Luonan Chen

发表

Quantifying pluripotency landscape of cell differentiation from scRNA-seq data by continuous birth-death process

Kazuyuki Aihara, Tiejun Li, Jifan Shi, 2019, PLoS Comput. Biol..

Autoreservoir computing for multistep ahead prediction based on the spatiotemporal information transformation

Kazuyuki Aihara, Luonan Chen, Pei Chen, 2020, Nature Communications.

Single-sample landscape entropy reveals the imminent phase transition during disease progression.

Rui Liu, Pei Chen, Luonan Chen, 2019, Bioinformatics.

A novel structure-based control method for controlling complex large scale nonlinear dynamical networks

Yan Li, Shao-Wu Zhang, Luonan Chen, 2019 .

Disease characterization using a partial correlation-based sample-specific network

Xiaoping Liu, Luonan Chen, Yanhong Huang, 2020, Briefings Bioinform..

Deep-joint-learning analysis model of single cell transcriptome and open chromatin accessibility data

Luonan Chen, Chunman Zuo, Luonan Chen, 2020, Briefings Bioinform..

Computational systems biology for omics data analysis

Luonan Chen, Luonan Chen, 2019, Journal of molecular cell biology.

Revealing dynamic regulations and the related key proteins of myeloma-initiating cells by integrating experimental data into a systems biological model

Xiaobo Zhou, Dan Wu, Luonan Chen, 2019, Bioinform..

A plausible accelerating function of intermediate states in cancer metastasis

Luonan Chen, Hanah Goetz, Juan R. Melendez-Alvarez, 2019, bioRxiv.

A novel network control model for identifying personalized driver genes in cancer

Tao Zeng, Shao-Wu Zhang, Yan Li, 2019, PLoS Comput. Biol..

Associating lncRNAs with small molecules via bilevel optimization reveals cancer-related lncRNAs

Yong Wang, Luonan Chen, Yongcui Wang, 2019, PLoS Comput. Biol..

CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis

Yang Wang, Yongqun He, Junguk Hur, 2020, Scientific Data.

ZokorDB: tissue specific regulatory network annotation for non-coding elements of plateau zokor

Yong Wang, Tao Zhang, Peng Shi, 2020, Quantitative Biology.

Network control principles for identifying personalized driver genes in cancer

Tatsuya Akutsu, Tao Zeng, Shao-Wu Zhang, 2019, Briefings Bioinform..

Spatiotemporal convolutional network for time-series prediction and causal inference pdf

Hao Peng, Luonan Chen, Hao Peng, 2021, ArXiv.

FPPI: Fusarium graminearum protein-protein interaction database.

Xing-Ming Zhao, Luonan Chen, Xingming Zhao, 2009, Journal of proteome research.

Oscillatory dynamics in a simple gene regulatory network mediated by small RNAs

Jianwei Shen, Zengrong Liu, Luonan Chen, 2009 .

Network‐Based Prediction of Protein Function

Luonan Chen, Xiang-Sun Zhang, Rui-Sheng Wang, 2009 .

Rewiring drug-activated p53-regulatory network from suppressing to promoting tumorigenesis.

Luonan Chen, Jiarui Wu, Naihe Jing, 2012, Journal of molecular cell biology.

Reinitiation enhances reliable transcriptional responses in eukaryotes

Kazuyuki Aihara, Bo Liu, Luonan Chen, 2014, Journal of The Royal Society Interface.

Systems biology for complex diseases.

Luonan Chen, Jiarui Wu, Luonan Chen, 2012, Journal of molecular cell biology.

Identifying critical transitions and their leading biomolecular networks in complex diseases

Kazuyuki Aihara, Rui Liu, Luonan Chen, 2012, Scientific Reports.

Limited ability driven phase transitions in the coevolution process in Axelrod's model

Kazuyuki Aihara, Bing Wang, Yuexing Han, 2009 .

Gene Function Prediction with the Shortest Path in Functional Linkage Graph

Xing-Ming Zhao, Kazuyuki Aihara, Luonan Chen, 2007 .

A new geometric-topological method to measure protein fold similarity

Yong Wang, Zikai Wu, Luonan Chen, 2007 .

Impulsive control of stochastic systems with applications in chaos control, chaos synchronization, and neural networks.

Kazuyuki Aihara, Luonan Chen, K. Aihara, 2008, Chaos.

