Improved and Promising Identificationof Human MicroRNAs by Incorporatinga High-Quality Negative Set. - Leyi Wei; Minghong Liao; Yue Gao 002; Rongrong Ji; Zengyou He; Quan Zou 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

mGOF-loc: A novel ensemble learning method for human protein subcellular localization prediction. - Leyi Wei; Minghong Liao; Xing Gao 004; Jingjing Wang; Weiqi Lin (Neurocomputing, 2016)

Exploring local discriminative information from evolutionary profiles for cytokine-receptor interaction prediction. - Leyi Wei; Bowen Zhang; Zhiyong Chen; Xing Gao 004; Minghong Liao (Neurocomputing, 2016)

A novel hierarchical selective ensemble classifier with bioinformatics application. - Leyi Wei; Shixiang Wan; Jiasheng Guo; Kelvin Kian Loong Wong (Artif. Intell. Medicine, 2017)

Improved prediction of protein-protein interactions using novel negative samples, features, and an ensemble classifier. - Leyi Wei; Pengwei Xing; Jian-Cang Zeng; Jin-Xiu Chen; Ran Su; Fei Guo 001 (Artif. Intell. Medicine, 2017)

Local-DPP: An improved DNA-binding protein prediction method by exploring local evolutionary information. - Leyi Wei; Jijun Tang; Quan Zou 001 (Inf. Sci., 2017)

Encoded Texture Features to Characterize Bone Radiograph Images. - Ran Su; Weijun Chen; Leyi Wei; Xiuting Li; Qiangguo Jin; Wenyuan Tao (ICPR, 2018)

ACPred-FL: a sequence-based predictor using effective feature representation to improve the prediction of anti-cancer peptides. - Leyi Wei; Chen Zhou; Huangrong Chen; Jiangning Song; Ran Su (Bioinform., 2018)

RA-UNet: A hybrid deep attention-aware network to extract liver and tumor in CT scans. - Qiangguo Jin; Zhao-Peng Meng; Changming Sun; Leyi Wei; Ran Su (CoRR, 2018)

Prediction of human protein subcellular localization using deep learning. - Leyi Wei; Yijie Ding; Ran Su; Jijun Tang; Quan Zou 001 (J. Parallel Distributed Comput., 2018)

LncPred-IEL: A Long Non-coding RNA Prediction Method using Iterative Ensemble Learning. - Yanzhen Xu; Xiaohan Zhao; Shuai Liu 017; Shichao Liu 002; Yanqing Niu; Wen Zhang 008; Leyi Wei (BIBM, 2019)

Identification and Prediction of Key Nucleotide Sites Using Machine Learning in Bioinformatics: A Brief Overview. - Jianhua Cai; Leyi Wei; Kun Zeng; Guobao Xiao (ISPA/BDCloud/SocialCom/SustainCom, 2019)

Discriminant Affinity Matrix for Deterministic Motion Trajectory Segmentation. - Guobao Xiao; Kun Zeng; Leyi Wei; Tao Wang 047; Taotao Lai (IEEE Access, 2019)

mAHTPred: a sequence-based meta-predictor for improving the prediction of anti-hypertensive peptides using effective feature representation. - Balachandran Manavalan; Shaherin Basith; Tae Hwan Shin; Leyi Wei; Gwang Lee (Bioinform., 2019)

Exploring sequence-based features for the improved prediction of DNA N4-methylcytosine sites in multiple species. - Leyi Wei; Shasha Luan; Luis Augusto Eijy Nagai; Ran Su; Quan Zou 001 (Bioinform., 2019)

Iterative feature representations improve N4-methylcytosine site prediction. - Leyi Wei; Ran Su; Shasha Luan; Zhijun Liao; Balachandran Manavalan; Quan Zou 001; Xiaolong Shi (Bioinform., 2019)

PEPred-Suite: improved and robust prediction of therapeutic peptides using adaptive feature representation learning. - Leyi Wei; Chen Zhou; Ran Su; Quan Zou 001 (Bioinform., 2019)

Integration of deep feature representations and handcrafted features to improve the prediction of N6-methyladenosine sites. - Leyi Wei; Ran Su; Bing Wang; Xiuting Li; Quan Zou 001; Xing Gao 004 (Neurocomputing, 2019)

