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T4SEfinder: a bioinformatics tool for genome-scale prediction of bacterial type IV secreted effectors using pre-trained protein language model

Published in Briefings in Bioinformatics, 2022

Recommended citation: Y Zhang†, Y Zhang†, Y Xiong, H Wang, Z Deng, J Song & HY Ou. (2022) T4SEfinder: a bioinformatics tool for genomescale prediction of bacterial type IV secreted effectors using pre-trained protein language model. Briefings in Bioinformatics, 23(1), bbab420.
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Unbiased curriculum learning enhanced global-local graph neural network for protein thermodynamic stability prediction

Published in Bioinformatics, 2023

Recommended citation: H Gong†, Y Zhang†, C Dong, Y Wang, G Chen, B Liang, H Li, L Liu, J Xu & G Li. (2023). Unbiased curriculum learning enhanced global-local graph neural network for protein thermodynamic stability prediction. Bioinformatics, 39(10), btad589.
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DeepSecE: a deep learning-based framework for multi-class prediction of secreted proteins in Gram-negative bacteria

Published in Research, 2023

Recommended citation: Y Zhang, J Guan, C Li, Z Wang, Z Deng, RB Gasser, J Song & HY Ou. (2023) DeepSecE: a deep learning-based framework for multi-class prediction of secreted proteins in Gram-negative bacteria. Research, 6, 0258.
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Supervised contrastive learning enhances MHC-II peptide binding affinity prediction

Published in bioRxiv, 2023

Recommended citation: LC Shen, L Yan, Z Liu, Y Zhang, Z Wang, Y Guo, J Rossjohn, J Song & DJ Yu. (2023) ConBoTNet: supervised contrastive learning enhances MHC-II peptide binding affinity prediction. bioRxiv, 2023.12.21.572942.
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Enhanced thermostability of Streptomyces mobaraensis transglutaminase via computation-aided site-directed mutations and structural analysis

Published in New Journal of Chemistry, 2024

Recommended citation: Y Li, B Wu, Y Zhang, L Liu, L Bai & T Shi. (2024) Enhanced thermostability of Streptomyces mobaraensis transglutaminase via computation-aided site-directed mutations and structural analysis. New Journal of Chemistry, 48(2), 591-602.
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TransEFVP: a two-stage approach for the prediction of human pathogenic variants based on protein sequence embedding fusion

Published in Journal of Chemical Information and Modeling, 2024

Recommended citation: Z Yan, F Ge, Y Liu, Y Zhang, F Li, J Song & DJ Yu. (2024) TransEFVP: a two-stage approach for the prediction of human pathogenic variants based on protein sequence embedding fusion. Journal of Chemical Information and Modeling, 64(4), 1407–1418.
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Histo-genomic knowledge distillation for cancer prognosis from histopathology whole slide images

Published in arXiv, 2024

Recommended citation: Z Wang, Y Zhang, Y Xu, S Imoto, H Chen & J Song (2024) Histo-genomic knowledge distillation for cancer prognosis from histopathology whole slide images. arXiv, 2403.10040.
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Transposition with Tn 3-family elements occurs through interaction with the host β-sliding clamp processivity factor

Published in Nucleic Acids Research, 2024

Recommended citation: Y Tang, J Zhang, J Guan, W Liang, MT Petassi, Y Zhang, X Jiang, M Wang, W Wu, HY Ou & JE Peters. (2024) Transposition with Tn 3-family elements occurs through interaction with the host β-sliding clamp processivity factor. Nucleic Acids Research, 52(17), 10416-10430.
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Epitope-anchored contrastive transfer learning for paired CD8+ T cell receptor-antigen recognition

Published in Nature Machine Intelligence, 2024

Recommended citation: Y Zhang, Z Wang, Y Jiang, DR Littler, M Gerstein, AW Purcell, J Rossjohn, HY Ou & J Song. (2024) Epitope-anchored contrastive transfer learning for paired CD8+ T cell receptor-antigen recognition. Nature Machine Intelligence, https://doi.org/10.1038/s42256-024-00913-8.
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T4SEfinder: a bioinformatics tool for genome-scale prediction of bacterial type IV secreted effectors using pre-trained protein language model.

Published: October 27, 2021

Genome-scale prediction of bacterial secreted effectors using pre-trained protein language model

Published: July 23, 2022

Teaching experience 1

Undergraduate course, University 1, Department, 2014

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