De novo prediction of RNA-protein interactions from sequence information.

Xiang-Sun Zhang, Yong Wang, Runsheng Chen, 2013, Molecular bioSystems.

Incremental stability analysis of stochastic hybrid systems

Kazuyuki Aihara, Luonan Chen, K. Aihara, 2013 .

Hunt for the tipping point during endocrine resistance process in breast cancer by dynamic network biomarkers

Kazuyuki Aihara, Luonan Chen, Haiyun Wang, 2018, Journal of molecular cell biology.

Unique Optimal Foldings of Proteins on a Triangular Lattice

Luonan Chen, Xiangsun Zhang, Zhenping Li, 2005, Applied bioinformatics.

Hubs with Network Motifs Organize Modularity Dynamically in the Protein-Protein Interaction Network of Yeast

Xiang-Sun Zhang, Guangxu Jin, Luonan Chen, 2007, PloS one.

A mathematical model of BCR-ABL autophosphorylation, signaling through the CRKL pathway, and Gleevec dynamics in chronic myeloid leukemia

Joseph J. DiStefano, Luonan Chen, Pep Charusanti, 2003 .

A parameter condition for ruling out multiple equilibria of the photosynthetic carbon metabolism

Xin Wang, Ruiqi Wang, Luonan Chen, 2011 .

A dynamical method to extract communities induced by low or middle-degree nodes

Xiang-Sun Zhang, Junhua Zhang, Luonan Chen, 2011, 2011 IEEE International Conference on Systems Biology (ISB).

Coexpression network analysis in chronic hepatitis B and C hepatic lesions reveals distinct patterns of disease progression to hepatocellular carcinoma.

Luonan Chen, Masao Honda, Shuichi Kaneko, 2012, Journal of molecular cell biology.

Detecting coherent local patterns from time series gene expression data by a temporal biclustering method

Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, 2011, 2011 IEEE International Conference on Systems Biology (ISB).

Detecting and analyzing differentially activated pathways in brain regions of Alzheimer's disease patients.

Xiang-Sun Zhang, Yong Wang, Weiming Xia, 2011, Molecular bioSystems.

Comparison of protein structures by multi-objective optimization.

Xiang-Sun Zhang, Yong Wang, Ling-Yun Wu, 2005, Genome informatics. International Conference on Genome Informatics.

Exploring the constrained maximum edge-weight connected graph problem

Xiang-Sun Zhang, Luonan Chen, Shihua Zhang, 2009 .

Constrained Subspace Clustering for Time Series Gene Expression Data

Luonan Chen, Jibin Qu, Michael Ng, 2010 .

Inferring gene regulatory networks from gene expression data by PC-algorithm based on conditional mutual information

Xing-Ming Zhao, Jin-Kao Hao, Luonan Chen, 2011 .

Global searching ability of chaotic neural networks

Kazuyuki Aihara, Luonan Chen, K. Aihara, 1999 .

Bridging protein local structures and protein functions

Xiang-Sun Zhang, Yong Wang, Ling-Yun Wu, 2008, Amino Acids.

Erratum: Quantitative function for community detection [Phys. Rev. E 77, 036109 (2008)]

Xiang-Sun Zhang, Rui-Sheng Wang, Luonan Chen, 2015 .

NOA: a novel Network Ontology Analysis method

Xiang-Sun Zhang, Yong Wang, Ling-Yun Wu, 2011, Nucleic acids research.

Identifying responsive functional modules from protein-protein interaction network

Zikai Wu, Luonan Chen, Xingming Zhao, 2009, Molecules and cells.

Bistability and Oscillations in Gene Regulation Mediated by Small Noncoding RNAs

Zengrong Liu, Ruiqi Wang, Luonan Chen, 2011, PloS one.

Prediction of Protein–Protein Interactions

Xiang-Sun Zhang, Rui-Sheng Wang, Luonan Chen, 2009 .

A network biology study on circadian rhythm by integrating various omics data.

Xiang-Sun Zhang, Yong Wang, Luonan Chen, 2009, Omics : a journal of integrative biology.

On the robust stability of time‐varying uncertain genetic regulatory networks

Kazuyuki Aihara, Graziano Chesi, Luonan Chen, 2011 .

Detecting early-warning signals of type 1 diabetes and its leading biomolecular networks by dynamical network biomarkers

Xing-Ming Zhao, Xiaoping Liu, Luonan Chen, 2013, BMC Medical Genomics.