DUNet: A deformable network for retinal vessel segmentation. - Qiangguo Jin; Zhaopeng Meng; Tuan D. Pham; Qi Chen; Leyi Wei; Ran Su (Knowl. Based Syst., 2019)

Developing a Multi-Dose Computational Model for Drug-Induced Hepatotoxicity Prediction Based on Toxicogenomics Data. - Ran Su; Huichen Wu; Bo Xu; Xiaofeng Liu 004; Leyi Wei (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Fast Prediction of Protein Methylation Sites Using a Sequence-Based Feature Selection Technique. - Leyi Wei; Pengwei Xing; Gaotao Shi; Zhiliang Ji; Quan Zou 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact. - Fuyi Li; Cunshuo Fan; Tatiana T. Marquez-Lago; André Leier; Jerico Nico De Leon Revote; Cangzhi Jia; Yan Zhu 006; Alexander Ian Smith; Geoffrey I. Webb; Quanzhong Liu; Leyi Wei; Jian Li 052; et al. (Briefings Bioinform., 2020)

CPPred-FL: a sequence-based predictor for large-scale identification of cell-penetrating peptides by feature representation learning. - Xiaoli Qiang; Chen Zhou; Xiucai Ye; Pufeng Du; Ran Su; Leyi Wei (Briefings Bioinform., 2020)

ACPred-Fuse: fusing multi-view information improves the prediction of anticancer peptides. - Bing Rao; Chen Zhou; Guoying Zhang; Ran Su; Leyi Wei (Briefings Bioinform., 2020)

Empirical comparison and analysis of web-based cell-penetrating peptide prediction tools. - Ran Su; Jie Hu; Quan Zou 001; Balachandran Manavalan; Leyi Wei (Briefings Bioinform., 2020)

MinE-RFE: determine the optimal subset from RFE by minimizing the subset-accuracy-defined energy. - Ran Su; Xinyi Liu; Leyi Wei (Briefings Bioinform., 2020)

Meta-GDBP: a high-level stacked regression model to improve anticancer drug response prediction. - Ran Su; Xinyi Liu; Guobao Xiao; Leyi Wei (Briefings Bioinform., 2020)

Comparative analysis and prediction of quorum-sensing peptides using feature representation learning and machine learning algorithms. - Leyi Wei; Jie Hu; Fuyi Li; Jiangning Song; Ran Su; Quan Zou 001 (Briefings Bioinform., 2020)

Identifying enhancer-promoter interactions with neural network based on pre-trained DNA vectors and attention mechanism. - Zengyan Hong; Xiangxiang Zeng; Leyi Wei; Xiangrong Liu (Bioinform., 2020)

Identification of expression signatures for non-small-cell lung carcinoma subtype classification. - Ran Su; Jiahang Zhang; Xiaofeng Liu 004; Leyi Wei (Bioinform., 2020)

Fusing convolutional neural network features with hand-crafted features for osteoporosis diagnoses. - Ran Su; Tianling Liu; Changming Sun; Qiangguo Jin; Rachid Jennane; Leyi Wei (Neurocomputing, 2020)

IEEE Access Special Section Editorial: Feature Representation and Learning Methods With Applications in Large-Scale Biological Sequence Analysis. - Feifei Cui; Quan Zou 001; Qin Ma 003; Leyi Wei; Jijun Tang; Dariusz Mrozek (IEEE Access, 2021)

Integrative machine learning framework for the identification of cell-specific enhancers from the human genome. - Shaherin Basith; Md. Mehedi Hasan 002; Gwang Lee; Leyi Wei; Balachandran Manavalan (Briefings Bioinform., 2021)

PSSP-MVIRT: peptide secondary structure prediction based on a multi-view deep learning architecture. - Xiao Cao; Wenjia He; Zitan Chen; Yifan Li; Kexin Wang; Hongbo Zhang; Lesong Wei; Lizhen Cui; Ran Su; Leyi Wei (Briefings Bioinform., 2021)

Iterative feature representation algorithm to improve the predictive performance of N7-methylguanosine sites. - Chichi Dai; Pengmian Feng; Lizhen Cui; Ran Su; Wei Chen 064; Leyi Wei (Briefings Bioinform., 2021)

