• Xu C, Xu E, Xiao Y, Yang D, Wu G, Chen M*. A multiscale model to explain the spatiotemporal progression of amyloid beta and tau pathology in Alzheimer’s disease. International Journal of Biological Macromolecules. 2025 May 1;310:142887. (IF 8.5) Corresponding author

• Liu S, Chen M, Cao X, Sheng Z, Sun J, Zhan J, Wang S, Wu G, Yang D. A Novel Joint Multi-Graph Learning Framework for Dynamic Functional Connectivity Network Estimation Across Multiple Time Scale. In 2025 IEEE 22nd International Symposium on Biomedical Imaging (ISBI) 2025 Apr 14 (pp. 1-4). IEEE.

• Rao H, Gu Y, Zhang JZ, Yu G, Cao Y, Chen M*. Hierarchical Gradient-Based Genetic Sampling for Accurate Prediction of Biological Oscillations. In Proceedings of the AAAI Conference on Artificial Intelligence 2025 Apr 11 (Vol. 39, No. 25, pp. 27126-27134). Corresponding author

• Chen C, Xu E, Yang D, Yan C, Wei T, Chen H, Wei Y, Chen M*. Chemical environment adaptive learning for optical band gap prediction of doped graphitic carbon nitride nanosheets. Neural Computing and Applications. 2025 Feb;37(5):3287-301. (IF 5.1) Corresponding author

• Yang D, Shen H, Chen M, Wang S, Chen J, Cai H, Chen X, Wu G, Zhu W. A novel Spatio-temporal hub identification in brain networks by learning dynamic graph embedding on Grassmannian manifolds. IEEE Transactions on Medical Imaging. 2024 Nov 19. (IF 9.8)

• Zhu W, Du Z, Xu Z, Yang D, Chen M, Song Q. Scrn: Single-cell gene regulatory network identification in alzheimer’s disease. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2024 Jul 8.

• Su J, Ma J, Tong S, Xu E, Chen M*. Multiscale attention wavelet neural operator for capturing steep trajectories in biochemical systems. In Proceedings of the AAAI Conference on Artificial Intelligence 2024 Mar 24 (Vol. 38, No. 13, pp. 15100-15107). Corresponding author

• Yang D, Zhao J, Chen M, Xue Y, Zhou J, Wang S, Wu G, Zhu W. Learning Functional Dynamics from a Multilayer Brain Network. In 2024 IEEE International Symposium on Biomedical Imaging (ISBI) 2024 May 27 (pp. 1-4). IEEE.

• Liu H, Marayati BF, de la Cerda D, Lemezis BM, Gao J, Song Q, Chen M, Reid KZ. The Cross-Regulation Between Set1, Clr4, and Lsd1/2 in Schizosaccharomyces pombe. PLoS Genetics. 2024 Jan 5;20(1):e1011107.

• Yang D, Shen H, Chen M, Xue Y, Wang S, Wu G, Zhu W.  Spatiotemporal Hub Identification in Brain Network by Learning Dynamic Graph Embedding on Grassmannian Manifold. The 26th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Vancouver, Canada, 2023.

• Wang J, Xu E, Xiao Y, Xu C and Chen M*. Modeling of AMPK Regulatory Network in Alzheimer’s Disease. In 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (pp. 3832-3839). Corresponding author

• Xu E, Zhang J, Li J, Song Q, Yang D, Wu G, Chen M*. Pathology Steered Stratification Network for Subtype Identification in Alzheimer’s Disease. Medical Physics, 2023. (IF 4.5) Corresponding author.

• Zhang J, Liu Q, Zhang H, Dai M, Song Q, Yang D, Wu G, M Chen*. Uncovering the System Vulnerability and Criticality of Human Brain under Evolving Neuropathological Events in Alzheimer’s Disease. Journal of Alzheimer’s, 2023. (IF 4.0) Corresponding author.

• Rao F, Chen M, Yang D, Morrell B, Song Q, Zhu W. scENT for revealing gene clusters from single-cell RNA-seq data. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2023.

• Jadhav S, Zhao J, Fan Y, Li J, Lin H, Yan C, Chen M*. Time-Varying Sequence Model. Mathematics. 2023.

• Qian W, Zhao C, Shao H, Chen M, Wang F, Hua M. Patient Similarity Learning with Selective Forgetting. IEEE International Conference on Bioinformatics and Biomedicine. 2022.

