Xiaoyu Wang

19 papers A* 1Journal 18
YearRankTypeTitle / Venue / Authors
2025 A* conf
CoPRA: Bridging Cross-domain Pretrained Sequence Models with Complex Structures for Protein-RNA Binding Affinity Prediction.
AAAI
Rong Han, Xiaohong Liu, Tong Pan, Jing Xu, Xiaoyu Wang, Wuyang Lan, Zhenyu Li, Zixuan Wang, Jiangning Song, Guangyu Wang, Ting Chen
2025 J jnl
Identifying Protein-Nucleotide Binding Residues via Grouped Multi-task Learning and Pre-trained Protein Language Models.
J. Chem. Inf. Model.
Jiashun Wu, Yan Liu, Ying Zhang, Xiaoyu Wang, He Yan, Yiheng Zhu, Jiangning Song, Dong-Jun Yu
2025 J jnl
MORE: a multi-omics data-driven hypergraph integration network for biomedical data classification and biomarker identification.
Briefings Bioinform.
Yuhan Wang, Zhikang Wang, Xuan Yu, Xiaoyu Wang, Jiangning Song, Dong-Jun Yu, Fang Ge
2025 J jnl
Multimodal geometric learning for antimicrobial peptide identification by leveraging alphafold2-predicted structures and surface features.
Briefings Bioinform.
Zehua Sun, Jing Xu, Yumeng Zhang, Yiwen Zhang, Zhikang Wang, Xiaoyu Wang, Shanshan Li, Yuming Guo, Hsin Hui Shen, Jiangning Song
2025 J jnl
SCREEN: A Graph-based Contrastive Learning Tool to Infer Catalytic Residues and Assess Enzyme Mutations.
Genom. Proteom. Bioinform.
Tong Pan, Yue Bi, Xiaoyu Wang, Ying Zhang, Geoffrey I. Webb, Robin B. Gasser, Lukasz A. Kurgan, Jiangning Song
2024 J jnl
CoPRA: Bridging Cross-domain Pretrained Sequence Models with Complex Structures for Protein-RNA Binding Affinity Prediction.
CoRR
Rong Han, Xiaohong Liu, Tong Pan, Jing Xu, Xiaoyu Wang, Wuyang Lan, Zhenyu Li, Zixuan Wang, Jiangning Song, Guangyu Wang, Ting Chen
2024 J jnl
Deep learning approaches for non-coding genetic variant effect prediction: current progress and future prospects.
Briefings Bioinform.
Xiaoyu Wang, Fuyi Li, Yiwen Zhang, Seiya Imoto, Hsin-Hui Shen, Shanshan Li, Yuming Guo, Jian Yang, Jiangning Song
2024 J jnl
GraphormerDTI: A graph transformer-based approach for drug-target interaction prediction.
Comput. Biol. Medicine
Mengmeng Gao, Daokun Zhang, Yi Chen, Yiwen Zhang, Zhikang Wang, Xiaoyu Wang, Shanshan Li, Yuming Guo, Geoffrey I. Webb, Anh T. N. Nguyen, Lauren T. May, Jiangning Song
2024 J jnl
MLSNet: a deep learning model for predicting transcription factor binding sites.
Briefings Bioinform.
Yuchuan Zhang, Zhikang Wang, Fang Ge, Xiaoyu Wang, Yiwen Zhang, Shanshan Li, Yuming Guo, Jiangning Song, Dong-Jun Yu
2024 J jnl
PmxPred: A data-driven approach for the identification of active polymyxin analogues against gram-negative bacteria.
Comput. Biol. Medicine
Xiaoyu Wang, Nitin Patil, Fuyi Li, Zhikang Wang, Haolan Zhan, Daniel Schmidt, Philip Thompson, Yuming Guo, Cornelia B. Landersdorfer, Hsin-Hui Shen, Anton Y. Peleg, Jian Li, Jiangning Song
2023 J jnl
SMG: self-supervised masked graph learning for cancer gene identification.
Briefings Bioinform.
Yan Cui, Zhikang Wang, Xiaoyu Wang, Yiwen Zhang, Ying Zhang, Tong Pan, Zhe Zhang, Shanshan Li, Yuming Guo, Tatsuya Akutsu, Jiangning Song
2023 J jnl
TIMER is a Siamese neural network-based framework for identifying both general and species-specific bacterial promoters.
Briefings Bioinform.
Yan Zhu, Fuyi Li, Xudong Guo, Xiaoyu Wang, Lachlan J. M. Coin, Geoffrey I. Webb, Jiangning Song, Cangzhi Jia
2023 J jnl
Targeting tumor heterogeneity: multiplex-detection-based multiple instance learning for whole slide image classification.
Bioinform.
Zhikang Wang, Yue Bi, Tong Pan, Xiaoyu Wang, Chris Bain, Richard Bassed, Seiya Imoto, Jianhua Yao, Roger J. Daly, Jiangning Song
2022 J jnl
ASPIRER: a new computational approach for identifying non-classical secreted proteins based on deep learning.
Briefings Bioinform.
Xiaoyu Wang, Fuyi Li, Jing Xu, Jia Rong, Geoffrey I. Webb, Zongyuan Ge, Jian Li, Jiangning Song
2022 J jnl
Multiplex-detection Based Multiple Instance Learning Network for Whole Slide Image Classification.
CoRR
Zhikang Wang, Yue Bi, Tong Pan, Xiaoyu Wang, Chris Bain, Richard Bassed, Seiya Imoto, Jianhua Yao, Jiangning Song
2022 J jnl
Positive-unlabeled learning in bioinformatics and computational biology: a brief review.
Briefings Bioinform.
Fuyi Li, Shuangyu Dong, André Leier, Meiya Han, Xudong Guo, Jing Xu, Xiaoyu Wang, Shirui Pan, Cangzhi Jia, Yang Zhang, Geoffrey I. Webb, Lachlan J. M. Coin, Chen Li, Jiangning Song
2022 J jnl
PreAcrs: a machine learning framework for identifying anti-CRISPR proteins.
BMC Bioinform.
Lin Zhu, Xiaoyu Wang, Fuyi Li, Jiangning Song
2022 J jnl
RBP-TSTL is a two-stage transfer learning framework for genome-scale prediction of RNA-binding proteins.
Briefings Bioinform.
Xinxin Peng, Xiaoyu Wang, Yuming Guo, Zongyuan Ge, Fuyi Li, Xin Gao, Jiangning Song
2021 J jnl
Leveraging the attention mechanism to improve the identification of DNA N6-methyladenine sites.
Briefings Bioinform.
Ying Zhang, Yan Liu, Jian Xu, Xiaoyu Wang, Xinxin Peng, Jiangning Song, Dong-Jun Yu