EP3: an ensemble predictor that accurately identifies type III secreted effectors. - Jing Li; Leyi Wei; Fei Guo 001; Quan Zou 001 (Briefings Bioinform., 2021)

Classification and gene selection of triple-negative breast cancer subtype embedding gene connectivity matrix in deep neural network. - Jin Liu; Ran Su; Jiahang Zhang; Leyi Wei (Briefings Bioinform., 2021)

Predicting drug-induced hepatotoxicity based on biological feature maps and diverse classification strategies. - Ran Su; Huichen Wu; Xinyi Liu; Leyi Wei (Briefings Bioinform., 2021)

Computational prediction and interpretation of cell-specific replication origin sites from multiple eukaryotes by exploiting stacking framework. - Leyi Wei; Wenjia He; Adeel Malik; Ran Su; Lizhen Cui; Balachandran Manavalan (Briefings Bioinform., 2021)

ATSE: a peptide toxicity predictor by exploiting structural and evolutionary information based on graph neural network and attention mechanism. - Lesong Wei; Xiucai Ye; Yuyang Xue; Tetsuya Sakurai; Leyi Wei (Briefings Bioinform., 2021)

Learning embedding features based on multisense-scaled attention architecture to improve the predictive performance of anticancer peptides. - Wenjia He; Yu Wang; Lizhen Cui; Ran Su; Leyi Wei (Bioinform., 2021)

iDNA-ABT: advanced deep learning model for detecting DNA methylation with adaptive features and transductive information maximization. - Yingying Yu; Wenjia He; Junru Jin; Guobao Xiao; Lizhen Cui; Rao Zeng; Leyi Wei (Bioinform., 2021)

FEGS: a novel feature extraction model for protein sequences and its applications. - Zengchao Mu; Ting Yu 010; Xiaoping Liu 002; Hongyu Zheng; Leyi Wei; Juntao Liu (BMC Bioinform., 2021)

Domain adaptation based self-correction model for COVID-19 infection segmentation in CT images. - Qiangguo Jin; Hui Cui 002; Changming Sun; Zhaopeng Meng; Leyi Wei; Ran Su (Expert Syst. Appl., 2021)

Identification of glioblastoma molecular subtype and prognosis based on deep MRI features. - Ran Su; Xiaoying Liu; Qiangguo Jin; Xiaofeng Liu 004; Leyi Wei (Knowl. Based Syst., 2021)

Protein subcellular localization based on deep image features and criterion learning strategy. - Ran Su; Linlin He; Tianling Liu; Xiaofeng Liu 004; Leyi Wei (Briefings Bioinform., 2021)

Semi-supervised Histological Image Segmentation via Hierarchical Consistency Enforcement. - Qiangguo Jin; Hui Cui 002; Changming Sun; Jiangbin Zheng 001; Leyi Wei; Zhenyu Fang; Zhaopeng Meng; Ran Su (MICCAI (2), 2022)

Accelerating bioactive peptide discovery via mutual information-based meta-learning. - Wenjia He; Yi Jiang; Junru Jin; Zhongshen Li; Jiaojiao Zhao; Balachandran Manavalan; Ran Su; Xin Gao 001; Leyi Wei (Briefings Bioinform., 2022)

SRDFM: Siamese Response Deep Factorization Machine to improve anti-cancer drug recommendation. - Ran Su; Yixuan Huang; De-gan Zhang; Guobao Xiao; Leyi Wei (Briefings Bioinform., 2022)

Distant metastasis identification based on optimized graph representation of gene interaction patterns. - Ran Su; Yingying Zhu; Quan Zou 001; Leyi Wei (Briefings Bioinform., 2022)

StackTADB: a stacking-based ensemble learning model for predicting the boundaries of topologically associating domains (TADs) accurately in fruit flies. - Hao Wu 062; Pengyu Zhang; Zhaoheng Ai; Leyi Wei; Hongming Zhang 002; Fan Yang 068; Lizhen Cui (Briefings Bioinform., 2022)

Predicting protein-peptide binding residues via interpretable deep learning. - Ruheng Wang; Junru Jin; Quan Zou 001; Kenta Nakai; Leyi Wei (Bioinform., 2022)

Multi-scale deep learning for the imbalanced multi-label protein subcellular localization prediction based on immunohistochemistry images. - Fengsheng Wang; Leyi Wei (Bioinform., 2022)