Modeling Biomolecular Networks in Cells

Kazuyuki Aihara, Chunguang Li, Luonan Chen, 2010 .

Detecting early‐warning signals of influenza outbreak based on dynamic network marker

Pei Chen, Xianghong Jasmine Zhou, Luonan Chen, 2018, Journal of cellular and molecular medicine.

Dynamics of gene regulatory networks with cell division cycle.

Kazuyuki Aihara, Ruiqi Wang, Luonan Chen, 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

Extracting Community Structure of Complex networks by Self-Organizing Maps

Rui-Sheng Wang, Luonan Chen, Luonan Chen, 2009 .

Identifying Responsive Modules by Mathematical Programming: An Application to Budding Yeast Cell Cycle

Luonan Chen, Guanying Piao, Jiarui Wu, 2012, PloS one.

DIPOS: database of interacting proteins in Oryza sativa.

Xing-Ming Zhao, Xiaoping Liu, Luonan Chen, 2011, Molecular bioSystems.

PPIM: A Protein-Protein Interaction Database for Maize1

Xing-Ming Zhao, Xin-Jian Xu, Luonan Chen, 2015, Plant Physiology.

Controlling the onset of Hopf bifurcation in the Hodgkin-Huxley model.

Kazuyuki Aihara, Luonan Chen, K. Aihara, 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

Detection of cellular rhythms and global stability within interlocked feedback systems.

Kazuyuki Aihara, Ruiqi Wang, Luonan Chen, 2007, Mathematical biosciences.

Prediction of S-Glutathionylation Sites Based on Protein Sequences

Xing-Ming Zhao, Luonan Chen, Xiaobo Zhou, 2013, PloS one.

Detecting thermophilic proteins through selecting amino acid and dipeptide composition features

Songyot Nakariyakul, Luonan Chen, Zhi-Ping Liu, 2011, Amino Acids.

Protein Subcellular Localization Prediction for Fusarium graminearum ∗

Xing-Ming Zhao, Luonan Chen, Chenglei Sun, 2009 .

Prediction of hot spots in protein interfaces using a random forest model with hybrid features.

Xiang-Sun Zhang, Luonan Chen, Zhi-Ping Liu, 2012, Protein engineering, design & selection : PEDS.

Detection for disease tipping points by landscape dynamic network biomarkers

Kazuyuki Aihara, Siyang Leng, Xiaoping Liu, 2018, National science review.

A mechanism of synchronization in interacting multi-cell genetic systems

Tianshou Zhou, Ruiqi Wang, Luonan Chen, 2005 .

Inferring transcriptional interactions and regulator activities from experimental data.

Xiang-Sun Zhang, Rui-Sheng Wang, Luonan Chen, 2007, Molecules and cells.

Excitation functions of coupling.

Tianshou Zhou, Ruiqi Wang, Luonan Chen, 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

Alignment of Protein Interaction Networks by Integer Quadratic Programming

Yong Wang, Xiang-Sun Zhang, Zhen-Ping Li, 2006, 2006 International Conference of the IEEE Engineering in Medicine and Biology Society.

Network-based biomarkers for complex diseases.

Xing-Ming Zhao, Luonan Chen, Xingming Zhao, 2014, Journal of theoretical biology.

Towards a critical transition theory under different temporal scales and noise strengths.

Jifan Shi, Luonan Chen, Tiejun Li, 2016, Physical review. E.

A sequence-based computational approach to predicting PDZ domain-peptide interactions.

Songyot Nakariyakul, Luonan Chen, Zhi-Ping Liu, 2014, Biochimica et biophysica acta.

Analytical distribution and tunability of noise in a model of promoter progress.

Tianshou Zhou, Luonan Chen, Jiajun Zhang, 2012, Biophysical journal.

Gene Toggle Switches Only with Positive Feedback Loops

Kazuyuki Aihara, Luonan Chen, Tetsuya J. Kobayashi, 2001 .

APG: an Active Protein-Gene Network Model to Quantify Regulatory Signals in Complex Biological Systems

Xiang-Sun Zhang, Huarong Zhou, Luonan Chen, 2013, Scientific Reports.

Data-driven systems biology approaches.

Luonan Chen, 2017, Journal of molecular cell biology.

Strange attractors in chaotic neural networks

Kazuyuki Aihara, Luonan Chen, K. Aihara, 2000 .