Welcome to BioAI-Lab

2025

GCNLA: Inferring Cell-Cell Interactions From Spatial Transcriptomics With Long Short-Term Memory and Graph Convolutional Networks.

Chao Yang, Xiuhao Fu, Zhenjie Luo, Leyi Wei, Jingbing Li, Feifei Cui, Quan Zou, Qingchen Zhang, and Zilong Zhang*, in IEEE Journal of Biomedical and Health Informatics. In press

A comprehensive review of computational methods for predicting DNA N4-methylcytosine sites.

Zihang Wang, Aoyun Geng, Junlin Xu, Yajie Meng, Zilong Zhang, Leyi Wei, Quan Zou, and Feifei Cui*, in International Journal of Biological Macromolecules. In press

NeuroCL: A Deep Learning Approach for Identifying Neuropeptides Based on Contrastive Learning.

Jian Liu, Aoyun Geng, Feifei Cui, Junlin Xu, Yajie Meng, Leyi Wei, Qingchen Zhang, Quan Zou, and Zilong Zhang*, in Analytical Biochemistry. In press

PLM-IL4: Enhancing IL-4-inducing peptide prediction with protein language model.

Ruiqi Liu, Shankai Yan, Zilong Zhang, Junlin Xu, Yajie Meng, Qingchen Zhang, Leyi Wei, Quan Zou, and Feifei Cui*, in Computational Biology and Chemistry. In press

DeepMaT: Prediction of Target Peptide Classification and Cleavage Site by Combining Mamba2 and Multiple Attention Mechanisms.

Qianmao Wen, Aoyun Geng, Junlin Xu, Yajie Meng, Leyi Wei, Zilong Zhang, Quan Zou, and Feifei Cui*, in Journal of Chemical Information and Modeling. In press

CNNCaps-DBP: Leveraging protein language models with attention-augmented convolution for DNA-binding protein prediction.

Ziyuan Yan, Aoyun Geng, Yazi Li, Jiajing Wang, Junlin Xu, Yajie Meng, Leyi Wei, Quan Zou, Zilong Zhang, Feifei Cuii*, in Neural Networks. In press

Progress and applications of single-cell RNA sequencing and spatial transcriptome technology in acute kidney injury research.

Chunyan Cui, Feifei Cui, Quan Zou, Zilong Zhang*, and Linpei Jia*, in Molecular Therapy Nucleic Acids. In press

ACP-EPC: an interpretable deep learning framework for anticancer peptide prediction utilizing pre-trained protein language model and multi-view feature extracting strategy.

Jingwei Lv, Kexin Li, Yike Wang, Junlin Xu, Yajie Meng, Feifei Cui, Leyi Wei, Qingchen Zhang, and Zilong Zhang*, in Molecular Diversity. In press

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, and Feifei Cui*, in Journal of Chemical Information and Modeling. In press

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, Qingchen Zhang, and Zilong Zhang*, in Journal of Chemical Information and Modeling. In press

PLPTP: A Motif-based Interpretable Deep Learning Framework Based on Protein Language Models for Peptide Toxicity Prediction.

Shun Gao, Yanna Jia, Feifei Cui, Junlin Xu, Yajie Meng, Leyi Wei, Qingchen Zhang, Quan Zou, and Zilong Zhang*, in Journal of Molecular Biology. In press

CasPro-ESM2: Accurate identification of Cas proteins integrating pre-trained protein language model and multi-scale convolutional neural network.

Chaorui Yan, Zilong Zhang, Junlin Xu, Yajie Meng, Shankai Yan, Leyi Wei, Quan Zou, Qingchen Zhang, and Feifei Cui*, in International Journal of Biological Macromolecules. In press

CPL‐Diff: A Diffusion Model for De Novo Design of Functional Peptide Sequences with Fixed Length.

Zhenjie Luo, Aoyun Geng, Leyi Wei, Quan Zou, Feifei Cui*, and Zilong Zhang*, in Advanced Science. In press

ACP-ESM2: Enhancing Anticancer Peptide Prediction with Pre-trained Protein Language Models.

Shun Gao, Yan Xia, Xingfeng Li, Feifei Cui, Qingchen Zhang, Quan Zou, and Zilong Zhang*, in IEEE-ACM Transactions on Computational Biology and Bioinformatics. In press

iBitter-GRE: A Novel Stacked Bitter Peptide Predictor with ESM-2 and Multi-View Features.

Jingwei Lv, Aoyun Geng, Zhuoyu Pan, Leyi Wei, Quan Zou, Zilong Zhang, and Feifei Cui*, in Journal of Molecular Biology. In press

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, Leyi Wei, and Feifei Cui*, in Journal of Chemical Information and Modeling. In press

A comprehensive review of deep learning-based approaches for drug–drug interaction prediction.

