团队主要围绕单细胞数据分析与处理、RNA结构预测、药物设计、生物医学图像处理等方向，以机器学习为主要工具开展系列研究，近五年来团队共获批国家自然科学基金8项，其中面上项目3项。在Chemical Reviews， PRE，Plos Computational Biology，Briefings in Bioinformatics, Biophysics Journal，JCIM等国内外知名期刊发表论文多篇。

1. 基于单细胞测序数据的基因转录爆发动力学机理研究，主持， 在研， 国家自科面上项目，直接经费：43.5万，2024.01-2017.12

2.纺织品智能化制造系统建模、分析与控制，主持，武汉市科技局， 在研， 地方政府合作项目 ，经费：10万元，2023.01-2024.12

3.企业供应链全生态数据管控分析平台开发， 已结题， 企业合作项目，经费：20万元， 2022.08-2023.08

4.核小体定位及其对表观遗传稳定性影响的数学建模与定量分析， 已结题， 国家自科面上项目，直接经费：45万元， 2020.01-2023.12

5.乙肝病毒的动力学模型重构及其动力学行为研究， 已结题， 国家自科青年项目， 经费：22万元，2015.01-2017.12

6.基于重构理论的基因表达数据分析， 已结题， 湖北省自科面上项目，经费：5万元，2014.01-2015.12

1. 基于单细胞测序数据的基因转录爆发动力学机理研究，主持， 在研， 国家自科面上项目，直接经费：43.5万，2024.01-2017.12

2.纺织品智能化制造系统建模、分析与控制，主持，武汉市科技局， 在研， 地方政府合作项目 ，经费：10万元，2023.01-2024.12

3.企业供应链全生态数据管控分析平台开发， 已结题， 企业合作项目，经费：20万元， 2022.08-2023.08

4.核小体定位及其对表观遗传稳定性影响的数学建模与定量分析， 已结题， 国家自科面上项目，直接经费：45万元， 2020.01-2023.12

5.乙肝病毒的动力学模型重构及其动力学行为研究， 已结题， 国家自科青年项目， 经费：22万元，2015.01-2017.12

6.基于重构理论的基因表达数据分析， 已结题， 湖北省自科面上项目，经费：5万元，2014.01-2015.12

2014.01-2015.12 基于重构理论的基因表达数据分析 已结题 湖北省自科面上项目

(1)Mengyuan Wang; Wenjie Cao; Yanbing Guo; Guilin Wang; Jian Jiang; Huahai Qiu; Ben-Gong Zhang, Inferring Transcriptional Bursting Kinetics Using Gene Expression Model with Memory and Crosstalk from scRNA-seq Data. Journal of Computational Biophysics and Chemistry, 23(6):765-779,2024 (SCI)

(2)Qiuyu Zhang, Wenjie Cao, Jiaqi Wang, Yihao Yin, Rui Sun, Zunyi Tian, Yalan Tan, Ben-gong Zhang, Transcriptional Bursting Dynamics in Gene Expression, frontiers in genetics, 15:1451461, 2024(SCI)

(3)Jian Jiang, Lu Ke, Long Chen, Bozheng Dou, Jie Liu, Yueying Zhu, Bengong Zhang, Tianshou Zhou, Guo-Wei Wei*, Transformer technology in molecular science. WIREs Comput Mol Sci. 2024;14:e1725.

(4)YZ Shi, Wu, H.; Li, S.-S.; Li, H.-Z.; Zhang, B.-G.; Tan, Y.-L. ABC2A: A Straightforward and Fast Method for the Accurate Back mapping of RNA Coarse-Grained Models to All-Atom Structures. Molecules, 2024, 29, 1244. (SCI)

(5)Yajie Meng, Yi Wang, Junlin Xu, Changcheng Lu, Xianfang Tang, Tao Peng, Bengong Zhang, Geng Tian, Jialiang Yang， Drug repositioning based on weighted local information augmented graph neural network, Briefings in Bioinformatics, Vol.25(1), 2024, bbad431, PP:1-12.(SCI, IF:9.5)

(6)Changfeng Han, Wenjie Cao, Cheng Li, Yanbing Guo, Yuebin Wang, Ya-Zhou Shi, Ben-Gong Zhang, MLBKFD: probabilistic model methods to infer pseudo trajectories from single-cell data, Journal of Computational Biophysics and Chemistry. 23(6):723-739,2024 (SCI, IF:2.2)

