Luonan Chen

206 papers A 1B 3C 2Misc 1Journal 150Unranked 44
YearRankTypeTitle / Venue / Authors
2026 J jnl
Enhancing detection of mild cognitive impairment and epilepsy using EEG-EGG integration via differential distribution analysis.
Biomed. Signal Process. Control.
Yusha Tang, Jing Ren, Peiluan Li, Wanlin Lai, Zijie Huang, Ruiqi Yang, Xinyun Xu, Luonan Chen, Lei Chen
2025 J jnl
A Time-Series Foundation Model by Universal Delay Embedding.
CoRR
Zijian Wang, Peng Tao, Jifan Shi, Rui Bao, Rui Liu, Luonan Chen
2025 J jnl
DNFE: Directed network flow entropy for detecting tipping points during biological processes.
PLoS Comput. Biol.
Xueqing Peng, Rui Qiao, Peiluan Li, Luonan Chen
2025 J jnl
Decoding the gut-brain axis: toward AI-driven integration of neuroimaging and gut microbiota in human health.
Vis. Comput.
Dezhi Wu, Hui Wang, Yueqiong Ni, Yurun Lu, Yong Wang, Huating Li, Luonan Chen
2025 J jnl
Delayformer: spatiotemporal transformation for predicting high-dimensional dynamics.
CoRR
Zijian Wang, Peng Tao, Luonan Chen
2025 J jnl
MCGAE: unraveling tumor invasion through integrated multimodal spatial transcriptomics.
Briefings Bioinform.
Yiwen Yang, Chengming Zhang, Zhaonan Liu, Kazuyuki Aihara, Chuanchao Zhang, Luonan Chen, Wu Wei
2025 J jnl
Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence.
CoRR
Yingying Sun, Jun A, Zhiwei Liu, Rui Sun, Liujia Qian, Samuel H. Payne, Wout Bittremieux, Markus Ralser, Chen Li, Yi Chen, Zhen Dong, Yasset Pérez-Riverol, Asif Khan, Chris Sander, Ruedi Aebersold, Juan Antonio Vizcaíno, Jonathan R. Krieger, Jianhua Yao, Han Wen, Linfeng Zhang, Yunping Zhu, Yue Xuan, Benjamin Boyang Sun, Liang Qiao, Henning Hermjakob, Haixu Tang, Huanhuan Gao, Yamin Deng, Qing Zhong, Cheng Chang, Nuno Bandeira, Ming Li, Weinan E, Siqi Sun, Yuedong Yang, Gilbert S. Omenn, Yue Zhang, Ping Xu, Yan Fu, Xiaowen Liu, Christopher M. Overall, Yu Wang, Eric W. Deutsch, Luonan Chen, Jürgen Cox, Vadim Demichev, Fuchu He, Jiaxing Huang, Huilin Jin, Chao Liu, Nan Li, Zhongzhi Luan, Jiangning Song, Kaicheng Yu, Wanggen Wan, Tai Wang, Kang Zhang, Le Zhang, Peter A. Bell, Matthias Mann, Bing Zhang, Tiannan Guo
2025 J jnl
Ultralow-dimensionality reduction for identifying critical transitions by spatial-temporal PCA.
CoRR
Pei Chen, Yaofang Suo, Rui Liu, Luonan Chen
2024 J jnl
Brain-inspired Chaotic Graph Backpropagation for Large-scale Combinatorial Optimization.
CoRR
Peng Tao, Kazuyuki Aihara, Luonan Chen
2024 J jnl
CIDER: Counterfactual-Invariant Diffusion-based GNN Explainer for Causal Subgraph Inference.
CoRR
Qibin Zhang, Chengshang Lyu, Lingxi Chen, Qiqi Jin, Luonan Chen
2024 J jnl
Deciphering interventional dynamical causality from non-intervention systems.
CoRR
Jifan Shi, Yang Li, Juan Zhao, Siyang Leng, Kazuyuki Aihara, Luonan Chen, Wei Lin
2024 J jnl
Dynamical causality under invisible confounders.
CoRR
Jinling Yan, Shao-Wu Zhang, Chihao Zhang, Weitian Huang, Jifan Shi, Luonan Chen
2024 J jnl
Multi-modal domain adaptation for revealing spatial functional landscape from spatially resolved transcriptomics.
Briefings Bioinform.
Lequn Wang, Yaofeng Hu, Kai Xiao, Chuanchao Zhang, Qianqian Shi, Luonan Chen
2024 J jnl
Revealing cell-cell communication pathways with their spatially coupled gene programs.
Briefings Bioinform.
Junchao Zhu, Hao Dai, Luonan Chen
2024 — conf
Survival Analysis of Histopathological Image Based on a Pretrained Hypergraph Model of Spatial Transcriptomics Data.
MICCAI (3)
Shangyan Cai, Weitian Huang, Weiting Yi, Bin Zhang, Yi Liao, Qiu Wang, Hongmin Cai, Luonan Chen, Weifeng Su
2023 J jnl
Cell-type annotation with accurate unseen cell-type identification using multiple references.
PLoS Comput. Biol.
Yi-Xuan Xiong, Meng-Guo Wang, Luonan Chen, Xiao-Fei Zhang
2023 J jnl
Contrastively generative self-expression model for single-cell and spatial multimodal data.
Briefings Bioinform.
Chengming Zhang, Yiwen Yang, Shijie Tang, Kazuyuki Aihara, Chuanchao Zhang, Luonan Chen
2023 J jnl
Predicting time series by data-driven spatiotemporal information transformation.
Inf. Sci.
Peng Tao, Xiaohu Hao, Jie Cheng, Luonan Chen
2023 J jnl
Robust joint clustering of multi-omics single-cell data via multi-modal high-order neighborhood Laplacian matrix optimization.
