DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction von You, Ronghui, Yao, Shuwei, Mamitsuka, Hiroshi, Zhu, Shanfeng

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Similarity-based machine learning methods for predicting drug-target interactions: a brief review von Ding, Hao, Takigawa, Ichigaku, Mamitsuka, Hiroshi, Zhu, Shanfeng

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GOLabeler: improving sequence-based large-scale protein function prediction by learning to rank von You, Ronghui, Zhang, Zihan, Xiong, Yi, Sun, Fengzhu, Mamitsuka, Hiroshi, Zhu, Shanfeng

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DeepMHCII: a novel binding core-aware deep interaction model for accurate MHC-II peptide binding affinity prediction von You, Ronghui, Qu, Wei, Mamitsuka, Hiroshi, Zhu, Shanfeng

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MetaBinner: a high-performance and stand-alone ensemble binning method to recover individual genomes from complex microbial communities von Wang, Ziye, Huang, Pingqin, You, Ronghui, Sun, Fengzhu, Zhu, Shanfeng

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HPOLabeler: improving prediction of human protein–phenotype associations by learning to rank von Liu, Lizhi, Huang, Xiaodi, Mamitsuka, Hiroshi, Zhu, Shanfeng

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DeepMeSH: deep semantic representation for improving large-scale MeSH indexing von Peng, Shengwen, You, Ronghui, Wang, Hongning, Zhai, Chengxiang, Mamitsuka, Hiroshi, Zhu, Shanfeng

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DrugE-Rank: improving drug-target interaction prediction of new candidate drugs or targets by ensemble learning to rank von Yuan, Qingjun, Gao, Junning, Wu, Dongliang, Zhang, Shihua, Mamitsuka, Hiroshi, Zhu, Shanfeng

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HPODNets: deep graph convolutional networks for predicting human protein–phenotype associations von Liu, Lizhi, Mamitsuka, Hiroshi, Zhu, Shanfeng

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Effective binning of metagenomic contigs using contrastive multi-view representation learning von Wang, Ziye, You, Ronghui, Han, Haitao, Liu, Wei, Sun, Fengzhu, Zhu, Shanfeng

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PLMSearch: Protein language model powers accurate and fast sequence search for remote homology von Liu, Wei, Wang, Ziye, You, Ronghui, Xie, Chenghan, Wei, Hong, Xiong, Yi, Yang, Jianyi, Zhu, Shanfeng

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MeSHLabeler: improving the accuracy of large-scale MeSH indexing by integrating diverse evidence von Liu, Ke, Peng, Shengwen, Wu, Junqiu, Zhai, Chengxiang, Mamitsuka, Hiroshi, Zhu, Shanfeng

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Author Correction: PLMSearch: Protein language model powers accurate and fast sequence search for remote homology von Liu, Wei, Wang, Ziye, You, Ronghui, Xie, Chenghan, Wei, Hong, Xiong, Yi, Yang, Jianyi, Zhu, Shanfeng

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Toward more accurate pan-specific MHC-peptide binding prediction: a review of current methods and tools von LIANMING ZHANG, UDAKA, Keiko, MAMITSUKA, Hiroshi, SHANFENG ZHU

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GrantExtractor: Accurate Grant Support Information Extraction from Biomedical Fulltext Based on Bi-LSTM-CRF von Dai, Suyang, Ding, Yuxia, Zhang, Zihan, Zuo, Wenxuan, Huang, Xiaodi, Zhu, Shanfeng

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TEPITOPEpan: extending TEPITOPE for peptide binding prediction covering over 700 HLA-DR molecules von Zhang, Lianming, Chen, Yiqing, Wong, Hau-San, Zhou, Shuigeng, Mamitsuka, Hiroshi, Zhu, Shanfeng

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Does Summarization Help Stock Prediction? A News Impact Analysis von Li, Xiaodong, Xie, Haoran, Song, Yangqiu, Zhu, Shanfeng, Li, Qing, Wang, Fu Lee

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ICH-LR2S2: a new risk score for predicting stroke-associated pneumonia from spontaneous intracerebral hemorrhage von Yan, Jing, Zhai, Weiqi, Li, Zhaoxia, Ding, LingLing, You, Jia, Zeng, Jiayi, Yang, Xin, Wang, Chunjuan, Meng, Xia, Jiang, Yong, Huang, Xiaodi, Wang, Shouyan, Wang, Yilong, Li, Zixiao, Zhu, Shanfeng, Wang, Yongjun, Zhao, Xingquan, Feng, Jianfeng

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Enhancing MEDLINE document clustering by incorporating MeSH semantic similarity von Zhu, Shanfeng, Zeng, Jia, Mamitsuka, Hiroshi

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HPOAnnotator: improving large-scale prediction of HPO annotations by low-rank approximation with HPO semantic similarities and multiple PPI networks von Gao, Junning, Liu, Lizhi, Yao, Shuwei, Huang, Xiaodi, Mamitsuka, Hiroshi, Zhu, Shanfeng

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