(7)Long Chen，Jian Jiang, Bozheng Dou, Hongsong Feng, Jie Liu, Yueying Zhu, Bengong Zhang, Tianshou Zhou, Guo-Wei Wei*，Machine learning study of the extended drug-target interaction network informed by pain related voltage-gated sodium channels，PAIN.Vol.165, 2024:908-921. （SCI， IF：7.4）

(8)Bozheng Dou, Zailiang Zhu, Ekaterina Merkurjev, Lu Ke, Long Chen, Jian Jiang, Yueying Zhu, Jie Liu, Bengong Zhang, Guo-Wei Wei，Machine Learning Methods for Small Data Challenges in Molecular Science，CHEMICAL REVIEWS.2023, 123( 13): 8736–8780. （SCI，IF：62.1）

(9)Mu, Z.-C.; Tan, Y.-L.; Liu, J.; Zhang, B.-G.; Shi, Y.-Z. Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding. Molecules，2023, 28, 4833. （SCI，IF：4.6）

(10)Zailiang Zhu,Bozheng Dou, Yukang Cao, Jian Jiang*, Yueying Zhu, Dong Chen, Hongsong Feng, Jie Liu, Bengong Zhang, Tianshou Zhou, and Guo-Wei Wei, TIDAL: Topology-Inferred Drug Addiction Learning, Journal of Chemical Information and Modeling 2023, 63, 5, 1472-1489. （SCI，IF：5.6）

(11)Ya-Lan Tan, Xunxun Wang, Shixiong Yu, Bengong Zhang and Zhi-Jie Tan, cgRNASP: coarse-grained statistical potentials with residue separation for RNA structure evaluation, NAR Genetics & Bioinformatics, 2023, Vol.5:1-14,lqad016（SCI，IF：4.6）

(12)Li huizhen, Wei Kanghui, Zhang Bengong, 3-D residual attention network for hyperspectral image classification, International Journal of Wavelets, Multiresolution and Information Processing, 2023,Vol. 21, No. 04, 2350004. （SCI，IF：1.4）

(13)Wang, Mengyuan, Jiatao Gan, Changfeng Han, Yanbing Guo, Kaihao Chen, Ya-zhou Shi, and Ben-gong Zhang. 2022. "Imputation Methods for scRNA Sequencing Data" Applied Sciences 12, no. 20: 10684. (SCI，IF：2.7)

(14) Mu Z-C, Tan Y-L, Zhang B-G, Liu J, Shi Y-Z Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions. PLoS Comput. Biol. (2022),18(10): e1010501.(SCI，IF：4.3)

(15) Wenjie Cao, Yazhou Shi, Huahai Qiu, Bengong Zhang*, SS-RNN: A strengthened skip algorithm for data classification based on recurrent neural networks. Frontiers in Genetics.Vol.12,2021,pp:1-13.(SCI)

(16)Huahai Qiu，Ben-gong Zhang, Tianshou Zhou, Explicit effect of stochastic reaction delay on gene expression, Physical Review E 101, 012405 (2020)(SCI)

(17)Ben-gong Zhang, HuahaiQiu, Jian Jiang, Jie Liu, Yazhou Shi, 3D structure stability of the HIV-1 TAR RNA in ion solutions:A coarse-grained model study, The Journal of Chemical Physics. 151, 165101，2019.(SCI)

(18)HuahaiQiu，Ben-gong Zhang, Tianshou Zhou, Influence of complex promoter structure on gene expression, Journal of Systems Science & Complexity, 32:600-614, 2019.(SCI)

(19)HuahaiQiu，Ben-gong Zhang, Tianshou Zhou, Analytical results for a generalized model of bursty gene

expression with molecular memory. Physical Review E 100, 012128 (2019).(SCI)

(20)Ya-Zhou Shi, Xiangpeng Li and Ben-Gong Zhang*. Traveling wave solutions of two nonlinear wave equations by (G’/G)-expansion method. Advances in Mathematical Physics, 2018, ID 8583418.（SCI）

(21)Ben-gong Zhang, Hongbo Fu, Wan li, Jicheng Liu, Weak order in averaging principle for stochastic differential equations with jumps. Advances in Difference Equations. (2018) 2018:197.(SCI)