Bioinform.
Hao Jiang, Senwen Zhan, Wai-Ki Ching, Luonan Chen
2023 J jnl
Single-cell causal network inferred by cross-mapping entropy.
Briefings Bioinform.
Lin Li, Rui Xia, Wei Chen, Qi Zhao, Peng Tao, Luonan Chen
2023 J jnl
Why Increase of Heterogeneity Signals Pre-Deterioration During Tumor Progression: A Unified Mathematical Model.
SIAM J. Appl. Math.
Yuanling Niu, Hao Kang, Pingyang Wang, Chenchen Guo, Fan Nie, Hongbin Ji, Jiarui Wu, Luonan Chen
2022 J jnl
A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology.
J. Biomed. Semant.
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
2022 J jnl
Brain-inspired chaotic backpropagation for MLP.
Neural Networks
Peng Tao, Jie Cheng, Luonan Chen
2022 J jnl
Deep latent space fusion for adaptive representation of heterogeneous multi-omics data.
Briefings Bioinform.
Chengming Zhang, Yabin Chen, Tao Zeng, Chuanchao Zhang, Luonan Chen
2022 J jnl
Detecting the critical states during disease development based on temporal network flow entropy.
Briefings Bioinform.
Rong Gao, Jinling Yan, Peiluan Li, Luonan Chen
2022 J jnl
Detection of Alzheimer's disease using features of brain region-of-interest-based individual network constructed with the sMRI image.
Comput. Medical Imaging Graph.
Jinwang Feng, Shaowu Zhang, Luonan Chen, Chunman Zuo, Alzheimer's Disease Neuroimaging Initiative
2022 J jnl
Extracting ROI-Based Contourlet Subband Energy Feature From the sMRI Image for Alzheimer's Disease Classification.
IEEE ACM Trans. Comput. Biol. Bioinform.
Jinwang Feng, Shaowu Zhang, Luonan Chen
2022 J jnl
Identifying network biomarkers of cancer by sample-specific differential network.
BMC Bioinform.
Yu Zhang, Xiao Chang, Jie Xia, Yanhong Huang, Shaoyan Sun, Luonan Chen, Xiaoping Liu
2022 J jnl
Predicting high-dimensional time series data with spatial, temporal and global information.
Inf. Sci.
Jining Wang, Chuan Chen, Zibin Zheng, Luonan Chen, Yuren Zhou
2022 J jnl
Single-cell RNA sequencing data analysis based on non-uniformε-neighborhood network.
Bioinform.
Junbo Jia, Luonan Chen
2022 J jnl
Spatiotemporal Transformer Neural Network for Time-Series Forecasting.
Entropy
Yujie You, Le Zhang, Peng Tao, Suran Liu, Luonan Chen
2022 J jnl
Time Series Prediction by Multi-task GPR with Spatiotemporal Information Transformation.
CoRR
Peng Tao, Xiaohu Hao, Jie Cheng, Luonan Chen
2022 J jnl
Transcriptome analysis method based on differential distribution evaluation.
Briefings Bioinform.
Yiwei Meng, Yanhong Huang, Xiao Chang, Xiaoping Liu, Luonan Chen
2021 J jnl
Advanced Single-cell Omics Technologies and Informatics Tools for Genomics, Proteomics, and Bioinformatics Analysis.
Genom. Proteom. Bioinform.
Luonan Chen, Rong Fan, Fuchou Tang
2021 J jnl
Alzheimer's disease classification using features extracted from nonsubsampled contourlet subband-based individual networks.
Neurocomputing
Jinwang Feng, Shaowu Zhang, Luonan Chen, Jie Xia
2021 J jnl
Deep cross-omics cycle attention model for joint analysis of single-cell multi-omics data.
Bioinform.
Chunman Zuo, Hao Dai, Luonan Chen
2021 J jnl
Deep-joint-learning analysis model of single cell transcriptome and open chromatin accessibility data.
Briefings Bioinform.
Chunman Zuo, Luonan Chen
2021 J jnl
Disease characterization using a partial correlation-based sample-specific network.
Briefings Bioinform.
Yanhong Huang, Xiao Chang, Yu Zhang, Luonan Chen, Xiaoping Liu
2021 J jnl
Revealing dynamic regulations and the related key proteins of myeloma-initiating cells by integrating experimental data into a systems biological model.
Bioinform.
Le Zhang, Guangdi Liu, Meijing Kong, Tingting Li, Dan Wu, Xiaobo Zhou, Chuanwei Yang, Lei Xia, Zhenzhou Yang, Luonan Chen
2021 J jnl
Spatiotemporal convolutional network for time-series prediction and causal inference.
CoRR
Hao Peng, Pei Chen, Rui Liu, Luonan Chen
2021 J jnl
c-CSN: Single-cell RNA Sequencing Data Analysis by Conditional Cell-specific Network.
Genom. Proteom. Bioinform.
Lin Li, Hao Dai, Zhaoyuan Fang, Luonan Chen
2020 — ed.
2020 IEEE International Conference on Big Data and Smart Computing, BigComp 2020, Busan, Korea (South), February 19-22, 2020
BigComp
Wookey Lee, Luonan Chen, Yang-Sae Moon, Julien Bourgeois, Mehdi Bennis, Yu-Feng Li, Young-Guk Ha, Hyuk-Yoon Kwon, Alfredo Cuzzocrea
2020 J jnl
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.
Ziwei Chen, Xiangqi Bai, Liang Ma, Xiawei Wang, Xiuqin Liu, Yuting Liu, Luonan Chen, Lin Wan
2020 J jnl
A plausible accelerating function of intermediate states in cancer metastasis.
