Selected Publications
（加粗为课题组成员，#为共同一作，*为通讯作者）
Computational Biology/Mathematical Biology/Bioinformatics
- Shuli Chen, Yuman Wang(2018级硕士，2021级博士), Da Zhou*, Jie Hu*. Bayesian inference of phenotypic plasticity of cancer cells based on dynamic model for temporal cell proportion Data. Biometrical Journal.
- Shaoqing Chen(2021级博士)#, Duo Xie#, Jiguang Wang, Zheng Hu*, Da Zhou*. Frequency-dependent selection of neoantigens fosters tumor immune escape and predicts immunotherapy response. Communications Biology, 7(2024): 770.
- Guohui Shi#, Yi Dai#, Da Zhou#, Mengmeng Chen, Jiaqi Zhang, Yilong Bi(2018级硕士), Shuai Liu, Qi Wu*. An alignment- and reference-free strategy using k-mer present pattern for population genomic analyses. Mycology, (2024).
- Kun Wang(2019级硕士，2022级博士), Liangzhen Hou, Zhaolian Lu, Xin Wang, Xiangwei Zhai, Zhike Zi, Weiwei Zhai, Xionglei He, Christina Curtis, Da Zhou*, Zheng Hu*. PhyloVelo enhances transcriptomic velocity field mapping using monotonically expressed genes. Nature Biotechnology, 42(2024): 778–789. (工作介绍)(被评为2023年中国生物信息学十大进展)
- Lili Jiang#, Sirong Chen#(2023级硕士), Yuanhui Wu, Da Zhou*, Lihua Duan*. Prediction of coronary heart disease in gout patients using machine learning models. Mathematical Biosciences and Engineering, 20(3) (2023): 4574-4591.
- Hui Chen#, Junqiu Wang#(2016级硕士), Yunsong Liu#, Ivy Quek Ee Ling, Chih Chuan Shih, Dafei Wu, Zhiyan Fu, Raphael Tze Chuen Lee, Miao Xu, Vincent T. Chow, Sebastian Maurer-Stroh, Da Zhou*, Jianjun Liu*, Weiwei Zhai*. MADE: A Computational Tool for Predicting Vaccine Effectiveness for the Influenza A(H3N2) Virus Adapted to Embryonated Eggs. Vaccines, 10(6) (2022), 907.
- Yuman Wang(2018级硕士，2021级博士), Jintong Zhao(2018级本科), Hye Jin Park, Da Zhou*. Effect of dedifferentiation on noise propagation in cellular hierarchy. Physical Review E, 105 (2022), 054409.
- Zhijie Wu(2018级硕士), Yuman Wang(2018级硕士，2021级博士), Kun Wang((2019级硕士，2022级博士), Da Zhou*. Stochastic stem cell models with mutation: A comparison of asymmetric and symmetric divisions. Mathematical Biosciences 332 (2021): 108541.
- Bin Wu*, Hye Jin Park, Lingshan Wu(2015级硕士), Da Zhou*. Evolution of cooperation driven by self-recommendation. Physical Review E 100.4 (2019): 042303.
- Da Zhou*, Yue Luo(2015级本科), David Dingli, Arne Traulsen*. The invasion of de-differentiating cancer cells into hierarchical tissues. PLoS Computational Biology 15.7 (2019): e1007167.
- Da Zhou, Shanjun Mao(2014级硕士), Jing Cheng, Kaiyi Chen, Xiaofang Cao, Jie Hu*. A Bayesian statistical analysis of stochastic phenotypic plasticity model of cancer cells. Journal of Theoretical Biology 454 (2018): 70-79.
- Bin Wu, Shanjun Mao(2014级硕士), Jiazeng Wang, Da Zhou*. Control of epidemics via social partnership adjustment. Physical Review E 94.6 (2016): 062314.
- Xiufang Chen, Yue Wang, Tianquan Feng, Ming Yi, Xingan Zhang*, Da Zhou*. The overshoot and phenotypic equilibrium in characterizing cancer dynamics of reversible phenotypic plasticity. Journal of Theoretical Biology 390 (2016): 40-49.
- Yuanling Niu, Yue Wang, and Da Zhou*. The phenotypic equilibrium of cancer cells: From average-level stability to path-wise convergence. Journal of Theoretical Biology 386 (2015): 7-17.
- Da Zhou, Yue Wang, Bin Wu. A multi-phenotypic cancer model with cell plasticity. Journal of Theoretical Biology 357 (2014): 35-45.