ToxIBTL: prediction of peptide toxicity based on information bottleneck and transfer learning. - Lesong Wei; Xiucai Ye; Tetsuya Sakurai; Zengchao Mu; Leyi Wei (Bioinform., 2022)

GSAML-DTA: An interpretable drug-target binding affinity prediction model based on graph neural networks with self-attention mechanism and mutual information. - Jiaqi Liao; Haoyang Chen; Lesong Wei; Leyi Wei (Comput. Biol. Medicine, 2022)

Deep convolutional neural networks with ensemble learning and transfer learning for automated detection of gastrointestinal diseases. - Qiaosen Su; Fengsheng Wang; Dong Chen; Gang Chen; Chao Li; Leyi Wei (Comput. Biol. Medicine, 2022)

MechRetro is a chemical-mechanism-driven graph learning framework for interpretable retrosynthesis prediction and pathway planning. - Yu Wang; Chao Pang; Yuzhe Wang; Yi Jiang; Junru Jin; Sirui Liang; Quan Zou 001; Leyi Wei (CoRR, 2022)

MSMG-Net: Multi-scale Multi-grained Supervised Metworks for Multi-task Image Manipulation Detection and Localization. - Fengsheng Wang; Leyi Wei (CoRR, 2022)

Multi-view deep learning based molecule design and structural optimization accelerates the SARS-CoV-2 inhibitor discovery. - Chao Pang; Yu Wang; Yi Jiang; Ruheng Wang; Ran Su; Leyi Wei (CoRR, 2022)

EOCSA: Predicting prognosis of Epithelial ovarian cancer with whole slide histopathological images. - Tianling Liu; Ran Su; Changming Sun; Xiuting Li; Leyi Wei (Expert Syst. Appl., 2022)

Recent Advances in the Prediction of Subcellular Localization of Proteins and Related Topics. - Kenta Nakai; Leyi Wei (Frontiers Bioinform., 2022)

PESA-Net: Permutation-Equivariant Split Attention Network for correspondence learning. - Zhen Zhong; Guobao Xiao; Shiping Wang; Leyi Wei; Xiaoqin Zhang 002 (Inf. Fusion, 2022)

Robust Feature Matching for Remote Sensing Image Registration via Guided Hyperplane Fitting. - Guobao Xiao; Huan Luo 001; Kun Zeng; Leyi Wei; Jiayi Ma 001 (IEEE Trans. Geosci. Remote. Sens., 2022)

A multi-label learning model for predicting drug-induced pathology in multi-organ based on toxicogenomics data. - Ran Su; Haitang Yang; Leyi Wei; Siqi Chen 001; Quan Zou 001 (PLoS Comput. Biol., 2022)

Shape-aware contrastive deep supervision for esophageal tumor segmentation from CT scans. - Qiangguo Jin; Hui Cui 002; Changming Sun; Jiapeng Huang; Ping Xuan; Yiyue Xu; Linlin Wang; Leilei Cao; Leyi Wei; Ran Su (BIBM, 2023)

Multi-modality Contrastive Learning for Sarcopenia Screening from Hip X-rays and Clinical Information. - Qiangguo Jin; Changjiang Zou; Hui Cui 002; Changming Sun; Shu-Wei Huang; Yi-Jie Kuo; Ping Xuan; Leilei Cao; Ran Su; Leyi Wei; Henry B. L. Duh; Yu-Pin Chen (MICCAI (6), 2023)

AFP-MFL: accurate identification of antifungal peptides using multi-view feature learning. - Yitian Fang; Fan Xu; Lesong Wei; Yi Jiang; Jie Chen 001; Leyi Wei; Dong-Qing Wei (Briefings Bioinform., 2023)

SiameseCPP: a sequence-based Siamese network to predict cell-penetrating peptides by contrastive learning. - Xin Zhang; Lesong Wei; Xiucai Ye; Kai Zhang; Saisai Teng; Zhongshen Li; Junru Jin; Min Jae Kim; Tetsuya Sakurai; Lizhen Cui; Balachandran Manavalan; Leyi Wei (Briefings Bioinform., 2023)

ExamPle: explainable deep learning framework for the prediction of plant small secreted peptides. - Zhongshen Li; Junru Jin; Yu Wang; Wentao Long; Yuanhao Ding; Haiyan Hu; Leyi Wei (Bioinform., 2023)