PLoS Comput. Biol.
Hanah Goetz, Juan Ramon Melendez-Alvarez, Luonan Chen, Xiao-Jun Tian
2020 — conf
CIDO: The Community-Based Coronavirus Infectious Disease Ontology.
ICBO/ODLS
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
2020 J jnl
Corrigendum to: Single-sample landscape entropy reveals the imminent phase transition during disease progression.
Bioinform.
Rui Liu, Pei Chen, Luonan Chen
2020 J jnl
Critical transitions and tipping points in EMT.
Quant. Biol.
Peng Wang, Luonan Chen
2020 — conf
Efficient Mining Closed k-Mers from DNA and Protein Sequences.
BigComp
Jingsong Zhang, Cheng Bi, Yinglin Wang, Tao Zeng, Bo Liao, Luonan Chen
2020 J jnl
Efficient Mining Multi-Mers in a Variety of Biological Sequences.
IEEE ACM Trans. Comput. Biol. Bioinform.
Jingsong Zhang, Jianmei Guo, Ming Zhang, Xiangtian Yu, Xiaoqing Yu, Weifeng Guo, Tao Zeng, Luonan Chen
2020 J jnl
Identification of Alzheimer's disease based on wavelet transformation energy feature of the structural MRI image and NN classifier.
Artif. Intell. Medicine
Jinwang Feng, Shao-Wu Zhang, Luonan Chen, Alzheimer's Disease Neuroimaging Initiative
2020 J jnl
Identification of Key Genes for the Ultrahigh Yield of Rice Using Dynamic Cross-tissue Network Analysis.
Genom. Proteom. Bioinform.
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
2020 J jnl
Kinase-substrate Edge Biomarkers Provide A More Accurate Prognostic Prediction in ER-negative Breast Cancer.
Genom. Proteom. Bioinform.
Yidi Sun, Chen Li, Shichao Pang, Qianlan Yao, Luonan Chen, Yixue Li, Rong Zeng
2020 — conf
Network biomarker for quantifying regular state of a biological system, and dynamic network biomarker for quantifying critical state of a biological system.
BIBM
Luonan Chen
2020 J jnl
Network control principles for identifying personalized driver genes in cancer.
Briefings Bioinform.
Weifeng Guo, Shaowu Zhang, Tao Zeng, Tatsuya Akutsu, Luonan Chen
2020 J jnl
Quantifying Direct Dependencies in Biological Networks by Multiscale Association Analysis.
IEEE ACM Trans. Comput. Biol. Bioinform.
Jifan Shi, Juan Zhao, Xiaoping Liu, Luonan Chen, Tiejun Li
2020 J jnl
Quantifying Waddington's epigenetic landscape: a comparison of single-cell potency measures.
Briefings Bioinform.
Jifan Shi, Andrew E. Teschendorff, Weiyan Chen, Luonan Chen, Tiejun Li
2020 J jnl
Single-sample landscape entropy reveals the imminent phase transition during disease progression.
Bioinform.
Rui Liu, Pei Chen, Luonan Chen
2020 J jnl
ZokorDB: tissue specific regulatory network annotation for non-coding elements of plateau zokor.
Quant. Biol.
Jingxue Xin, Junjun Hao, Lang Chen, Tao Zhang, Lei Li, Luonan Chen, Wenmin Zhao, Xuemei Lu, Peng Shi, Yong Wang
2019 J jnl
A Semisupervised Classification Approach for Multidomain Networks With Domain Selection.
IEEE Trans. Neural Networks Learn. Syst.
Chuan Chen, Jingxue Xin, Yong Wang, Luonan Chen, Michael K. Ng
2019 J jnl
A novel network control model for identifying personalized driver genes in cancer.
PLoS Comput. Biol.
Weifeng Guo, Shao-Wu Zhang, Tao Zeng, Yan Li, Jianxi Gao, Luonan Chen
2019 J jnl
Associating lncRNAs with small molecules via bilevel optimization reveals cancer-related lncRNAs.
PLoS Comput. Biol.
Yongcui Wang, Shilong Chen, Luonan Chen, Yong Wang
2019 J jnl
Quantifying pluripotency landscape of cell differentiation from scRNA-seq data by continuous birth-death process.
PLoS Comput. Biol.
Jifan Shi, Tiejun Li, Luonan Chen, Kazuyuki Aihara
2019 J jnl
Systems biology intertwines with single cell and AI.
BMC Bioinform.
Yong Wang, Xiang-Sun Zhang, Luonan Chen
2019 J jnl
Victors: a web-based knowledge base of virulence factors in human and animal pathogens.
Nucleic Acids Res.
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
2018 J jnl
Discovering personalized driver mutation profiles of single samples in cancer by network control strategy.
Bioinform.
Weifeng Guo, Shao-Wu Zhang, Li-Li Liu, Fei Liu, Qianqian Shi, Lei Zhang, Ying Tang, Tao Zeng, Luonan Chen
2018 J jnl
Improved flower pollination algorithm for identifying essential proteins.
BMC Syst. Biol.
Xiujuan Lei, Ming Fang, Fang-Xiang Wu, Luonan Chen
2018 J jnl
Integrating data- and model-driven strategies in systems biology.
BMC Syst. Biol.
Yong Wang, Xiang-Sun Zhang, Luonan Chen
2018 J jnl
Single cell clustering based on cell-pair differentiability correlation and variance analysis.
Bioinform.
Hao Jiang, Lydia L. Sohn, Haiyan Huang, Luonan Chen
2017 J jnl
Comparative network stratification analysis for identifying functional interpretable network biomarkers.
BMC Bioinform.
Chuanchao Zhang, Juan Liu, Qianqian Shi, Tao Zeng, Luonan Chen
2017 J jnl
Detecting causality from short time-series data based on prediction of topologically equivalent attractors.
