chen:
Inference of Gene Regulatory Network Based on Local Bayesian Networks. PLoS Comput. Biol. 12(8) (2016) - [c46]Chuanchao Zhang, Juan Liu, Qianqian Shi, Xiangtian Yu, Tao Zeng, Luonan Chen:
Integration of multiple heterogeneous omics data. BIBM 2016: 564-569 - 2015
- [j76]Takayuki Ishizaki, Kenji Kashima, Antoine Girard, Jun-ichi Imura, Luonan Chen, Kazuyuki Aihara:
Clustered model reduction of positive directed networks. Autom. 59: 238-247 (2015) - [j75]Xing-Ming Zhao, Keqin Liu, Guanghui Zhu, Feng He, Béatrice Duval, Jean-Michel Richer, De-Shuang Huang, Changjun Jiang, Jin-Kao Hao, Luonan Chen:
Identifying cancer-related microRNAs based on gene expression data. Bioinform. 31(8): 1226-1234 (2015) - [j74]Xindong Zhang, Lin Gao, Zhi-Ping Liu, Luonan Chen:
Identifying module biomarker in type 2 diabetes mellitus by discriminative area of functional activity. BMC Bioinform. 16: 92:1-92:10 (2015) - [j73]Xinan Yang, Meiyi Li, Bin Wang, Wanqi Zhu, Aurelie Desgardin, Kenan Onel, Jill de Jong, Jianjun Chen, Luonan Chen, John M. Cunningham:
Systematic computation with functional gene-sets among leukemic and hematopoietic stem cells reveals a favorable prognostic signature for acute myeloid leukemia. BMC Bioinform. 16: 97:1-97:21 (2015) - [j72]Ben-gong Zhang, Gouhei Tanaka, Kazuyuki Aihara, Masao Honda, Shuichi Kaneko, Luonan Chen:
Dynamics of an HBV Model with Drug Resistance Under Intermittent Antiviral Therapy. Int. J. Bifurc. Chaos 25(7): 1540011:1-1540011:12 (2015) - [j71]Shi-Hua Zhang, Luonan Chen:
Guest Editorial for Special Section on ISB/TBC 2014. IEEE ACM Trans. Comput. Biol. Bioinform. 12(5): 1074-1075 (2015) - [j70]Hao Kang, Kwang-Hyun Cho, Xiaohua Douglas Zhang, Tao Zeng, Luonan Chen:
Inferring Sequential Order of Somatic Mutations during Tumorgenesis based on Markov Chain Model. IEEE ACM Trans. Comput. Biol. Bioinform. 12(5): 1094-1103 (2015) - [c45]Chuanchao Zhang, Juan Liu, Qianqian Shi, Tao Zeng, Luonan Chen:
Identification of phenotypic networks based on whole transcriptome by comparative network decomposition. BIBM 2015: 189-194 - [i2]Hui-Jia Li, Hao Wang, Luonan Chen:
Measuring robustness of community structure in complex networks. CoRR abs/1503.08012 (2015) - [i1]Hui-Jia Li, Junhua Zhang, Zhi-Ping Liu, Luonan Chen, Xiang-Sun Zhang:
Identifying overlapping communities in social networks using multi-scale local information expansion. CoRR abs/1503.08024 (2015) - 2014
- [j69]Meiyi Li, Tao Zeng, Rui Liu, 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 Bioinform. 15(2): 229-243 (2014) - [j68]Xiangtian Yu, Guojun Li, Luonan Chen:
Prediction and early diagnosis of complex diseases by edge-network. Bioinform. 30(6): 852-859 (2014) - [j67]Rui Liu, Xiangtian Yu, Xiaoping Liu, Dong Xu, Kazuyuki Aihara, Luonan Chen:
Identifying critical transitions of complex diseases based on a single sample. Bioinform. 30(11): 1579-1586 (2014) - [j66]Yixue Li, Luonan Chen:
Big Biological Data: Challenges and Opportunities. Genom. Proteom. Bioinform. 12(5): 187-189 (2014) - [j65]Huanfei Ma, Tianshou Zhou, Kazuyuki Aihara, Luonan Chen:
Predicting Time Series from Short-Term High-Dimensional Data. Int. J. Bifurc. Chaos 24(12) (2014) - [j64]Andrew E. Teschendorff, Xiaoping Liu, Helena Carén, Steve M. Pollard, Stephan Beck, Martin Widschwendter, Luonan Chen:
The Dynamics of DNA Methylation Covariation Patterns in Carcinogenesis. PLoS Comput. Biol. 10(7) (2014) - [c44]Tao Zeng, Ziming Wang, Luonan Chen:
Detecting Phosphorylation Determined Active Protein Interaction Network during Cancer Development by Robust Network Component Analysis. DTMBIO@CIKM 2014: 49 - [c43]Luonan Chen, Doheon Lee, Hua Xu, Min Song:
DTMBIO 2014: International Workshop on Data and Text Mining in Biomedical Informatics. CIKM 2014: 2090-2091 - [e2]Doheon Lee, Luonan Chen, Min Song, Hua Xu:
Proceedings of the ACM 8th International Workshop on Data and Text Mining in Bioinformatics, DTMBIO@CIKM 2014, Shanghai, China, November 7, 2014. ACM 2014, ISBN 978-1-4503-1275-2 [contents] - 2013
- [j63]Xiaoping Liu, Xiaodong Zhang, Weihua Tang, Luonan Chen, Xing-Ming Zhao:
eFG: an electronic resource for Fusarium graminearum. Database J. Biol. Databases Curation 2013 (2013) - [j62]Xiujun Zhang, Keqin Liu, Zhi-Ping Liu, Béatrice Duval, Jean-Michel Richer, Xing-Ming Zhao, Jin-Kao Hao, Luonan Chen:
NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference. Bioinform. 29(1): 106-113 (2013) - [j61]Chao Zhang, Jiguang Wang, Kristina Hanspers, Dong Xu, Luonan Chen, Alexander R. Pico:
NOA: a cytoscape plugin for network ontology analysis. Bioinform. 29(16): 2066-2067 (2013) - [j60]Yong Wang, Xiang-Sun Zhang, Luonan Chen:
Computational systems biology in the big data era. BMC Syst. Biol. 7(S-2): S1 (2013) - [j59]Zhiyuan Yang, Yan Zhang, Luonan Chen:
Investigation of anti-cancer mechanisms by comparative analysis of naked mole rat and rat. BMC Syst. Biol. 7(S-2): S5 (2013) - [j58]Zhenshu Wen, Zhi-Ping Liu, Zhengrong Liu, Yan Zhang, Luonan Chen:
Research and applications: An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer. J. Am. Medical Informatics Assoc. 20(4): 659-667 (2013) - [j57]Rui Liu, Kazuyuki Aihara, Luonan Chen:
Dynamical network biomarkers for identifying critical transitions and their driving networks of biologic processes. Quant. Biol. 1(2): 105-114 (2013) - [c42]Luonan Chen:
Identifying Critical Transitions of Biological Processes by Dynamical Network Biomarkers. ISBRA 2013: 2 - 2012
- [j56]Xiujun Zhang, Xing-Ming Zhao, Kun He, Le Lu, Yongwei Cao, Jingdong Liu, Jin-Kao Hao, Zhi-Ping Liu, Luonan Chen:
Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information. Bioinform. 28(1): 98-104 (2012) - [j55]Keqin Liu, Zhi-Ping Liu, Jin-Kao Hao, Luonan Chen, Xing-Ming Zhao:
Identifying dysregulated pathways in cancers from pathway interaction networks. BMC Bioinform. 13: 126 (2012) - [j54]Zhi-Ping Liu, Jiguang Wang, Yu-Qing Qiu, Ross K. K. Leung, Xiang-Sun Zhang, Stephen Kwok-Wing Tsui, Luonan Chen:
Inferring a protein interaction map of Mycobacterium tuberculosis based on sequences and interologs. BMC Bioinform. 13(S-7): S6 (2012) - [j53]Hee Lee, Taejeong Bae, Ji-Hyun Lee, Dae Kim, Young Oh, Yeongjun Jang, Ji-Tea Kim, Jong Jun Lee, Alessio Innocenti, Claudiu T. Supuran, Luonan Chen, Kyoohyoung Rho, Sunghoon Kim:
Rational drug repositioning guided by an integrated pharmacological network of protein, disease and drug. BMC Syst. Biol. 6: 80 (2012) - [j52]Yong Wang, Xiang-Sun Zhang, Luonan Chen:
Modelling biological systems from molecules to dynamical networks. BMC Syst. Biol. 6(S-1): S1 (2012) - [j51]Tao Zeng, Luonan Chen:
Tracing dynamic biological processes during phase transition. BMC Syst. Biol. 6(S-1): S12 (2012) - [j50]Guanying Piao, Shigeru Saito, Yidan Sun, Zhi-Ping Liu, Yong Wang, Xiao Han, Jiarui Wu, Huarong Zhou, Luonan Chen, Katsuhisa Horimoto:
A computational procedure for identifying master regulator candidates: a case study on diabetes progression in Goto-Kakizaki rats. BMC Syst. Biol. 6(S-1): S2 (2012) - [j49]Tao Zeng, Luonan Chen:
Correction: Tracing dynamic biological processes during phase transition. BMC Syst. Biol. 6(S-1): S23 (2012) - [j48]Xiaoping Liu, Zhi-Ping Liu, Xing-Ming Zhao, Luonan Chen:
Identifying disease genes and module biomarkers by differential interactions. J. Am. Medical Informatics Assoc. 19(2): 241-248 (2012) - [j47]Luonan Chen, Michael K. Ng:
Guest Editorial: Bioinformatics and Computational Systems Biology. IEEE ACM Trans. Comput. Biol. Bioinform. 9(4): 945-946 (2012) - [c41]Ben-gong Zhang, Gouhei Tanaka, Luonan Chen, Kazuyuki Aihara:
Dynamical modeling of chronic myeloid leukemia progression and the development of mutations. BIBM Workshops 2012: 130-135 - [c40]Hailong Zhu, R. Shyama Prasad Rao, Luonan Chen:
Reconstructing dynamic gene regulatory network for the development process of hepatocellular carcinoma. BIBM Workshops 2012: 159-165 - [c39]Takayuki Ishizaki, Kenji Kashima, Antoine Girard, Jun-ichi Imura, Luonan Chen, Kazuyuki Aihara:
Clustering-based ℌ2-state aggregation of positive networks and its application to reduction of chemical master equations. CDC 2012: 4175-4180 - [c38]Hongjuan Zhang, Zikai Wu, Shuxue Ding, Luonan Chen:
A fixed-point blind source extraction algorithm and its application to ECG data analysis. ISB 2012: 73-78 - [c37]Xinrong Zhou, Katsuhisa Horimoto, Shigeru Saito, Luonan Chen, Huarong Zhou:
Network clustering along diabetes progression in three tissues of Goto-Kakizaki rats. ISB 2012: 86-91 - [c36]Zhi-Ping Liu, Wanwei Zhang, Katsuhisa Horimoto, Luonan Chen:
A Gaussian graphical model for identifying significantly responsive regulatory networks from time series gene expression data. ISB 2012: 142-147 - [c35]Tao Zeng, Ruozhao Wang, Luonan Chen:
Module network rewiring in response to therapy. ISB 2012: 197-202 - [c34]Zikai Wu, Yong Wang, Luonan Chen:
A new method to identify repositioned drugs for prostate cancer. ISB 2012: 280-284 - [c33]Zhiyuan Yang, Yan Zhang, Luonan Chen:
in silico identification of novel cancer-related genes by comparative genomics of naked mole rat and rat. ISB 2012: 285-290 - [c32]Fu-Yan Hu, Xing-Ming Zhao, Nelson L. S. Tang, Yan Zhang, Luonan Chen:
Comparative analysis of protein-coding genes and long non-coding RNAs of prostate cancer between Caucasian and Chinese populations. ISB 2012: 291-296 - [c31]Yang Liu, Jin Zhou, Zhi-Ping Liu, Luonan Chen, Michael K. Ng:
Construction and analysis of genome-wide SNP networks. ISB 2012: 327-332 - 2011
- [j46]Ruiqi Wang, Kaihui Liu, Luonan Chen, Kazuyuki Aihara:
Neural fate decisions mediated by trans-activation and cis-inhibition in Notch signaling. Bioinform. 27(22): 3158-3165 (2011) - [j45]Yong Wang, Xiang-Sun Zhang, Luonan Chen:
Computational systems biology: integration of sequence, structure, network, and dynamics. BMC Syst. Biol. 5(S-1): S1 (2011) - [j44]Hong-Bo Lei, Ji-Feng Zhang, Luonan Chen:
Multi-equilibrium property of metabolic networks: SSI module. BMC Syst. Biol. 5(S-1): S15 (2011) - [j43]Huarong Zhou, Shigeru Saito, Guanying Piao, Zhi-Ping Liu, Jiguang Wang, Katsuhisa Horimoto, Luonan Chen:
Network screening of Goto-Kakizaki rat liver microarray data during diabetic progression. BMC Syst. Biol. 5(S-1): S16 (2011) - [c30]Zhi-Ping Liu, Jiguang Wang, Yu-Qing Qiu, Ross K. K. Leung, Xiang-Sun Zhang, Stephen Kwok-Wing Tsui, Luonan Chen:
Inferring Protein-Protein Interactions Based on Sequences and Interologs in Mycobacterium Tuberculosis. ICIC (3) 2011: 91-96 - 2010
- [j42]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. Bioinform. 26(13): 1616-1622 (2010) - [j41]Yu-Qing Qiu, Shi-Hua Zhang, Xiang-Sun Zhang, Luonan Chen:
Detecting disease associated modules and prioritizing active genes based on high throughput data. BMC Bioinform. 11: 26 (2010) - [j40]Yong Wang, Xiang-Sun Zhang, Luonan Chen:
Optimization meets systems biology. BMC Syst. Biol. 4(S-2): S1 (2010) - [j39]Zhi-Ping Liu, Yong Wang, Xiang-Sun Zhang, Luonan Chen:
Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer's disease brains. BMC Syst. Biol. 4(S-2): S11 (2010) - [j38]Chenglei Sun, Xing-Ming Zhao, Weihua Tang, Luonan Chen:
FGsub: Fusarium graminearum protein subcellular localizations predicted from primary structures. BMC Syst. Biol. 4(S-2): S12 (2010) - [j37]Zikai Wu, Xing-Ming Zhao, Luonan Chen:
A systems biology approach to identify effective cocktail drugs. BMC Syst. Biol. 4(S-2): S7 (2010) - [j36]Luonan Chen, Xiang-Sun Zhang:
Editorial. J. Syst. Sci. Complex. 23(5): 883 (2010) - [j35]Zhen-Ping Li, Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen:
Self-organizing map of complex networks for community detection. J. Syst. Sci. Complex. 23(5): 931-941 (2010) - [j34]Dengyu Liu, Xiao Chang, Zengrong Liu, Luonan Chen, Ruiqi Wang:
The effect of coupled feedback on noise filtering in signal transduction networks. J. Syst. Sci. Complex. 23(5): 942-950 (2010) - [c29]Zhi-Ping Liu, Xiang-Sun Zhang, Luonan Chen:
Inferring gene regulatory networks from expression data with prior knowledge by linear programming. ICMLC 2010: 3067-3072 - [p2]Zhao Song, Luonan Chen, Dong Xu:
Bioinformatics Methods for Protein Identification Using Peptide Mass Fingerprinting. Proteome Bioinformatics 2010: 7-22 - [e1]Taesung Park, Stephen Kwok-Wing Tsui, Luonan Chen, Michael K. Ng, Limsoon Wong, Xiaohua Hu:
2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010, Hong Kong, China, December 18-21, 2010, Proceedings. IEEE Computer Society 2010, ISBN 978-1-4244-8306-8 [contents]
2000 – 2009
- 2009
- [j33]Rui-Sheng Wang, Guangxu Jin, Xiang-Sun Zhang, Luonan Chen:
Modeling post-transcriptional regulation activity of small non-coding RNAs in Escherichia coli. BMC Bioinform. 10(S-4) (2009) - [j32]Yi Wang, Jianwei Shen, Baoguo Niu, Zengrong Liu, Luonan Chen:
Robustness of interval gene networks with multiple time-varying delays and noise. Neurocomputing 72(13-15): 3303-3310 (2009) - [j31]Xing-Ming Zhao, Rui-Sheng Wang, Luonan Chen, Kazuyuki Aihara:
Automatic Modeling of Signaling Pathways by Network Flow Model. J. Bioinform. Comput. Biol. 7(2): 309-322 (2009) - [j30]Ling-Yun Wu, Zhen-Ping Li, Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen:
