学术论文：

1.Zhang J, Zhu D, Zhou H, Wang X, Jiang H, Zhu Y, Wang S*. Precise 5′-leader engineering and its potential applications in plant improvement. New Crops. 2025; (In press)

2.Li X, Gui J, Xue W, Wang B, Chen K, Wei P, Xia J*, Yue Z*. Reusability Report: A Distributed Strategy for Solving Combinatorial Optimization Problems with Hypergraph Neural Networks. Nature Machine Intelligence. 2025 Dec;7:1870-1878. (IF: 16.0)

3.Ji H*, Tang R, Cha Y, Wang H, Hao Y, Dong X, Chen J, Yang W, Peng Y, Chen Y, Han Q, Zhang J, Zhu G, Su C, He F, Liu B, Kong F, Li X. Domestication-mediated growth confines soybean basal branching by upregulating GmBRC1a and GmBRC1b. New Phytologist. 2025 Dec;248:2850-2864. (IF: 8.3)

4.Li B, Li X, Wang Y, Liu X, Li K, Li R, Faiz MU, Darlington UT, Rao Z, Wu Q, Yue Y, Wang S, Fei Z, Liu Y, Zheng Y, Yue J. KPGD: A Kiwifruit Pangenome Database for Comprehensive Mining of Genetic Diversity in the Genus Actinidia. Plant Communications. 2025 Aug;6(8):101373. (IF: 11.6)

5.Wang X, Li X#, Xiang Y, Xu T, Yue Z, Gu L. MDAGCN: Predicting mutation-drug associations through signed graph convolutional networks via graph sampling. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2025 Jul-Aug;22(4):1428-1440. (IF: 3.6)

6.Shi H, Xu T, Li X, Gao Q, Xiong Z, Xia J, Yue Z*. DRExplainer: Quantifiable Interpretability in Drug Response Prediction with Directed Graph Convolutional Network. Artificial Intelligence in Medicine. 2025 May;163:103101. (IF: 6.1)

7.Niu Q*, Xu Y, Huang H, Li L, Tang D, Wu S, Liu P, Liu R, Ma Y, Zhang B, Zhu JK, Lang Z. Two transcription factors play critical roles in mediating epigenetic regulation of fruit ripening in tomato. Proceedings of the National Academy of Sciences of the United States of America. 2025 Apr;122(15):e2422798122. (IF: 9.4)

8.Jiang Y, Xiao Z, Luo Z, Zhou S, Tong C, Jin S, Liu X, Qin R, Xu R, Pan L, Li J, Wei P*. Improving plant C-to-G base editors with a cold-adapted glycosylase and TadA-8e variants. Trends in Biotechnology. 2025 Apr:S0167-7799(25)00086-1. (IF: 14.3)

9.Zhou Q, Gao Q, Gao Y, Zhang Y, Chen Y, Li M, Wei P*, Yue Z*. BES-Designer: A Web Tool to Design Guide RNAs for Base Editing to Simplify Library. Interdisciplinary Sciences: Computational Life Sciences. 2025 Mar;17(1):134-139. (IF: 3.9)

10.Xiang Y, Li X, Gao Q, Xia J, Yue Z*. ExplainMIX: Explaining Drug Response Prediction in Directed Graph Neural Networks with Multi-Omics Fusion. IEEE Journal of Biomedical and Health Informatics. 2025 Mar;PP. doi: 10.1109/JBHI.2025.3550353. (IF: 6.7)

11.Guo P, Chong L, Jiao Z, Xu R, Niu Q*, Zhu Y. Salt stress activates the CDK8-AHL10-SUVH2/9 module to dynamically regulate salt tolerance in Arabidopsis. Nature Communications. 2025 Mar;16(1):2454. (IF: 14.7)

12.Gao Q, Xu T, Li X, Gao W, Shi H, Zhang Y, Chen J, Yue Z*. Interpretable Dynamic Directed Graph Convolutional Network for Multi-Relational Prediction of Missense Mutation and Drug Response. IEEE Journal of Biomedical and Health Informatics. 2025 Feb;29(2):1514-1524. (IF: 6.7)

13.Hu S*, Lu P, Feng Y, Chen A, Han G*. Elucidating the role of the genus Pseudomonas involved in coumarin degradation. Environmental Research. 2025 Feb;266:120603. (IF: 7.7)

14.Zhao J, Liu H, Kang L, Gao W, Lu Q, Rao Y, Yue Z*. deep-AMPpred: A Deep Learning Method for Identifying Antimicrobial Peptides and Their Functional Activities. Journal of Chemical Information and Modeling. 2025 Jan;65(2):997-1008. (IF: 5.7)

15.Liu Y, Han Q, Zhang J, Zhang X, Chen Y, Li M, Hao Y, Hong Y, Tang R, Ferguson BJ, Gresshoff PM, Kuai J, Zhou G, Li X, Ji H*. Soybean nodulation shapes the rhizosphere microbiome to increase rapeseed yield. Journal of Advanced Research. 2025 Sep;75:95-110. (IF: 13.0)

16.Wan S#, Liu H#, Zhu G#, Geng Y, Li W, Chen L, Zhang Y*, Han G*. Decoding Oxygen Preference: Machine Learning Discovers Functional Genes in Bacteria. Genomics. 2025 Sep;117(5):111095. (IF: 3.0)

17.Liu H#, Zhu G#, Chen L, Ye H, Zhang Y*, Han G*. Machine Learning Prediction of Bacterial Optimal Growth Temperature from Protein Domain Signatures Reveals Thermoadaptation Mechanisms. BMC Genomics. 2025 Oct;26(1):957. (IF: 3.7)

18.Li W#, Zhu G#, Zubair M, Guo C, Zhang L, Lu P, Yan Y, Chu Y, Zhang H, Han G*. Deep Learning-Driven Discovery of Novel Antimicrobial Peptides from Large-Scale Protist Genomes and Experimental Characterization. Journal of Chemical Information and Modeling. 2025 Oct;65(19):9962-9973. (IF: 5.3)

19.Liu Q, Liu H, Shi X, Xu C, Xie Y, Hu S, Zhang Y, Han G*. Rapid Key Gene Discovery for Bacterial Shape: A Cross-Species Machine Learning Approach. BMC Microbiology. 2025 Nov;25:705. (IF: 4.2)

20.Jing F#, Geng L#, Zhang Y, Xie H, Zhu J-K, Zhu J. A genotype-independent and highly efficient Agrobacterium-mediated soybean genetic transformation system. Journal of Integrative Plant Biology. 2025 Dec 3. doi: 10.1111/jipb.70102. Epub ahead of print. (IF 9.3)

21.姜昊、张琳杰、蔡嘉茹、王雪晴、卢杰、周毅、朱玉磊、王升星*，小麦HBD基因家族全基因组鉴定及功能分析。 华北农学报，2025，40(4):29-40.(IF: 1.9)

22.张志翔、喻思媛、沈卓凡、姜昊、王升星*，植物DNA损伤修复及基因组编辑应用进展。基因组学与应用生物学，2025，44(7): 716-728. (IF: 0.5)

23.Lu Q, Xu J, Zhang R, Liu H, Wang M, Liu X, Yue Z*, Gao Y. RiceSNP-ABST: A Deep Learning Approach to Identify Abiotic Stress-Associated Single Nucleotide Polymorphisms in Rice. Briefings in Bioinformatics. 2024 Nov;26(1):bbae702. (IF: 6.8)