BMC Syst. Biol.
Ben-gong Zhang, Weibo Li, Yazhou Shi, Xiaoping Liu, Luonan Chen
2017 J jnl
Differential function analysis: identifying structure and activation variations in dysregulated pathways.
Sci. China Inf. Sci.
Chuanchao Zhang, Juan Liu, Qianqian Shi, Tao Zeng, Luonan Chen
2017 — conf
Mining K-mers of Various Lengths in Biological Sequences.
ISBRA
Jingsong Zhang, Jianmei Guo, Xiaoqing Yu, Xiangtian Yu, Weifeng Guo, Tao Zeng, Luonan Chen
2017 J jnl
Pattern fusion analysis by adaptive alignment of multiple heterogeneous omics data.
Bioinform.
Qianqian Shi, Chuanchao Zhang, Minrui Peng, Xiangtian Yu, Tao Zeng, Juan Liu, Luonan Chen
2017 J jnl
Quantifying critical states of complex diseases using single-sample dynamic network biomarkers.
PLoS Comput. Biol.
Xiaoping Liu, Xiao Chang, Rui Liu, Xiangtian Yu, Luonan Chen, Kazuyuki Aihara
2017 J jnl
Understanding biological systems through the lens of data.
BMC Syst. Biol.
Yong Wang, Xiang-Sun Zhang, Luonan Chen
2016 J jnl
Big-data-based edge biomarkers: study on dynamical drug sensitivity and resistance in individuals.
Briefings Bioinform.
Tao Zeng, Wanwei Zhang, Xiangtian Yu, Xiaoping Liu, Meiyi Li, Luonan Chen
2016 J jnl
CMIP: a software package capable of reconstructing genome-wide regulatory networks using gene expression data.
BMC Bioinform.
Guangyong Zheng, Yaochen Xu, Xiujun Zhang, Zhi-Ping Liu, Zhuo Wang, Luonan Chen, Xin-Guang Zhu
2016 J jnl
Detecting critical state before phase transition of complex biological systems by hidden Markov model.
Bioinform.
Pei Chen, Rui Liu, Yongjun Li, Luonan Chen
2016 J jnl
Inference of Gene Regulatory Network Based on Local Bayesian Networks.
PLoS Comput. Biol.
Fei Liu, Shao-Wu Zhang, Weifeng Guo, Ze-Gang Wei, Luonan Chen
2016 — conf
Integration of multiple heterogeneous omics data.
BIBM
Chuanchao Zhang, Juan Liu, Qianqian Shi, Xiangtian Yu, Tao Zeng, Luonan Chen
2015 J jnl
Clustered model reduction of positive directed networks.
Autom.
Takayuki Ishizaki, Kenji Kashima, Antoine Girard, Jun-ichi Imura, Luonan Chen, Kazuyuki Aihara
2015 J jnl
Dynamics of an HBV Model with Drug Resistance Under Intermittent Antiviral Therapy.
Int. J. Bifurc. Chaos
Ben-gong Zhang, Gouhei Tanaka, Kazuyuki Aihara, Masao Honda, Shuichi Kaneko, Luonan Chen
2015 J jnl
Guest Editorial for Special Section on ISB/TBC 2014.
IEEE ACM Trans. Comput. Biol. Bioinform.
Shi-Hua Zhang, Luonan Chen
2015 — conf
Identification of phenotypic networks based on whole transcriptome by comparative network decomposition.
BIBM
Chuanchao Zhang, Juan Liu, Qianqian Shi, Tao Zeng, Luonan Chen
2015 J jnl
Identifying cancer-related microRNAs based on gene expression data.
Bioinform.
Xing-Ming Zhao, Keqin Liu, Guanghui Zhu, Feng He, Béatrice Duval, Jean-Michel Richer, De-Shuang Huang, Changjun Jiang, Jin-Kao Hao, Luonan Chen
2015 J jnl
Identifying module biomarker in type 2 diabetes mellitus by discriminative area of functional activity.
BMC Bioinform.
Xindong Zhang, Lin Gao, Zhi-Ping Liu, Luonan Chen
2015 J jnl
Identifying overlapping communities in social networks using multi-scale local information expansion.
CoRR
Hui-Jia Li, Junhua Zhang, Zhi-Ping Liu, Luonan Chen, Xiang-Sun Zhang
2015 J jnl
Inferring Sequential Order of Somatic Mutations during Tumorgenesis based on Markov Chain Model.
IEEE ACM Trans. Comput. Biol. Bioinform.
Hao Kang, Kwang-Hyun Cho, Xiaohua Douglas Zhang, Tao Zeng, Luonan Chen
2015 J jnl
Measuring robustness of community structure in complex networks.
CoRR
Hui-Jia Li, Hao Wang, Luonan Chen
2015 J jnl
Systematic computation with functional gene-sets among leukemic and hematopoietic stem cells reveals a favorable prognostic signature for acute myeloid leukemia.
BMC Bioinform.
Xinan Yang, Meiyi Li, Bin Wang, Wanqi Zhu, Aurelie Desgardin, Kenan Onel, Jill de Jong, Jianjun Chen, Luonan Chen, John M. Cunningham
2014 J jnl
Big Biological Data: Challenges and Opportunities.
Genom. Proteom. Bioinform.
Yixue Li, Luonan Chen
2014 A conf
DTMBIO 2014: International Workshop on Data and Text Mining in Biomedical Informatics.
CIKM
Luonan Chen, Doheon Lee, Hua Xu, Min Song
2014 — conf
Detecting Phosphorylation Determined Active Protein Interaction Network during Cancer Development by Robust Network Component Analysis.