MPI-VGAE: protein-metabolite enzymatic reaction link learning by variational graph autoencoders. - Cheng Wang; Chuang Yuan; Yahui Wang; Ranran Chen; Yuying Shi; Tao Zhang 127; Fuzhong Xue; Gary J. Patti; Leyi Wei; Qingzhen Hou (Briefings Bioinform., 2023)

DrugormerDTI: Drug Graphormer for drug-target interaction prediction. - Jiayue Hu; Yu Wang; Chao Pang; Junru Jin; Nhat Truong Pham; Balachandran Manavalan; Leyi Wei (Comput. Biol. Medicine, 2023)

CoraL: interpretable contrastive meta-learning for the prediction of cancer-associated ncRNA-encoded small peptides. - Zhongshen Li; Junru Jin; Wenjia He; Wentao Long; Haoqing Yu; Xin Gao 001; Kenta Nakai; Quan Zou 001; Leyi Wei (Briefings Bioinform., 2023)

PLPMpro: Enhancing promoter sequence prediction with prompt-learning based pre-trained language model. - Zhongshen Li; Junru Jin; Wentao Long; Leyi Wei (Comput. Biol. Medicine, 2023)

Rm-LR: A long-range-based deep learning model for predicting multiple types of RNA modifications. - Sirui Liang; Yanxi Zhao; Junru Jin; Jianbo Qiao; Ding Wang; Yu Wang; Leyi Wei (Comput. Biol. Medicine, 2023)

MolFPG: Multi-level fingerprint-based Graph Transformer for accurate and robust drug toxicity prediction. - Saisai Teng; Chenglin Yin; Yu Wang; Xiandong Chen; Zhongmin Yan; Lizhen Cui; Leyi Wei (Comput. Biol. Medicine, 2023)

A general hypergraph learning algorithm for drug multi-task predictions in micro-to-macro biomedical networks. - Shuting Jin; Yue Hong; Li Zeng; Yinghui Jiang; Yuan Lin; Leyi Wei; Zhuohang Yu; Xiangxiang Zeng; Xiangrong Liu (PLoS Comput. Biol., 2023)

DeepProSite: structure-aware protein binding site prediction using ESMFold and pretrained language model. - Yitian Fang; Yi Jiang; Leyi Wei; Qin Ma 003; Zhixiang Ren; Qianmu Yuan; Dong-Qing Wei (Bioinform., 2023)

MolCAP: Molecular Chemical reActivity Pretraining and prompted-finetuning enhanced molecular representation learning. - Yu Wang; Jingjie Zhang; Junru Jin; Leyi Wei (Comput. Biol. Medicine, 2023)

ConPep: Prediction of peptide contact maps with pre-trained biological language model and multi-view feature extracting strategy. - Qingxin Wei; Ruheng Wang; Yi Jiang; Leyi Wei; Yu Sun; Jie Geng; Ran Su (Comput. Biol. Medicine, 2023)

Advanced deep learning methods for molecular property prediction. - Chao Pang; Henry H. Y. Tong; Leyi Wei (Quant. Biol., 2023)

MSKI-Net: Towards modality-specific knowledge interaction for glioma survival prediction. - Ran Su; Jin Xiao; Hui Cui 002; Ping Xuan; Xikang Feng; Leyi Wei; Qiangguo Jin (BIBM, 2024)

Location Embedding Based Pairwise Distance Learning for Fine-Grained Diagnosis of Urinary Stones. - Qiangguo Jin; Jiapeng Huang; Changming Sun; Hui Cui 002; Ping Xuan; Ran Su; Leyi Wei; Yu-Jie Wu; Chia-An Wu; Henry B. L. Duh; Yueh-Hsun Lu (MICCAI (11), 2024)

CELA-MFP: a contrast-enhanced and label-adaptive framework for multi-functional therapeutic peptides prediction. - Yitian Fang; Mingshuang Luo; Zhixiang Ren; Leyi Wei; Dong-Qing Wei (Briefings Bioinform., 2024)

Therapeutic peptides identification via kernel risk sensitive loss-based k-nearest neighbor model and multi-Laplacian regularization. - Wenyu Zhang; Yijie Ding; Leyi Wei; Xiaoyi Guo; Fengming Ni (Briefings Bioinform., 2024)