Self-organizing map approaches for the haplotype assembly problem. Math. Comput. Simul. 79(10): 3026-3037 (2009) - [j29]Jiguang Wang, Shi-Hua Zhang, Yong Wang, Luonan Chen, Xiang-Sun Zhang:
Disease-Aging Network Reveals Significant Roles of Aging Genes in Connecting Genetic Diseases. PLoS Comput. Biol. 5(9) (2009) - [j28]Yong Wang, Ling-Yun Wu, Ji-Hong Zhang, Zhong-Wei Zhan, Xiang-Sun Zhang, Luonan Chen:
Evaluating Protein Similarity from Coarse Structures. IEEE ACM Trans. Comput. Biol. Bioinform. 6(4): 583-593 (2009) - [c28]Xing-Ming Zhao, Luonan Chen:
A New Balanced Ensemble Classifier for Predicting Fungi Protein Subcellular Localization Based on Protein Primary Structures. BMEI 2009: 1-5 - [c27]Hong-Bo Lei, Xin Wang, Ruiqi Wang, Xin-Guang Zhu, Luonan Chen, Ji-Feng Zhang:
Analysis on steady states of photosynthetic carbon metabolic system. CDC 2009: 5643-5648 - [c26]Bing Wang, Yuexing Han, Luonan Chen, Kazuyuki Aihara:
Multiple Phase Transitions in the Culture Dissemination. Complex (1) 2009: 286-290 - [c25]Yu Lu, Luonan Chen:
Analysis and Optimality on Network Traffic Flows. CSIE (2) 2009: 39-43 - [c24]Zhi-Ping Liu, Yong Wang, Tieqiao Wen, Xiang-Sun Zhang, Weiming Xia, Luonan Chen:
Dynamically dysfunctional protein interactions in the development of Alzheimer's disease. SMC 2009: 4262-4267 - [p1]Shi-Hua Zhang, Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen:
Fuzzy System Methods in Modeling Gene Expression and Analyzing Protein Networks. Fuzzy Systems in Bioinformatics and Computational Biology 2009: 165-189 - 2008
- [j27]Xing-Ming Zhao, Yong Wang, Luonan Chen, Kazuyuki Aihara:
Gene function prediction using labeled and unlabeled data. BMC Bioinform. 9 (2008) - [j26]Shihua Zhang, Xiang-Sun Zhang, Luonan Chen:
Biomolecular network querying: a promising approach in systems biology. BMC Syst. Biol. 2: 5 (2008) - [j25]Xing-Ming Zhao, Luonan Chen, Kazuyuki Aihara:
Protein function prediction with the shortest path in functional linkage graph and boosting. Int. J. Bioinform. Res. Appl. 4(4): 375-384 (2008) - [j24]Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, Luonan Chen:
Protein cavity clustering based on community structure of pocket similarity network. Int. J. Bioinform. Res. Appl. 4(4): 445-460 (2008) - [j23]Guoguang He, Luonan Chen, Kazuyuki Aihara:
Associative memory with a controlled chaotic neural network. Neurocomputing 71(13-15): 2794-2805 (2008) - [j22]Rui-Sheng Wang, Shi-Hua Zhang, Yong Wang, Xiang-Sun Zhang, Luonan Chen:
Clustering complex networks and biological networks by nonnegative matrix factorization with various similarity measures. Neurocomputing 72(1-3): 134-141 (2008) - [j21]Ruiqi Wang, Chunguang Li, Luonan Chen, Kazuyuki Aihara:
Modeling and Analyzing Biological Oscillations in Molecular Networks. Proc. IEEE 96(8): 1361-1385 (2008) - [c23]Xing-Ming Zhao, Rui-Sheng Wang, Luonan Chen, Kazuyuki Aihara:
Automatic Modeling of Signal Pathways from Protein-Protein Interaction Networks. APBC 2008: 287-296 - [c22]Rui-Sheng Wang, Guangxu Jin, Xiang-Sun Zhang, Luonan Chen:
Reconstruction of Regulator Activity in E. coli Post-Transcription Processes. BIBM 2008: 339-342 - [c21]Mingyu You, Guo-Zheng Li, Luonan Chen, Jianhua Tao:
A Novel Classifier Based on Enhanced Lipschitz Embedding for Speech Emotion Recognition. ICIC (1) 2008: 482-490 - [c20]Xing-Ming Zhao, Luonan Chen:
Domain-Domain Interaction Identification with a Feature Selection Approach. PRIB 2008: 178-186 - 2007
- [j20]Zhen-Ping Li, Shi-Hua Zhang, Yong Wang, Xiang-Sun Zhang, Luonan Chen:
Alignment of molecular networks by integer quadratic programming. Bioinform. 23(13): 1631-1639 (2007) - [j19]Rui-Sheng Wang, Yong Wang, Xiang-Sun Zhang, Luonan Chen:
Inferring transcriptional regulatory networks from high-throughput data. Bioinform. 23(22): 3056-3064 (2007) - [j18]Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Luonan Chen, Xiang-Sun Zhang:
Predicting gene ontology functions from protein's regional surface structures. BMC Bioinform. 8 (2007) - [j17]Rui-Sheng Wang, Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, Luonan Chen:
Analysis on multi-domain cooperation for predicting protein-protein interactions. BMC Bioinform. 8 (2007) - [j16]Chunguang Li, Luonan Chen, Kazuyuki Aihara:
Stochastic synchronization of genetic oscillator networks. BMC Syst. Biol. 1: 6 (2007) - [j15]Yong Wang, Ling-Yun Wu, Luonan Chen, Xiang-Sun Zhang:
Supervised classification of protein structures based on convex hull representation. Int. J. Bioinform. Res. Appl. 3(2): 123-144 (2007) - [j14]Chunguang Li, Luonan Chen, Kazuyuki Aihara:
A Systems Biology Perspective on Signal Processing in Genetic Network Motifs [Life Sciences]. IEEE Signal Process. Mag. 24(2): 136-147 (2007) - [j13]Chunguang Li, Luonan Chen, Kazuyuki Aihara:
Stochastic Stability of Genetic Networks With Disturbance Attenuation. IEEE Trans. Circuits Syst. II Express Briefs 54-II(10): 892-896 (2007) - [c19]Huibo Lou, Chengxiong Mao, Jiming Lu, Dan Wang, Luonan Chen:
Double Three-Level Inverter Based Variable Frequency Drive with Minimal Total Harmonic Distortion Using Particle Swarm Optimization. ICIC (1) 2007: 461-472 - [c18]Rui-Sheng Wang, Shi-Hua Zhang, Xiang-Sun Zhang, Luonan Chen:
Identifying Modules in Complex Networks by a Graph-Theoretical Method and Its Application in Protein Interaction Networks. ICIC (2) 2007: 1090-1101 - [c17]Jianbao Zhang, Zengrong Liu, Ying Li, Luonan Chen:
Frequency Synchronization of a Set of Cells Coupled by Quorum Sensing. LSMS (2) 2007: 21-27 - [c16]Rui-Sheng Wang, Yong Wang, Xiang-Sun Zhang, Luonan Chen:
Detecting Community Structure in Complex Networks by Optimal Rearrangement Clustering. PAKDD Workshops 2007: 119-130 - 2006
- [j12]Ruiqi Wang, Luonan Chen, Kazuyuki Aihara:
Synchronizing a multicellular system by external input: an artificial control strategy. Bioinform. 22(14): 1775-1781 (2006) - [j11]Yong Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, Luonan Chen:
Inferring gene regulatory networks from multiple microarray datasets. Bioinform. 22(19): 2413-2420 (2006) - [j10]Chunguang Li, Luonan Chen, Kazuyuki Aihara:
Transient Resetting: A Novel Mechanism for Synchrony and Its Biological Examples. PLoS Comput. Biol. 2(8) (2006) - [j9]Luonan Chen, Ruiqi Wang:
Designing Gene Regulatory Networks With Specified Functions. IEEE Trans. Circuits Syst. I Regul. Pap. 53-I(11): 2444-2450 (2006) - [j8]Chunguang Li, Luonan Chen, Kazuyuki Aihara:
Stability of Genetic Networks With SUM Regulatory Logic: Lur'e System and LMI Approach. IEEE Trans. Circuits Syst. I Regul. Pap. 53-I(11): 2451-2458 (2006) - [c15]Zhao Song, Luonan Chen, Chao Zhang, Dong Xu:
Design and Implementation of Probability-Based Scoring Function for Peptide Mass Fingerprinting Protein Identification. EMBC 2006: 4556-4559 - [c14]Zhen-Ping Li, Yong Wang, Shihua Zhang, Xiang-Sun Zhang, Luonan Chen:
Alignment of Protein Interaction Networks by Integer Quadratic Programming. EMBC 2006: 5527-5530 - [c13]Yong Wang, Trupti Joshi, Dong Xu, Xiang-Sun Zhang, Luonan Chen:
Supervised Inference of Gene Regulatory Networks by Linear Programming. ICIC (3) 2006: 551-561 - [c12]Shu Fan, Chengxiong Mao, Jiadong Zhang, Luonan Chen:
Forecasting Electricity Demand by Hybrid Machine Learning Model. ICONIP (2) 2006: 952-963 - [c11]Luonan Chen, Ruiqi Wang, Xiabo Zhou, S. Wong:
Designing synthetic biological networks. ISCAS 2006 - [c10]Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, Luonan Chen:
Automatic Classification of Protein Structures Based on Convex Hull Representation by Integrated Neural Network. TAMC 2006: 505-514 - 2005
- [j7]Luonan Chen, Tianshou Zhou, Yun Tang:
Protein structure alignment by deterministic annealing. Bioinform. 21(1): 51-62 (2005) - [j6]Luonan Chen, Ruiqi Wang, Tianshou Zhou, Kazuyuki Aihara:
Noise-induced cooperative behavior in a multicell system. Bioinform. 21(11): 2722-2729 (2005) - [j5]Zhen-Ping Li, Wenfeng Zhou, Xiang-Sun Zhang, Luonan Chen:
A parsimonious tree-grow method for haplotype inference. Bioinform. 21(17): 3475-3481 (2005) - [j4]Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, Luonan Chen:
Exploring Protein's Optimal Hp Configurations by Self-organizing Mapping. J. Bioinform. Comput. Biol. 3(2): 385-400 (2005) - [j3]Tianshou Zhou, Luonan Chen, Yun Tang, Xiang-Sun Zhang:
Aligning Multiple Protein Structures by Deterministic Annealing. J. Bioinform. Comput. Biol. 3(4): 837-860 (2005) - [c9]Luonan Chen, Ruiqi Wang, Kazuyuki Aihara:
Reducing Gene Regulatory Networks by Decomposition. CSB Workshops 2005: 17-18 - [c8]Luonan Chen, Ruiqi Wang, Zhujun Jing, Kazuyuki Aihara:
Cooperative dynamics coordinated by stochastic noise in a multi-cell system. ISCAS (5) 2005: 4791-4794 - [c7]Shu Fan, Chengxiong Mao, Luonan Chen:
Peak Load Forecasting Using the Self-organizing Map. ISNN (3) 2005: 640-647 - 2004
- [c6]Ruiqi Wang, Junya Nakai, Mitsuyasu Seo, Luonan Chen:
Designing Synthetic Biological Systems by Multiple Time Scale Networks. CSB 2004: 748-749 - 2003
- [j2]Rong Yuan, Zhujun Jing, Luonan Chen:
Uniform asymptotic stability of hybrid dynamical systems with delay. IEEE Trans. Autom. Control. 48(2): 344-348 (2003) - [c5]Luonan Chen:
Multiple Protein Structure Alignment by Deterministic Annealing. CSB 2003: 609-610 - 2002
- [c4]Tetsuya Kobayashi, Luonan Chen, Kazuyuki Aihara:
Design of Genetic Switches with Only Positive Feedback Loops. CSB 2002: 151- - [c3]Luonan Chen, Tetsuya Kobayashi, Kazuyuki Aihara:
Designing Oscillators in Synthetic Gene Networks Based on Multi-Scale Dynamics. CSB 2002: 336
1990 – 1999
- 1998
- [c2]Luonan Chen, Kazuyuki Aihara:
Bifurcation analysis of hybrid dynamical systems. SMC 1998: 857-862 - 1995
- [j1]Luonan Chen, Kazuyuki Aihara:
Chaotic simulated annealing by a neural network model with transient chaos. Neural Networks 8(6): 915-930 (1995) - [c1]Luonan Chen, Kazuyuki Aihara:
An application of mean field theory to optimal power flow. ICNN 1995: 887-892
Coauthor Index
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