DTMBIO@CIKM
Tao Zeng, Ziming Wang, Luonan Chen
2014 J jnl
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.
Meiyi Li, Tao Zeng, Rui Liu, Luonan Chen
2014 J jnl
Identifying critical transitions of complex diseases based on a single sample.
Bioinform.
Rui Liu, Xiangtian Yu, Xiaoping Liu, Dong Xu, Kazuyuki Aihara, Luonan Chen
2014 J jnl
Predicting Time Series from Short-Term High-Dimensional Data.
Int. J. Bifurc. Chaos
Huanfei Ma, Tianshou Zhou, Kazuyuki Aihara, Luonan Chen
2014 J jnl
Prediction and early diagnosis of complex diseases by edge-network.
Bioinform.
Xiangtian Yu, Guojun Li, Luonan Chen
2014 — ed.
Proceedings of the ACM 8th International Workshop on Data and Text Mining in Bioinformatics, DTMBIO@CIKM 2014, Shanghai, China, November 7, 2014
DTMBIO@CIKM
Doheon Lee, Luonan Chen, Min Song, Hua Xu
2014 J jnl
The Dynamics of DNA Methylation Covariation Patterns in Carcinogenesis.
PLoS Comput. Biol.
Andrew E. Teschendorff, Xiaoping Liu, Helena Carén, Steve M. Pollard, Stephan Beck, Martin Widschwendter, Luonan Chen
2013 J jnl
Computational systems biology in the big data era.
BMC Syst. Biol.
Yong Wang, Xiang-Sun Zhang, Luonan Chen
2013 J jnl
Dynamical network biomarkers for identifying critical transitions and their driving networks of biologic processes.
Quant. Biol.
Rui Liu, Kazuyuki Aihara, Luonan Chen
2013 — conf
Identifying Critical Transitions of Biological Processes by Dynamical Network Biomarkers.
ISBRA
Luonan Chen
2013 J jnl
Investigation of anti-cancer mechanisms by comparative analysis of naked mole rat and rat.
BMC Syst. Biol.
Zhiyuan Yang, Yan Zhang, Luonan Chen
2013 J jnl
NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference.
Bioinform.
Xiujun Zhang, Keqin Liu, Zhi-Ping Liu, Béatrice Duval, Jean-Michel Richer, Xing-Ming Zhao, Jin-Kao Hao, Luonan Chen
2013 J jnl
NOA: a cytoscape plugin for network ontology analysis.
Bioinform.
Chao Zhang, Jiguang Wang, Kristina Hanspers, Dong Xu, Luonan Chen, Alexander R. Pico
2013 J jnl
Research and applications: An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer.
J. Am. Medical Informatics Assoc.
Zhenshu Wen, Zhi-Ping Liu, Zhengrong Liu, Yan Zhang, Luonan Chen
2012 — conf
A Gaussian graphical model for identifying significantly responsive regulatory networks from time series gene expression data.
ISB
Zhi-Ping Liu, Wanwei Zhang, Katsuhisa Horimoto, Luonan Chen
2012 J jnl
A computational procedure for identifying master regulator candidates: a case study on diabetes progression in Goto-Kakizaki rats.
BMC Syst. Biol.
Guanying Piao, Shigeru Saito, Yidan Sun, Zhi-Ping Liu, Yong Wang, Xiao Han, Jiarui Wu, Huarong Zhou, Luonan Chen, Katsuhisa Horimoto
2012 — conf
A fixed-point blind source extraction algorithm and its application to ECG data analysis.
ISB
Hongjuan Zhang, Zikai Wu, Shuxue Ding, Luonan Chen
2012 — conf
A new method to identify repositioned drugs for prostate cancer.
ISB
Zikai Wu, Yong Wang, Luonan Chen
2012 — conf
Clustering-based ℌ2-state aggregation of positive networks and its application to reduction of chemical master equations.
CDC
Takayuki Ishizaki, Kenji Kashima, Antoine Girard, Jun-ichi Imura, Luonan Chen, Kazuyuki Aihara
2012 — conf
Comparative analysis of protein-coding genes and long non-coding RNAs of prostate cancer between Caucasian and Chinese populations.
ISB
Fu-Yan Hu, Xing-Ming Zhao, Nelson L. S. Tang, Yan Zhang, Luonan Chen
2012 — conf
Construction and analysis of genome-wide SNP networks.
ISB
Yang Liu, Jin Zhou, Zhi-Ping Liu, Luonan Chen, Michael K. Ng
2012 J jnl
Correction: Tracing dynamic biological processes during phase transition.
BMC Syst. Biol.
Tao Zeng, Luonan Chen
2012 — conf
Dynamical modeling of chronic myeloid leukemia progression and the development of mutations.
BIBM Workshops
Ben-gong Zhang, Gouhei Tanaka, Luonan Chen, Kazuyuki Aihara
2012 J jnl
Guest Editorial: Bioinformatics and Computational Systems Biology.
IEEE ACM Trans. Comput. Biol. Bioinform.
Luonan Chen, Michael K. Ng
2012 J jnl
Identifying disease genes and module biomarkers by differential interactions.
J. Am. Medical Informatics Assoc.
Xiaoping Liu, Zhi-Ping Liu, Xing-Ming Zhao, Luonan Chen
2012 J jnl
Identifying dysregulated pathways in cancers from pathway interaction networks.
BMC Bioinform.
Keqin Liu, Zhi-Ping Liu, Jin-Kao Hao, Luonan Chen, Xing-Ming Zhao
2012 J jnl
Inferring a protein interaction map of Mycobacterium tuberculosis based on sequences and interologs.
BMC Bioinform.
