1.Ronghui You, Wei Qu, Hiroshi Mamitsuka, Shanfeng Zhu*, DeepMHCII: A Novel Binding Core-Aware Deep Interaction Model for Accurate MHC II-peptide Binding Affinity Prediction. ISMB2022, In Press

2.Ronghui You, Shuwei Yao, Hiroshi Mamitsuka, Shanfeng Zhu*, DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction. Bioinformatics (ISMB/ECCB2021), 37(S1) i262-i271

3.Lizhi Liu, Xiaodi Huang, Hiroshi Mamitsuka, Shanfeng Zhu*, HPOFiller: Identifying Missing Protein-phenotype Associations by Graph Convolutional Network. Bioinformatics, 37 (19), 3328–3336, (2021)

4.Shuwei Yao, Ronghui You, Shaojun Wang, Yi Xiong, Xiaodi Huang, Shanfeng Zhu*. NetGO 2.0: improving large-scale protein function prediction with massive sequence, text, domain, family and network information. Nucleic Acids Res. 49(W1):W469-475 (2021)

5.Junyi Bian, Li Huang, Xiaodi Huang, Hong Zhou and Shanfeng Zhu*.GrantRel: Grant Information Extraction via Joint Entity and Relation Extraction. Findings of ACL2021, 2674-2685

6.Ronghui You, Yuxuan Liu, Hiroshi Mamitsuka, Shanfeng Zhu*. BERTMeSH: deep contextual representation learning for large-scale high-performance MeSH indexing with full text. Bioinformatics, 37(5): 684-692 (2021)

7.Suyang Dai, Ronghui You, Zhiyong Lu, Xiaodi Huang, Hiroshi Mamitsuka, Shanfeng Zhu*: FullMeSH: improving large-scale MeSH indexing with full text. Bioinformatics. 36(5): 1533-1541(2020)

8.Ronghui You, Zihan Zhang, Ziye Wang, Suyang Dai, Hiroshi Mamitsuka, Shanfeng Zhu*: AttentionXML: Label Tree-based Attention-Aware Deep Model for High-Performance Extreme Multi-Label Text Classification. NeurIPS 2019: 5812-5822(2019)(First Place of BioASQ 8a and 7a)

9.Shengwen Peng, Ronghi You, Hongning Wang, Hiroshi Mamitsuka, Shanfeng Zhu*, DeepMeSH: Deep Semantic Representation for Improving Large-scale MeSH Indexing. Bioinformatics(ISMB2016), 2016，32(12) i70-79(First Place of BioASQ 5a and 4a)

10.Ke Liu, Shengwen Peng, Junqiu Wu, Chengxiang Zhai, Hiroshi Mamitsuka, Shanfeng Zhu*, MeSHLabeler: Improving the Accuracy of large-scale MeSH indexing by Integrating Diverse Evidence. Bioinformatics(ISMB2015), 2015, 31(12): i339-i347(First Place of BioASQ 3a and 2a)

11.Junning Gao, Makoto Yamada, Samuel Kaski, Hiroshi Mamitsuka, Shanfeng Zhu*, A Robust Convex Formulation for Ensemble Clustering. Proceedings of the 25th International Joint Conference on Artificial Intelligence (IJCAI 2016),New York,USA Jul. 2015,AAAI Press,1476-1482

12.Xiaodong Zheng, Shanfeng Zhu*, Junning Gao, Hiroshi Mamitsuka, Instance-wise Weighted Nonnegative Matrix Factorization for Aggregating Partitions with Locally Reliable Clusters. Proceedings of the 24th International Joint Conference on Artificial Intelligence(IJCAI 2015),Buenos Aires, Argentina Jul. 2015, AAAI Press,4091-4097.

13.Lizhi Liu, Xiaodi Huang, Hiroshi Mamitsuka, Shanfeng Zhu*, HPOLabeler: Improving prediction of human protein-phenotype associations by learning to rank. Bioinformatics 36(14)4180-4188(2020)

14.Ronghui You, Shuwei Yao, Yi Xiong, Xiaodi Huang, Fengzhu Sun, Hiroshi Mamituska, Shanfeng Zhu*, NetGO: improving large-scale protein function prediction with massive network information. Nucleic Acids Research,47(W1),W379–W387(2019)

15.Ronghui You, Zhihan Zhang, Yi Xiong, Fengzhu Sun, Hiroshi Mamitsuka, Shanfeng Zhu* GOLabeler: Improving Sequence-based Large-scale Protein Function Prediction by Learning to Rank. Bioinformatics 34(14)2465-2473,(2018) （First Place in CAFA3）

16.Ziye Wang, Zhengyang Wang, Yang Young Lu, Fengzhu Sun*, Shanfeng Zhu* SolidBin: improving metagenome binning with semi-supervised normalized cut. Bioinformatics 35(21): 4229-4238(2019)

17.Qingjun Yuan, Junning Gao, Dongliang Wu, Shihua Zhang, Hiroshi Mamitsuka, Shanfeng Zhu*, DrugE-Rank: improving drug–target interaction prediction of new candidate drugs or targets by ensemble learning to rank. Bioinformatics(ISMB2016)，2016 32(12). i18-27