(22)Yi Yang, Qi Gu, Ben-Gong Zhang, Ya-Zhou Shi and Zhi-Gang Shao*. A novel knowledge-based potential for RNA 3D structure evaluation. Chin. Phys. B 27(3) 038701, 2018 .(SCI)

(23)BG. Zhang, W. Li, Y. Shi, X. Liu and L. Chen, Detecting Causal Gene Regulations from Short Time-series Data Based on Prediction of Topologically Equivalent Attractors, BMC Systems Biology, 2017, 11（Supp 7）：128. (SCI)

(24)BG. Zhang, W. Li, X. Li, Peakons and new exact solitary wave solutions of extended quantum Zakharov-Kuznetsov equation. Physics of Plasmas 24, 062113 (2017) (SCI)

(25)Li SY, Li Y, B. Zhang, Some singular solutions and their limit forms for generalizedCalogero–Bogoyavlenskii–Schiff equation, Nonlinear Dyn. (2016) 85:1665–1677 (SCI)

(26)B. Zhang, G. Tanaka, L. Chen, K. Aihara, Dynamics of an HBV model with drug resistance under intermittent antiviral therapy, Int. J. Bifurcation Chaos. Vol. 25, No. 7 (2015)1540011. (SCI)

(27)Ben-gong Zhang, Analytical and Multishaped Solitary Wave Solutions for Extended Reduced Ostrovsky Equation, Abstract and Applied Analysis, ID 670847 (2013). (SCI),

(28)Ben-gong Zhang,Luonan Chen, K. Aihara, Incremental stability analysis of stochastic hybrid systems, Nonlinear Analysis: RWA, 14 (2013) 1225-1234 (SCI)

(29)Ben-gong Zhang, Zheng-rong Liu, Qing Xiao. New exact solitary wave and multiple soliton solutions of quantum Zakharov–Kuznetsov equation. Applied Mathematics and Computation 217 (2010) 392-402 (SCI)

(30)Ben-gong Zhang,zheng-rong Liu，Jian-feng Mao. New exact solutions of mCH and mDP equations by auxiliary equation method. Applied Mathematics and Computation. 217 (2010) 1306-1314 (SCI)

(31)Chao-hong Pan, Zheng-rong Liu, Ben-gong Zhang. A simple method and its applications to nonlinear partial differential equations. Applied Mathematics and Computation, 217(2010): 4197-4204 (SCI)

(32)Ming Song, Chenxi Yang, Bengong Zhang. Exact solitary wave solutions of the Kadomtsov–Petviashvili–Benjamin–Bona–Mahony equation. Applied Mathematics and Computation.217 (2010) 4:1334–1339 (SCI).

(33)Ben-gong Zhang, Shao-yong Li, Zheng-rong Liu. Homotopy perturbation method for modified Camassa–Holm and Degasperis–Procesi equations, Physics Letters A 372(2008):1867-1872. (SCI)

专利与软著：

(1)张本龚，曹文洁，时亚洲等，一种基于神经网络的建模方法及装置，发明专利，授权专利号：ZL202110099795.6

(2)魏康辉，张本龚，李会珍，朱在亮， 高光谱图像分析可视化系统V1.0，登记号：2022SR0492537，全部权利（原始取得），2022年4月

(3)张本龚，陈俊超等，基于深度卷积神经网络的时间序列图像分类系统V1.0，

登记号：2021SR 0672760，全部权利（原始取得），2021年3月

(4)张本龚，曹文洁，基于Seurat工具的单细胞数据整合与分析系统V1.0，登记号：2020SR1246962全部权利（原始取得），2020年7月

(5) 张本龚，熊珍珍，曹文洁，王婷，张承，基于SC3工具的单细胞数据聚类与分析系统V1.0，登记号：2021SR0320174，全部权利（原始取得），2020年12月

(6) 张本龚，曹文洁，熊珍珍，王婷，张承，基于SNN-Clip工具的单细胞数据整合与分析系统V1.0，登记号：2021SR0320173，全部权利（原始取得），2020年12月

(7) 张本龚，王婷，曹文洁，熊珍珍，张承，基于Scanpy工具的单细胞数据聚类与分析系统V1.0，登记号：2021SR0340985，全部权利（原始取得），2020年12月

(8) 刘杰，张本龚，李丽，织物瑕疵检测系统V1.0，登记号：2020SR1238578，全部权利（原始取得），2020年2月