Zhi-Ping Liu, Jiguang Wang, Yu-Qing Qiu, Ross K. K. Leung, Xiang-Sun Zhang, Stephen Kwok-Wing Tsui, Luonan Chen
2012 J jnl
Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information.
Bioinform.
Xiujun Zhang, Xing-Ming Zhao, Kun He, Le Lu, Yongwei Cao, Jingdong Liu, Jin-Kao Hao, Zhi-Ping Liu, Luonan Chen
2012 J jnl
Modelling biological systems from molecules to dynamical networks.
BMC Syst. Biol.
Yong Wang, Xiang-Sun Zhang, Luonan Chen
2012 — conf
Module network rewiring in response to therapy.
ISB
Tao Zeng, Ruozhao Wang, Luonan Chen
2012 — conf
Network clustering along diabetes progression in three tissues of Goto-Kakizaki rats.
ISB
Xinrong Zhou, Katsuhisa Horimoto, Shigeru Saito, Luonan Chen, Huarong Zhou
2012 J jnl
Rational drug repositioning guided by an integrated pharmacological network of protein, disease and drug.
BMC Syst. Biol.
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
2012 — conf
Reconstructing dynamic gene regulatory network for the development process of hepatocellular carcinoma.
BIBM Workshops
Hailong Zhu, R. Shyama Prasad Rao, Luonan Chen
2012 J jnl
Tracing dynamic biological processes during phase transition.
BMC Syst. Biol.
Tao Zeng, Luonan Chen
2012 — conf
in silico identification of novel cancer-related genes by comparative genomics of naked mole rat and rat.
ISB
Zhiyuan Yang, Yan Zhang, Luonan Chen
2011 J jnl
Computational systems biology: integration of sequence, structure, network, and dynamics.
BMC Syst. Biol.
Yong Wang, Xiang-Sun Zhang, Luonan Chen
2011 — conf
Inferring Protein-Protein Interactions Based on Sequences and Interologs in Mycobacterium Tuberculosis.
ICIC (3)
Zhi-Ping Liu, Jiguang Wang, Yu-Qing Qiu, Ross K. K. Leung, Xiang-Sun Zhang, Stephen Kwok-Wing Tsui, Luonan Chen
2011 J jnl
Multi-equilibrium property of metabolic networks: SSI module.
BMC Syst. Biol.
Hong-Bo Lei, Ji-Feng Zhang, Luonan Chen
2011 J jnl
Network screening of Goto-Kakizaki rat liver microarray data during diabetic progression.
BMC Syst. Biol.
Huarong Zhou, Shigeru Saito, Guanying Piao, Zhi-Ping Liu, Jiguang Wang, Katsuhisa Horimoto, Luonan Chen
2011 J jnl
Neural fate decisions mediated by
Bioinform.
Ruiqi Wang, Kaihui Liu, Luonan Chen, Kazuyuki Aihara
2010 — ed.
2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010, Hong Kong, China, December 18-21, 2010, Proceedings
BIBM
Taesung Park, Stephen Kwok-Wing Tsui, Luonan Chen, Michael K. Ng, Limsoon Wong, Xiaohua Hu
2010 J jnl
A systems biology approach to identify effective cocktail drugs.
BMC Syst. Biol.
Zikai Wu, Xing-Ming Zhao, Luonan Chen
2010 — ch.
Bioinformatics Methods for Protein Identification Using Peptide Mass Fingerprinting.
Proteome Bioinformatics
Zhao Song, Luonan Chen, Dong Xu
2010 J jnl
Detecting disease associated modules and prioritizing active genes based on high throughput data.
BMC Bioinform.
Yu-Qing Qiu, Shi-Hua Zhang, Xiang-Sun Zhang, Luonan Chen
2010 J jnl
Editorial.
J. Syst. Sci. Complex.
Luonan Chen, Xiang-Sun Zhang
2010 J jnl
FGsub: Fusarium graminearum protein subcellular localizations predicted from primary structures.
BMC Syst. Biol.
Chenglei Sun, Xing-Ming Zhao, Weihua Tang, Luonan Chen
2010 J jnl
Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer's disease brains.
BMC Syst. Biol.
Zhi-Ping Liu, Yong Wang, Xiang-Sun Zhang, Luonan Chen
2010 Misc conf
Inferring gene regulatory networks from expression data with prior knowledge by linear programming.
ICMLC
Zhi-Ping Liu, Xiang-Sun Zhang, Luonan Chen
2010 J jnl
Optimization meets systems biology.
BMC Syst. Biol.
Yong Wang, Xiang-Sun Zhang, Luonan Chen
2010 J jnl
Prediction of protein-RNA binding sites by a random forest method with combined features.
Bioinform.
Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, Luonan Chen
2010 J jnl
Self-organizing map of complex networks for community detection.
J. Syst. Sci. Complex.
Zhen-Ping Li, Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen
2010 J jnl
The effect of coupled feedback on noise filtering in signal transduction networks.
J. Syst. Sci. Complex.
Dengyu Liu, Xiao Chang, Zengrong Liu, Luonan Chen, Ruiqi Wang
2009 — conf
A New Balanced Ensemble Classifier for Predicting Fungi Protein Subcellular Localization Based on Protein Primary Structures.
BMEI
Xing-Ming Zhao, Luonan Chen
2009 — conf
Analysis and Optimality on Network Traffic Flows.
CSIE (2)
Yu Lu, Luonan Chen
2009 — conf
Analysis on steady states of photosynthetic carbon metabolic system.
CDC
Hong-Bo Lei, Xin Wang, Ruiqi Wang, Xin-Guang Zhu, Luonan Chen, Ji-Feng Zhang
2009 J jnl
Automatic Modeling of Signaling Pathways by Network Flow Model.
