An integrated virtual cell approach towards elucidating the systems pharmacology of antibiotics against Pseudomonas aeruginosa

Research output

Research output per year 2018 2020 2021 2022 2025

• 42 Article
• 3 Review Article

Research output per year

Research output per year

Search results

• 2025

  Two decades of advances in sequence-based prediction of MoRFs, disorder-to-order transitioning binding regions

  Song, J. & Kurgan, L., 2025, In: Expert Review of Proteomics. 22, 1, p. 1-9 9 p.

  Research output: Contribution to journal › Article › Research › peer-review
• 2024

  Epitope-anchored contrastive transfer learning for paired CD8+ T cell receptor–antigen recognition

  Zhang, Y., Wang, Z., Jiang, Y., Littler, D. R., Gerstein, M., Purcell, A. W., Rossjohn, J., Ou, H. Y. & Song, J., Nov 2024, In: Nature Machine Intelligence. 6, 11, p. 1344–1358 15 p.

  Research output: Contribution to journal › Article › Research › peer-review
  2 Citations (Scopus)

• PmxPred: A data-driven approach for the identification of active polymyxin analogues against gram-negative bacteria

  Wang, X., Patil, N., Li, F., Wang, Z., Zhan, H., Schmidt, D. F., Thompson, P. E., Guo, Y., Landersdorfer, C. B., Shen, H-H., Peleg, A. Y., Li, J. & Song, J., 2024, In: Computers in Biology and Medicine. 168, 10 p., 107681.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access
  9 Citations (Scopus)
• 2023

  iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities

  Xu, J., Li, F., Li, C., Guo, X., Landersdorfer, C. B., Shen, H-H., Peleg, A. Y., Li, J., Imoto, S., Yao, J., Akutsu, T. & Song, J., Jul 2023, In: Briefings in Bioinformatics. 24, 4, 20 p., bbad240.

  Research output: Contribution to journal › Article › Research › peer-review
  41 Citations (Scopus)

• Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues

  Zhang, Y., Wang, Z., Zhang, Y., Li, S., Guo, Y., Song, J. & Yu, D-J., 1 Dec 2023, In: Bioinformatics. 39, 12, 8 p., btad709.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access
  6 Citations (Scopus)

• Prediction of Multiple Types of RNA Modifications via Biological Language Model

  Zhang, Y., Ge, F., Li, F., Yang, X., Song, J. & Yu, D-J., Sept 2023, In: IEEE/ACM Transactions on Computational Biology and Bioinformatics. 20, 5, p. 3205-3214 10 p.

  Research output: Contribution to journal › Article › Research › peer-review
  11 Citations (Scopus)

• SMG: self-supervised masked graph learning for cancer gene identification

  Cui, Y., Wang, Z., Wang, X., Zhang, Y., Zhang, Y., Pan, T., Zhang, Z., Li, S., Guo, Y., Akutsu, T. & Song, J., Nov 2023, In: Briefings in Bioinformatics. 24, 6, 13 p., bbad406.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access
  7 Citations (Scopus)

• TripletCell: a deep metric learning framework for accurate annotation of cell types at the single-cell level

  Liu, Y., Wei, G., Shen, L-C., Gasser, R. B., Song, J., Chen, D. & Yu, D-J., May 2023, In: Briefings in Bioinformatics. 24, 3, p. 1-11 11 p.

  Research output: Contribution to journal › Article › Research › peer-review
  7 Citations (Scopus)
• 2022

  ASPIRER: A new computational approach for identifying non-classical secreted proteins based on deep learning

  Wang, X., Li, F., Xu, J., Rong, J., Webb, G. I., Ge, Z., Li, J. & Song, J., Mar 2022, In: Briefings in Bioinformatics. 23, 2, p. 1-12 12 p., bbac031.

  Research output: Contribution to journal › Article › Research › peer-review
  20 Citations (Scopus)

• BigFiRSt: A Software Program Using Big Data Technique for Mining Simple Sequence Repeats From Large-Scale Sequencing Data

  Chen, J., Li, F., Wang, M., Li, J., Marquez-Lago, T. T., Leier, A., Revote, J., Li, S., Liu, Q. & Song, J., 18 Jan 2022, In: Frontiers in Big Data. 4, 16 p., 727216.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access
  2 Citations (Scopus)

• Clarion is a multi-label problem transformation method for identifying mRNA subcellular localizations

  Bi, Y., Li, F., Guo, X., Wang, Z., Pan, T., Guo, Y., Webb, G. I., Yao, J., Jia, C. & Song, J., 19 Nov 2022, In: Briefings in Bioinformatics. 23, 6, p. 1-12 12 p.