Deep Generative Models in De Novo Drug Molecule Generation. - Chao Pang; Jianbo Qiao; Xiangxiang Zeng; Quan Zou 001; Leyi Wei (J. Chem. Inf. Model., 2024)

AttenSyn: An Attention-Based Deep Graph Neural Network for Anticancer Synergistic Drug Combination Prediction. - Tianshuo Wang; Ruheng Wang; Leyi Wei (J. Chem. Inf. Model., 2024)

CACPP: A Contrastive Learning-Based Siamese Network to Identify Anticancer Peptides Based on Sequence Only. - Xuetong Yang; Junru Jin; Ruheng Wang; Zhongshen Li; Yu Wang; Leyi Wei (J. Chem. Inf. Model., 2024)

MucLiPred: Multi-Level Contrastive Learning for Predicting Nucleic Acid Binding Residues of Proteins. - Jiashuo Zhang 002; Ruheng Wang; Leyi Wei (J. Chem. Inf. Model., 2024)

Moss-m7G: A Motif-Based Interpretable Deep Learning Method for RNA N7-Methlguanosine Site Prediction. - Yanxi Zhao; Junru Jin; Wenjia Gao; Jianbo Qiao; Leyi Wei (J. Chem. Inf. Model., 2024)

Multi-CGAN: Deep Generative Model-Based Multiproperty Antimicrobial Peptide Design. - Haoqing Yu; Ruheng Wang; Jianbo Qiao; Leyi Wei (J. Chem. Inf. Model., 2024)

StructuralDPPIV: a novel deep learning model based on atom structure for predicting dipeptidyl peptidase-IV inhibitory peptides. - Ding Wang; Junru Jin; Zhongshen Li; Yu Wang; Mushuang Fan; Sirui Liang; Ran Su; Leyi Wei (Bioinform., 2024)

NanoCon: contrastive learning-based deep hybrid network for nanopore methylation detection. - Chenglin Yin; Ruheng Wang; Jianbo Qiao; Hua Shi; Hongliang Duan; Xinbo Jiang; Saisai Teng; Leyi Wei (Bioinform., 2024)

Inter- and intra-uncertainty based feature aggregation model for semi-supervised histopathology image segmentation. - Qiangguo Jin; Hui Cui 002; Changming Sun; Yang Song; Jiangbin Zheng 001; Leilei Cao; Leyi Wei; Ran Su (Expert Syst. Appl., 2024)

Towards retraining-free RNA modification prediction with incremental learning. - Jianbo Qiao; Junru Jin; Haoqing Yu; Leyi Wei (Inf. Sci., 2024)

Iterative clustering algorithm G-DESC-E and pan-cancer key gene analysis based on single-cell sequencing data. - Ke Wu; Changming Sun; Jie Geng; Ping Wang; Qi Dai; Leyi Wei; Ran Su (Briefings Bioinform., 2025)

MCAMEF-BERT: an efficient deep learning method for RNA N7-methylguanosine site prediction via multi-branch feature integration. - Junlei Yu; Wenjia Gao; Siqi Chen 001; Ronglin Lu; Jianbo Qiao; Junru Jin; Leyi Wei; Hua Shi; Zilong Zhang; Feifei Cui; Xinbo Jiang; Zhongmin Yan (Briefings Bioinform., 2025)

PLM-IL4: Enhancing IL-4-inducing peptide prediction with protein language model. - Ruiqi Liu; Shankai Yan; Zilong Zhang; Junlin Xu; Yajie Meng; Qingchen Zhang 001; Leyi Wei; Quan Zou 001; Feifei Cui (Comput. Biol. Chem., 2025)

PKDF-Net: Anticancer peptide prediction via a prior-knowledge-aware dual-path feature-entangled network. - Qiangguo Jin; Ankang Wu; Leyi Wei; Hui Cui 002; Ping Xuan; Xikang Feng; Ran Su (Eng. Appl. Artif. Intell., 2025)

ACP-CLB: An Anticancer Peptide Prediction Model Based on Multichannel Discriminative Processing and Integration of Large Pretrained Protein Language Models. - Aoyun Geng; Zhenjie Luo; Aohan Li; Zilong Zhang; Quan Zou 001; Leyi Wei; Feifei Cui (J. Chem. Inf. Model., 2025)