J. Bioinform. Comput. Biol.
Xing-Ming Zhao, Rui-Sheng Wang, Luonan Chen, Kazuyuki Aihara
2009 J jnl
Disease-Aging Network Reveals Significant Roles of Aging Genes in Connecting Genetic Diseases.
PLoS Comput. Biol.
Jiguang Wang, Shi-Hua Zhang, Yong Wang, Luonan Chen, Xiang-Sun Zhang
2009 B conf
Dynamically dysfunctional protein interactions in the development of Alzheimer's disease.
SMC
Zhi-Ping Liu, Yong Wang, Tieqiao Wen, Xiang-Sun Zhang, Weiming Xia, Luonan Chen
2009 J jnl
Evaluating Protein Similarity from Coarse Structures.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yong Wang, Ling-Yun Wu, Ji-Hong Zhang, Zhong-Wei Zhan, Xiang-Sun Zhang, Luonan Chen
2009 — ch.
Fuzzy System Methods in Modeling Gene Expression and Analyzing Protein Networks.
Fuzzy Systems in Bioinformatics and Computational Biology
Shi-Hua Zhang, Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen
2009 J jnl
Modeling post-transcriptional regulation activity of small non-coding RNAs in
BMC Bioinform.
Rui-Sheng Wang, Guangxu Jin, Xiang-Sun Zhang, Luonan Chen
2009 — conf
Multiple Phase Transitions in the Culture Dissemination.
Complex (1)
Bing Wang, Yuexing Han, Luonan Chen, Kazuyuki Aihara
2009 J jnl
Robustness of interval gene networks with multiple time-varying delays and noise.
Neurocomputing
Yi Wang, Jianwei Shen, Baoguo Niu, Zengrong Liu, Luonan Chen
2009 J jnl
Self-organizing map approaches for the haplotype assembly problem.
Math. Comput. Simul.
Ling-Yun Wu, Zhen-Ping Li, Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen
2008 — conf
A Novel Classifier Based on Enhanced Lipschitz Embedding for Speech Emotion Recognition.
ICIC (1)
Mingyu You, Guo-Zheng Li, Luonan Chen, Jianhua Tao
2008 J jnl
Associative memory with a controlled chaotic neural network.
Neurocomputing
Guoguang He, Luonan Chen, Kazuyuki Aihara
2008 B conf
Automatic Modeling of Signal Pathways from Protein-Protein Interaction Networks.
APBC
Xing-Ming Zhao, Rui-Sheng Wang, Luonan Chen, Kazuyuki Aihara
2008 J jnl
Biomolecular network querying: a promising approach in systems biology.
BMC Syst. Biol.
Shihua Zhang, Xiang-Sun Zhang, Luonan Chen
2008 J jnl
Clustering complex networks and biological networks by nonnegative matrix factorization with various similarity measures.
Neurocomputing
Rui-Sheng Wang, Shi-Hua Zhang, Yong Wang, Xiang-Sun Zhang, Luonan Chen
2008 — conf
Domain-Domain Interaction Identification with a Feature Selection Approach.
PRIB
Xing-Ming Zhao, Luonan Chen
2008 J jnl
Gene function prediction using labeled and unlabeled data.
BMC Bioinform.
Xing-Ming Zhao, Yong Wang, Luonan Chen, Kazuyuki Aihara
2008 J jnl
Modeling and Analyzing Biological Oscillations in Molecular Networks.
Proc. IEEE
Ruiqi Wang, Chunguang Li, Luonan Chen, Kazuyuki Aihara
2008 J jnl
Protein cavity clustering based on community structure of pocket similarity network.
Int. J. Bioinform. Res. Appl.
Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, Luonan Chen
2008 J jnl
Protein function prediction with the shortest path in functional linkage graph and boosting.
Int. J. Bioinform. Res. Appl.
Xing-Ming Zhao, Luonan Chen, Kazuyuki Aihara
2008 — conf
Reconstruction of Regulator Activity in E. coli Post-Transcription Processes.
BIBM
Rui-Sheng Wang, Guangxu Jin, Xiang-Sun Zhang, Luonan Chen
2007 J jnl
A Systems Biology Perspective on Signal Processing in Genetic Network Motifs [Life Sciences].
IEEE Signal Process. Mag.
Chunguang Li, Luonan Chen, Kazuyuki Aihara
2007 J jnl
Alignment of molecular networks by integer quadratic programming.
Bioinform.
Zhen-Ping Li, Shi-Hua Zhang, Yong Wang, Xiang-Sun Zhang, Luonan Chen
2007 J jnl
Analysis on multi-domain cooperation for predicting protein-protein interactions.
BMC Bioinform.
Rui-Sheng Wang, Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, Luonan Chen
2007 — conf
Detecting Community Structure in Complex Networks by Optimal Rearrangement Clustering.
PAKDD Workshops
Rui-Sheng Wang, Yong Wang, Xiang-Sun Zhang, Luonan Chen
2007 — conf
Double Three-Level Inverter Based Variable Frequency Drive with Minimal Total Harmonic Distortion Using Particle Swarm Optimization.
ICIC (1)
Huibo Lou, Chengxiong Mao, Jiming Lu, Dan Wang, Luonan Chen
2007 — conf
Frequency Synchronization of a Set of Cells Coupled by Quorum Sensing.
LSMS (2)
Jianbao Zhang, Zengrong Liu, Ying Li, Luonan Chen
2007 — conf
Identifying Modules in Complex Networks by a Graph-Theoretical Method and Its Application in Protein Interaction Networks.
ICIC (2)
Rui-Sheng Wang, Shi-Hua Zhang, Xiang-Sun Zhang, Luonan Chen
2007 J jnl
Inferring transcriptional regulatory networks from high-throughput data.
Bioinform.