  Research output: Contribution to journal › Article › Research › peer-review
  19 Citations (Scopus)

• csORF-finder: an effective ensemble learning framework for accurate identification of multi-species coding short open reading frames

  Zhang, M., Zhao, J., Li, C., Ge, F., Wu, J., Jiang, B., Song, J. & Song, X., Nov 2022, In: Briefings in Bioinformatics. 23, 6, 18 p., bbac392.

  Research output: Contribution to journal › Article › Research › peer-review
  15 Citations (Scopus)

• Enhancing Characteristic Gene Selection and Tumor Classification by the Robust Laplacian Supervised Discriminative Sparse PCA

  Zhang, L. X., Yan, H., Liu, Y., Xu, J., Song, J. & Yu, D-J., 11 Apr 2022, In: Journal of Chemical Information and Modeling. 62, 7, p. 1794-1807 14 p.

  Research output: Contribution to journal › Article › Research › peer-review
  3 Citations (Scopus)

• iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets

  Chen, Z., Liu, X., Zhao, P., Li, C., Wang, Y., Li, F., Akutsu, T., Bain, C., Gasser, R. B., Li, J., Yang, Z., Gao, X., Kurgan, L. & Song, J., 5 Jul 2022, In: Nucleic Acids Research. 50, W1, p. W434-W447 14 p.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access
  43 Citations (Scopus)

• Improving the prediction of DNA-protein binding by integrating multi-scale dense convolutional network with fault-tolerant coding

  Yin, Y. H., Shen, L. C., Jiang, Y., Gao, S., Song, J. & Yu, D-J., 1 Nov 2022, In: Analytical Biochemistry. 656, 11 p., 114878.

  Research output: Contribution to journal › Article › Research › peer-review
  7 Citations (Scopus)

• Prediction of disease-associated nsSNPs by integrating multi-scale ResNet models with deep feature fusion

  Ge, F., Zhang, Y., Xu, J., Muhammad, A., Song, J. & Yu, D. J., Jan 2022, In: Briefings in Bioinformatics. 23, 1, p. 1-21 21 p., bbab530.

  Research output: Contribution to journal › Article › Research › peer-review
  21 Citations (Scopus)

• RBP-TSTL is a two-stage transfer learning framework for genome-scale prediction of RNA-binding proteins

  Peng, X., Wang, X., Guo, Y., Ge, Z., Li, F., Gao, X. & Song, J., Jul 2022, In: Briefings in Bioinformatics. 23, 4, p. 1-15 15 p.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access
  17 Citations (Scopus)
• 2021

  A Deep Learning-Based Method for Identification of Bacteriophage-Host Interaction

  Li, M., Wang, Y., Li, F., Zhao, Y., Liu, M., Zhang, S., Bin, Y., Smith, A. I., Webb, G. I., Li, J., Song, J. & Xia, J., Sept 2021, In: IEEE/ACM Transactions on Computational Biology and Bioinformatics. 18, 5, p. 1801-1810 10 p.

  Research output: Contribution to journal › Article › Research › peer-review
  44 Citations (Scopus)

• BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria

  Wang, J., Li, J., Hou, Y., Dai, W., Xie, R., Marquez-Lago, T. T., Leier, A., Zhou, T., Torres, V., Hay, I., Stubenrauch, C., Zhang, Y., Song, J. & Lithgow, T., 8 Jan 2021, In: Nucleic Acids Research. 49, D1, p. D651-D659 9 p.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access
  36 Citations (Scopus)

• Comprehensive assessment of machine learning-based methods for predicting antimicrobial peptides

  Xu, J., Li, F., Leier, A., Xiang, D., Shen, H-H., Marquez Lago, T. T., Li, J., Yu, D-J. & Song, J., Sept 2021, In: Briefings in Bioinformatics. 22, 5, p. 1-22 22 p.