• Chen M, Jia S, Xue M, Huang H, Xu Z, Yang D, Zhu W, Song Q. Dual-Stream Subspace Clustering Network for Revealing Gene Targets in Alzheimer’s Disease. Computers in Biology and Medicine. 2022. (IF 4.6)

• Song Q, Zhu X, Jin L, Chen M, Zhang W, Su J. SMGR: a joint statistical method for integrative analysis of single-cell multi-omics data. NAR Genomics and Bioinformatics. 2022. (IF 8.3)

• Chen J, Xu E, Wei Y, Chen M*, Wei T, Zheng S. Graph Clustering Analyses of Discontinuous Molecular Dynamics Simulations: Study of Lysozyme Adsorption on a Graphene Surface. Langmuir. 2022. (IF 4.3) Co-corresponding author

• Chen M, Xu C, Xu Z, He W, Zhang H, Su J, Song Q. Uncovering the dynamic effects of DEX treatment on lung cancer by integrating bioinformatic inference and multiscale modeling of scRNA-seq and proteomics data. Computers in Biology and Medicine. 2022. (IF 4.6)

• Li W, Zhao J, Shen C, Zhang J, Hu J, Xiao M, Zhang J, Chen M*. Regional Brain Fusion: Graph Convolutional Network for Alzheimer’s Disease Prediction and Analysis. Frontiers in Neuroinformatics. 2022. (IF 4.8) Corresponding author

• Li W, Yan C, Chen M, Li Q, Zhu W, Wu G, Yang D. Characterizing Network Selectiveness to the Dynamic Spreading of Neuropathological Events in Alzheimer’s Disease, Journal of Alzheimer’s Disease, 2022. (IF 4.5)

• Xu C, Hollis H, Dai M, Yao X, Watson LT, Cao Y, Chen M*. Modeling the temporal dynamics of master regulators and CtrA proteolysis in Caulobacter crescentus cell cycle. PLOS Computational Biology, 2022. (IF 4.4) Corresponding author

• Yang D, Li W, Zhang J, Shen H, Chen M*, Zhu W, Wu G. A neuropathological hub identification for Alzheimer’s disease via joint analysis of topological structure and neuropathological burden. IEEE International Symposium on Biomedical Imaging, 2022. Corresponding author

• Liu Q, Yang D, Zhang J, Wei Z, Wu G, Chen M*. Analyzing the Spatiotemporal Interaction and Propagation of ATN Biomarkers in Alzheimer’s Disease Using Longitudinal Neuroimaging Data. IEEE International Symposium on Biomedical Imaging, 2021. Corresponding author

• Zhang J, Yang D, He W, Wu G, Chen M*. A Network-Guided Reaction-Diffusion Model of AT[N] Biomarkers in Alzheimer’s Disease. The 20th IEEE International Conference on BioInformatics and BioEngineering, 2020. Corresponding author

• Chen M, Ahmadian M, Watson LT, Cao Y. Finding acceptable parameter regions of stochastic Hill functions for multisite phosphorylation mechanism. J Chem Phys. 2020;152(12):124108. doi:10.1063/1.5143004

• Chen M, Cao Y. Analysis and remedy of negativity problem in hybrid stochastic simulation algorithm and its application. BMC Bioinformatics. 2019, 20:315. PMCID: PMC6584509.

• Chen M, Wang S, Cao Y. Accuracy Analysis of Hybrid Stochastic Simulation Algorithm on Linear Chain Reaction Systems. Bull Math Biol. 2019, 81(8):3024-3052. doi:10.1007/s11538-018-0461-z

• Chen M, Amos BD, Watson LT, Tyson JJ, Cao Y, Shaffer CA, Trosset MW, Oguz C, Kakoti G. Quasi-Newton stochastic optimization algorithm for parameter estimation of a stochastic model of the budding yeast cell cycle. IEEE/ACM Trans Comput Biol Bioinform. 2019, 16(1):301-311. doi:10.1109/TCBB.2017.2773083

• Chen M, Cao Y, Watson LT. Parameter estimation of stochastic models based on limited data. ACM SIGBioinformatics Record. 2018, 7(3):1-3.

• Li F, Chen M, Erban R, Cao Y. Reaction time for trimolecular reactions in compartment-based reaction-diffusion models. J Chem Phys. 2018, 148(20):204108.

• Chen M, Li F, Wang S, Cao Y. Stochastic modeling and simulation of reaction-diffusion system with Hill function dynamics. BMC Syst Biol. 2017, 11:21. PMCID: PMC5374650. doi: 10.1186/s12918-017-0401-9

• Wang S, Ahmadian M, Chen M, Tyson J, Cao Y. A hybrid stochastic model of budding yeast cell cycle control Mechanism. Proc. 7th ACM Int. Conf. on Bioinformatics, Computational Biology, and Health Informatics, 2016, 261-270. doi: 10.1145/2975167.2975194

• Li F, Subramanian K, Chen M, Tyson JJ, Cao Y. A stochastic spatiotemporal model of a response-regulator network in the Caulobacter crescentus cell cycle. Phys Biol. 2016, 13(3):035007.

• Chen M, Li F, Subramanian K, Tyson J, Cao Y. Two-dimensional model of bipolar PopZ polymerization in Caulobacter crescentus. Proc. 6th ACM Int. Conf. on Bioinformatics, Computational Biology, and Health Informatics, 2015, 37-46. doi: 10.1145/2808719.2808723