Rui-Sheng Wang, Yong Wang, Xiang-Sun Zhang, Luonan Chen
2007 J jnl
Predicting gene ontology functions from protein's regional surface structures.
BMC Bioinform.
Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Luonan Chen, Xiang-Sun Zhang
2007 J jnl
Stochastic Stability of Genetic Networks With Disturbance Attenuation.
IEEE Trans. Circuits Syst. II Express Briefs
Chunguang Li, Luonan Chen, Kazuyuki Aihara
2007 J jnl
Stochastic synchronization of genetic oscillator networks.
BMC Syst. Biol.
Chunguang Li, Luonan Chen, Kazuyuki Aihara
2007 J jnl
Supervised classification of protein structures based on convex hull representation.
Int. J. Bioinform. Res. Appl.
Yong Wang, Ling-Yun Wu, Luonan Chen, Xiang-Sun Zhang
2006 — conf
Alignment of Protein Interaction Networks by Integer Quadratic Programming.
EMBC
Zhen-Ping Li, Yong Wang, Shihua Zhang, Xiang-Sun Zhang, Luonan Chen
2006 C conf
Automatic Classification of Protein Structures Based on Convex Hull Representation by Integrated Neural Network.
TAMC
Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, Luonan Chen
2006 — conf
Design and Implementation of Probability-Based Scoring Function for Peptide Mass Fingerprinting Protein Identification.
EMBC
Zhao Song, Luonan Chen, Chao Zhang, Dong Xu
2006 J jnl
Designing Gene Regulatory Networks With Specified Functions.
IEEE Trans. Circuits Syst. I Regul. Pap.
Luonan Chen, Ruiqi Wang
2006 C conf
Designing synthetic biological networks.
ISCAS
Luonan Chen, Ruiqi Wang, Xiabo Zhou, S. Wong
2006 — conf
Forecasting Electricity Demand by Hybrid Machine Learning Model.
ICONIP (2)
Shu Fan, Chengxiong Mao, Jiadong Zhang, Luonan Chen
2006 J jnl
Inferring gene regulatory networks from multiple microarray datasets.
Bioinform.
Yong Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, Luonan Chen
2006 J jnl
Stability of Genetic Networks With SUM Regulatory Logic: Lur'e System and LMI Approach.
IEEE Trans. Circuits Syst. I Regul. Pap.
Chunguang Li, Luonan Chen, Kazuyuki Aihara
2006 — conf
Supervised Inference of Gene Regulatory Networks by Linear Programming.
ICIC (3)
Yong Wang, Trupti Joshi, Dong Xu, Xiang-Sun Zhang, Luonan Chen
2006 J jnl
Synchronizing a multicellular system by external input: an artificial control strategy.
Bioinform.
Ruiqi Wang, Luonan Chen, Kazuyuki Aihara
2006 J jnl
Transient Resetting: A Novel Mechanism for Synchrony and Its Biological Examples.
PLoS Comput. Biol.
Chunguang Li, Luonan Chen, Kazuyuki Aihara
2005 J jnl
A parsimonious tree-grow method for haplotype inference.
Bioinform.
Zhen-Ping Li, Wenfeng Zhou, Xiang-Sun Zhang, Luonan Chen
2005 J jnl
Aligning Multiple Protein Structures by Deterministic Annealing.
J. Bioinform. Comput. Biol.
Tianshou Zhou, Luonan Chen, Yun Tang, Xiang-Sun Zhang
2005 — conf
Cooperative dynamics coordinated by stochastic noise in a multi-cell system.
ISCAS (5)
Luonan Chen, Ruiqi Wang, Zhujun Jing, Kazuyuki Aihara
2005 J jnl
Exploring Protein's Optimal Hp Configurations by Self-organizing Mapping.
J. Bioinform. Comput. Biol.
Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, Luonan Chen
2005 J jnl
Noise-induced cooperative behavior in a multicell system.
Bioinform.
Luonan Chen, Ruiqi Wang, Tianshou Zhou, Kazuyuki Aihara
2005 — conf
Peak Load Forecasting Using the Self-organizing Map.
ISNN (3)
Shu Fan, Chengxiong Mao, Luonan Chen
2005 J jnl
Protein structure alignment by deterministic annealing.
Bioinform.
Luonan Chen, Tianshou Zhou, Yun Tang
2005 — conf
Reducing Gene Regulatory Networks by Decomposition.
CSB Workshops
Luonan Chen, Ruiqi Wang, Kazuyuki Aihara
2004 — conf
Designing Synthetic Biological Systems by Multiple Time Scale Networks.
CSB
Ruiqi Wang, Junya Nakai, Mitsuyasu Seo, Luonan Chen
2003 — conf
Multiple Protein Structure Alignment by Deterministic Annealing.
CSB
Luonan Chen
2003 J jnl
Uniform asymptotic stability of hybrid dynamical systems with delay.
IEEE Trans. Autom. Control.
Rong Yuan, Zhujun Jing, Luonan Chen
2002 — conf
Design of Genetic Switches with Only Positive Feedback Loops.
CSB
Tetsuya Kobayashi, Luonan Chen, Kazuyuki Aihara
2002 — conf
Designing Oscillators in Synthetic Gene Networks Based on Multi-Scale Dynamics.
CSB
Luonan Chen, Tetsuya Kobayashi, Kazuyuki Aihara
1998 B conf
Bifurcation analysis of hybrid dynamical systems.
SMC
Luonan Chen, Kazuyuki Aihara
1995 — conf
An application of mean field theory to optimal power flow.
ICNN
Luonan Chen, Kazuyuki Aihara
1995 J jnl
Chaotic simulated annealing by a neural network model with transient chaos.
Neural Networks
Luonan Chen, Kazuyuki Aihara