Yan Xia, An Xiong, Zilong Zhang*, Quan Zou*, and Feifei Cui*, in Briefings in Functional Genomics. In press

PROTCROWN: A Manually Curated Resource of Protein Corona Data for Unlocking the Potential of Protein–Nanoparticle Interactions.

Yunyun Su, Xiuhao Fu, Leyi Wei, Zilong Zhang*, Quan Zou*, and Feifei Cui*, in Nano Letters. In press

A comprehensive review of approaches for spatial domain recognition of spatial transcriptomes.

Ziyi Wang, Aoyun Geng, Hao Duan, Feifei Cui, Quan Zou, and Zilong Zhang*, in Briefings in Functional Genomics. In press

msBERT-Promoter: a multi-scale ensemble predictor based on BERT pre-trained model for the two-stage prediction of DNA promoters and their strengths.

Yazi Li, Xiaoman Wei, Qinglin Yang, An Xiong, Xingfeng Li, Quan Zou, Feifei Cui*, and Zilong Zhang*, in BMC biology. In press

Voting-ac4C:Pre-trained large RNA language model enhances RNA N4-acetylcytidine site prediction.

Yanna Jia, Zilong Zhang, Shankai Yan, Qingchen Zhang, Leyi Wei, and Feifei Cui*, in International Journal of Biological Macromoleculess. In press

MVST: Identifying spatial domains of spatial transcriptomes from multiple views using multi-view graph convolutional networks.

Hao Duan, Qingchen Zhang, Feifei Cui*, Quan Zou*, and Zilong Zhang*, in PLOS Computational Biology. In press

Machine learning enables comprehensive prediction of the relative protein abundance of multiple proteins on the protein corona.

Xiuhao Fu, Chao Yang, Yunyun Su, Chunling Liu, Haoye Qiu, Yanyan Yu, Gaoxing Su, Qingchen Zhang, Leyi Wei, and Feifei Cui*, in Research. In press

MultiFeatVotPIP: a voting-based ensemble learning framework for predicting proinflammatory peptides.

Chaorui Yan, Aoyun Geng, Zhuoyu Pan, Zilong Zhang, and Feifei Cui*, in Briefings in Bioinformatics. In press

DPNN-ac4C: A Dual-Path Neural Network with self-attention mechanism for identification of N4‑acetylcytidine (ac4C) in mRNA.

Jiahao Yuan, Ziyi Wang, Zhuoyu Pan, Aohan Li, Zilong Zhang, and Feifei Cui*, in Bioinformatics. In press

Hyb_SEnc: An Antituberculosis Peptide Predictor Based on a Hybrid Feature Vector and Stacked Ensemble Learning.

Xiuhao Fu, Xiaofeng Zang, Chunling Liu, Xingfeng Li, Qingchen Zhang, Zilong Zhang*, Quan Zou*, and Feifei Cui*, in IEEE/ACM Transactions on Computational Biology and Bioinformatics. In press

AGF-PPIS: a protein–protein interaction site predictor based on an attention mechanism and graph convolutional networks.

Xiuhao Fu, Ye Yuan, Haoye Qiu, Haodong Suo, Yingying Song, Anqi Li, Yupeng Zhang, Cuilin Xiao, Yazi Li, Lijun Dou, Zilong Zhang* and Feifei Cui*, in Methods. In press

Machine learning-based prediction model for distant metastasis of breast cancer.

Hao Duan, Yu Zhang, Haoye Qiu, Xiuhao Fu, Chunling Liu, Xiaofeng Zang, Anqi Xu, Ziyue Wu, Xingfeng Li, Qingchen Zhang, Zilong Zhang and Feifei Cui*, in Computers in Biology and Medicine. In press

Single-cell transcriptome analysis reveals immune microenvironment changes and insights into the transition from DCIS to IDC with associated prognostic genes.

Yidi Sun, Zhuoyu Pan, Ziyi Wang, Haofei Wang, Leyi Wei, Feifei Cui*, Quan Zou*, and Zilong Zhang*, in Journal of Translational Medicine. In press

Integration tools for scRNA-seq data and spatial transcriptomics sequencing data.

Chaorui Yan, Yanxu Zhu, Miao Chen, Kainan Yang, Feifei Cui*, Quan Zou*, and Zilong Zhang*, in Briefings in Functional Genomics. In press

PEL-PVP: Application of plant vacuolar protein discriminator based on PEFT ESM-2 and bilayer LSTM in an unbalanced dataset.

Cuilin Xiao, Zheyu Zhou, Jiayi She, Jinfen Yin, Feifei Cui, and Zilong Zhang*, in International Journal of Biological Macromolecules. In press

PSAC-6mA: 6mA site identifier using self-attention capsule network based on sequence-positioning.