AVP-HNCL: Innovative Contrastive Learning with a Queue-Based Negative Sampling Strategy for Dual-Phase Antiviral Peptide Prediction. - Yuanhao Li; Aoyun Geng; Zheyu Zhou; Feifei Cui; Junlin Xu; Yajie Meng; Leyi Wei; Quan Zou 001; Qingchen Zhang 001; Zilong Zhang (J. Chem. Inf. Model., 2025)

m5U-HybridNet: Integrating an RNA Foundation Model with CNN Features for Accurate Prediction of 5-Methyluridine Modification Sites. - Xinyu Li; Zhenjie Luo; Jingwei Lv; Chao Yang; Shankai Yan; Junlin Xu; Yajie Meng; Leyi Wei; Zilong Zhang; Quan Zou 001; Feifei Cui (J. Chem. Inf. Model., 2025)

GICL: A Cross-Modal Drug Property Prediction Framework Based on Knowledge Enhancement of Large Language Models. - Na Li; Jianbo Qiao; Fei Gao; Yanling Wang; Hua Shi; Zilong Zhang; Feifei Cui; Lichao Zhang; Leyi Wei (J. Chem. Inf. Model., 2025)

NeuroPred-AIMP: Multimodal Deep Learning for Neuropeptide Prediction via Protein Language Modeling and Temporal Convolutional Networks. - Jinjin Li; Shuwen Xiong; Hua Shi; Feifei Cui; Zilong Zhang; Leyi Wei (J. Chem. Inf. Model., 2025)

Deep Learning in Antimicrobial Peptide Prediction. - Changhang Lin; Shuwen Xiong; Feifei Cui; Zilong Zhang; Hua Shi; Leyi Wei (J. Chem. Inf. Model., 2025)

Integrating Protein Language Models and Geometric Deep Learning for Peptide Toxicity Prediction. - Yanling Wang; Na Li; Xiao Wang; Feng Cao; Shuwen Xiong; Leyi Wei (J. Chem. Inf. Model., 2025)

UMPPI: Unveiling Multilevel Protein-Peptide Interaction Prediction via Language Models. - Shuwen Xiong; Jiajie Cai; Hua Shi; Feifei Cui; Zilong Zhang; Leyi Wei (J. Chem. Inf. Model., 2025)

Iterative pseudo-labeling based adaptive copy-paste supervision for semi-supervised tumor segmentation. - Qiangguo Jin; Hui Cui 002; Junbo Wang; Changming Sun; Yimiao He; Ping Xuan; Linlin Wang; Cong Cong; Leyi Wei; Ran Su (Knowl. Based Syst., 2025)

Elucidating spatiotemporal chromatin dynamics with multi-stage differential variations from Hi-C. - Zhongshen Li; Jixiang Yu; Shen You; Leyi Wei; Qiuzhen Lin; Xiangtao Li; Ka-Chun Wong (Knowl. Based Syst., 2025)

Taco-DDI: accurate prediction of drug-drug interaction events using graph transformer-based architecture and dynamic co-attention matrices. - Jianbo Qiao; Xu Guo; Junru Jin; Ding Wang; Kefei Li; Wenjia Gao; Feifei Cui; Zilong Zhang; Hua Shi; Leyi Wei (Neural Networks, 2025)

Multi-Modal Deep Representation Learning Accurately Identifies and Interprets Drug-Target Interactions. - Jiayue Hu; Yuhang Liu; Xiangxiang Zeng; Quan Zou 001; Ran Su; Leyi Wei (IEEE J. Biomed. Health Informatics, 2025)

Multiview Deep Learning-Based Molecule Design and Structural Optimization Accelerates Inhibitor Discover. - Chao Pang; Yu Wang; Yi Jiang; Ruheng Wang; Xiaojun Yao; Quan Zou 001; Xiangxiang Zeng; Ran Su; Leyi Wei (IEEE Trans. Neural Networks Learn. Syst., 2025)

xBitterT5: an explainable transformer-based framework with multimodal inputs for identifying bitter-taste peptides. - Nguyen Doan Hieu Nguyen; Nhat Truong Pham; Duong Thanh Tran; Leyi Wei; Adeel Malik; Balachandran Manavalan (J. Cheminformatics, 2025)