- Da Zhou, Dingming Wu, Zhe Li, Minping Qian, Michael Q Zhang*. Population dynamics of cancer cells with cell state conversions. Quantitative biology 1.3 (2013): 201-208.
- Da Zhou* and Hong Qian*. Fixation, transient landscape, and diffusion dilemma in stochastic evolutionary game dynamics. Physical Review E 84.3 (2011): 031907.
- Da Zhou*, Bin Wu, and Hao Ge. Evolutionary stability and quasi-stationary strategy in stochastic evolutionary game dynamics. Journal of Theoretical Biology 264.3 (2010): 874-881.
AI for Chemistry/Machine Learning
- Zhuoying Xu(2021级硕士)#, Yingjun Zhu（2021级硕士）#, Binbin Hong, Xinlin Wu, Jingwen Zhang, Da Zhou*, Yu Liu*. Correlating Measures of Hierarchical Structures in Artificial Neural Networks with Their Performance. npj Complexity, 1, 15(2024). (工作介绍) (被选为Nature Portfolio’s Nobel Prize in Physics 2024 cross-journal collection)
- Xinru He#, Yuming Su#, Jieyu Zhu#, Nan Fang, YangTao Chen, Huichong Liu, Da Zhou*, Cheng Wang*. Uncovering the influence of the modifier redox potential on CO2 reduction through combined data-driven machine learning and hypothesis-driven experimentation. Journel of Materials Chemistry A, 11(2023): 18106-18114. （入选该杂志2023年热点文章 HOT Papers）
- Liang Zhang(2020级博士), Longqiang Yi, Yu Liu, Cheng wang, Da Zhou*. Motif Entropy Graph Kernel. Pattern Recognition, 140 (2023): 109544.
- Yuming Su#, Yiheng Dai#, Yifan Zeng, Caiyun Wei, Yangtao Chen, Fuchun Ge, Peikun Zheng, Da Zhou*, Pavlo O Dral*, Cheng Wang*. Interpretable Machine Learning of Two-Photon Absorption. Advanced Science, 10(8) (2023): 2204902.
- Ying Guo#, Xinru He#, Yuming Su, Yiheng Dai, Mingcan Xie, Shuangli Yang, Jiawei Chen, Kun Wang(2019级硕士，2022级博士), Da Zhou*, Cheng Wang*. Machine-Learning-Guided Discovery and Optimization of Additives in Preparing Cu Catalysts for CO2 Reduction. Journal of the American Chemical Society 143.15 (2021): 5755-5762. (工作介绍)（入选杂志2021高被引论文）
- Chuanyu Xu(2016级硕士，福建省优秀学术硕士论文), Xiuchong Wang, Binbin Hu, Da Zhou*, Yu Dong, Chengfu Huo, Weijun Ren. Graph Attention Networks for New Product Sales Forecasting in E-Commerce. DASFAA, 2021. (CCF-B类会议)
- Peican Chen, Zeyu Tang(2016级硕士), Zhongming Zeng, Xuefu Hu, Liangping Xiao, Yi Liu, Xudong Qian, Chunyu Deng(2014级本科), Ruiyun Huang, Jingzheng Zhang, Yilong Bi(2018级硕士), Rongkun Lin, Yang Zhou, Honggang Liao, Da Zhou*, Cheng Wang*, Wenbin Lin. Machine-learning-guided morphology engineering of nanoscale metal-organic frameworks. Matter 2, 6 (2020): 1651-1666. (中国科学报报道, Cell出版社工作介绍)
- Chuanyu Xu(2016级硕士，福建省优秀学术硕士论文), Dong Wang, Zhihong Zhang*, Beizhan Wang, Da Zhou, Guijun Ren, Lu Bai, Lixin Cui, Edwin R Hancock. Depth-based subgraph convolutional neural networks, ICPR, 2018. (Best Scientific paper, 最佳科学论文奖)
Miscellaneous
- Kai Wang(2022级硕士), Xiaoyu Xu, Yinping Zheng, Da Zhou, Shihui Guo*, Yipeng Qin, Xiaohu Guo. Computational design of wiring layout on tight suits with minimal motion resistance. SIGGRAPH Asia, 2023. (CCF-A类会议)
- Jizhong Zhao#, Danwei Chen#(2020级硕士), Li Zhao, Yating Shi, Shihui Guo, Zhongguan Zhu, Jiarong Liu, Wanjing Li, Wentao Lei, Haixia Chen, Yi Chen, Da Zhou, Ronghui Wu*, Wenxi Guo*. Self-powered speech recognition system for deaf users. Cell Reports Physical Science, 3 (2022), 101168.