Zheyu Zhou, Cuilin Xiao, Jinfen Yin, Jiayi She, Hao Duan, Chunling Liu, Xiuhao Fu, Feifei Cui, Qi Qi, and Zilong Zhang*, in Computers in Biology and Medicine. In press

A comprehensive survey of dimensionality reduction and clustering methods for single-cell and spatial transcriptomics data.

Yidi Sun, Lingling Kong, Jiayi Huang, Hongyan Deng, Xinling Bian, Xingfeng Li, Feifei Cui, Lijun Dou, Chen Cao, Quan Zou and Zilong Zhang*, in Briefings in Functional Genomics . In press

RAVAR: a curated repository for rare variant–trait associations.

Chen Cao, Mengting Shao, Chunman Zuo, Devin Kwok, Lin Liu, Yuli Ge, Zilong Zhang, Feifei Cui, Mingshuai Chen, and Rui Fan, in Nucleic Acids Research . In press

AIPPT: Predicts anti-inflammatory peptides using the most characteristic subset of bases and sequences by stacking ensemble learning strategies.

Ruiqi Liu, Xiuhao Fu, Shankai Yan, Zilong Zhang, and Feifei Cui*, in 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). Istanbul, Turkiye, 2023, pp. 23-29.In press

Human-Spa: An Online Platform Based on Spatial Transcriptome Data for Diseases of Human Systems.

17. Yunyun Su, Shiyu Yan, Chen Cao, Feifei Cui, Quan Zou*, and Zilong Zhang*, in 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 5-8 Dec, 2023. 293-298. In press

webSCST: an interactive web application for single−cell RNA−sequencing data and spatial transcriptomic data integration.

Zilong Zhang#, Feifei Cui#, Wei Su, Lijun Dou, Anqi Xu, Chen Cao, Quan Zou*.Bioinformatics,2022.Doi: 10.1093/bioinformatics/btac350.In press

DeepMC-iNABP: Deep learning for multiclass identification and classification of nucleic acid-binding proteins.

Feifei Cui#, Shuang Li#, Zilong Zhang, Miaomiao Sui, Chen Cao, Abd El-Latif Hesham, Quan Zou*. Computational and Structural Biotechnology Journal,2022.In press

Protein−DNA/RNA interactions: Machine intelligence tools and approaches in the era of artificial intelligence and big data.

Feifei Cui, Zilong Zhang, Chen Cao, Quan Zou, Dong Chen*, Xi Su*.Proteomics,2022.Doi: 10.1002/pmic.202100197.In press

iKcr_CNN: A novel computational tool for imbalance classification of human nonhistone crotonylation sites based on convolutional neural networks with focal loss.

Lijun Dou, Zilong Zhang, Lei Xu*, Quan Zou*.Computational and Structural Biotechnology Journal,2022.In press

webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study.

Chen Cao, Jianhau Wang, Devin Kwok, Feifei Cui, Zilong Zhang, Da Zhao, Mulin Jun Li, Quan Zou*.Nucleic acids research,2022.In press

Toward smarter management and recovery of municipal solid waste: A critical review on deep learning approaches.

Kunsen Lin, Youcai Zhao, Jia-Hong Kuo, Hao Deng, Feifei Cui, Zilong Zhang, Meilan Zhang, Chunlong Zhao, Xiaofeng Gao*, Tao Zhou*, Tao Wang*.Journal of Cleaner Production,2022.In press

Anticancer peptides prediction with deep representation learning features.

Zhibin Lv#, Feifei Cui#, Quan Zou*, Lichao Zhang*, Lei Xu*.Briefings in Bioinformatics,2021.In press

Sequence representation approaches for sequence−based protein prediction tasks that use deep learning.

Feifei Cui, Zilong Zhang, Quan Zou*. Briefings in Functional Genomics,2021.In press

Briefings in functional genomics special section editorial: analysis of integrated multiple omics data.

Feifei Cui, Liang Cheng *, Quan Zou *.Briefings in Functional Genomics,2021.In press

IEEE Access Special Section Editorial: Feature Representation and Learning Methods With Applications in Large−Scale Biological Sequence Analysis.

Feifei Cui, Quan Zou*, Qin Ma, Leyi Wei, Jijun Tang and Dariusz Mrozek. IEEE Access,2021.In press

"CPL‐Diff: A Diffusion Model for De Novo Design of Functional Peptide Sequences with Fixed Length."

"Machine learning enables comprehensive prediction of the relative protein abundance of multiple proteins on the protein corona."

"PROTCROWN: A Manually Curated Resource of Protein Corona Data for Unlocking the Potential of Protein–Nanoparticle Interactions. "

Publications

# These authors contributed equally to the paper as first authors

* To whom correspondence should be addressed

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