  Research output: Contribution to journal › Article › Research › peer-review
  88 Citations (Scopus)

• Computational identification of eukaryotic promoters based on cascaded deep capsule neural networks

  Zhu, Y., Li, F., Xiang, D., Akutsu, T., Song, J. & Jia, C., Jul 2021, In: Briefings in Bioinformatics. 22, 4, 11 p., bbaa299.

  Research output: Contribution to journal › Article › Research › peer-review
  49 Citations (Scopus)

• DeepBL: a deep learning-based approach for in silico discovery of beta-lactamases

  Wang, Y., Li, F., Bharathwaj, M. A., Rosas, N. C., Leier, A., Akutsu, T., Webb, G. I., Marquez-Lago, T. T., Li, J., Lithgow, T. & Song, J., Jul 2021, In: Briefings in Bioinformatics. 22, 4, 12 p., bbaa301.

  Research output: Contribution to journal › Article › Research › peer-review
  10 Citations (Scopus)

• DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy

  Xie, R., Li, J., Wang, J., Dai, W., Leier, A., Marquez-Lago, T. T., Akutsu, T., Lithgow, T., Song, J. & Zhang, Y., 20 May 2021, In: Briefings in Bioinformatics. 22, 3, 15 p., bbaa125.

  Research output: Contribution to journal › Article › Research › peer-review
  56 Citations (Scopus)

• Formator: Predicting Lysine Formylation Sites Based on the Most Distant Undersampling and Safe-Level Synthetic Minority Oversampling

  Jia, C., Zhang, M., Fan, C., Li, F. & Song, J., Sept 2021, In: IEEE/ACM Transactions on Computational Biology and Bioinformatics. 18, 5, p. 1937-1945 9 p.

  Research output: Contribution to journal › Article › Research › peer-review
  18 Citations (Scopus)

• ILearnPlus: A comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization

  Chen, Z., Zhao, P., Li, C., Li, F., Xiang, D., Chen, Y., Akutsu, T., Daly, R. J., Webb, G. I., Zhao, Q., Kurgan, L. & Song, J., 4 Jun 2021, In: Nucleic Acids Research. 49, 10, 19 p., e60.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access
  175 Citations (Scopus)

• Improving protein fold recognition using triplet network and ensemble deep learning

  Liu, Y., Han, K., Zhu, Y. H., Zhang, Y., Shen, L. C., Song, J. & Yu, D. J., Nov 2021, In: Briefings in Bioinformatics. 22, 6, p. 1-16 16 p.

  Research output: Contribution to journal › Article › Research › peer-review
  11 Citations (Scopus)

• Leveraging the attention mechanism to improve the identification of DNA N6-methyladenine sites

  Zhang, Y., Liu, Y., Xu, J., Wang, X., Peng, X., Song, J. & Yu, D. J., Nov 2021, In: Briefings in Bioinformatics. 22, 6, p. 1-13 13 p.

  Research output: Contribution to journal › Article › Research › peer-review
  29 Citations (Scopus)

• Porpoise: a new approach for accurate prediction of RNA pseudouridine sites

  Li, F., Guo, X., Jin, P., Chen, J., Xiang, D., Song, J. & Coin, L. J. M., 5 Nov 2021, In: Briefings in Bioinformatics. 22, 6, p. 1-12 12 p.

  Research output: Contribution to journal › Article › Research › peer-review
  46 Citations (Scopus)
• 2020

  An Interpretable Prediction Model for Identifying N⁷-Methylguanosine Sites Based on XGBoost and SHAP

  Bi, Y., Xiang, D., Ge, Z., Li, F., Jia, C. & Song, J., 4 Dec 2020, In: Molecular Therapy - Nucleic Acids. 22, p. 362-372 11 p.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access

  File
  123 Citations (Scopus)

• Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences

  Chen, Z., Zhao, P., Li, F., Wang, Y., Smith, A. I., Webb, G. I., Akutsu, T., Baggag, A., Bensmail, H. & Song, J., 25 Sept 2020, In: Briefings in Bioinformatics. 21, 5, p. 1676-1696 21 p., bbz112.

  Research output: Contribution to journal › Article › Research › peer-review
  106 Citations (Scopus)

• iLearn: an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data

  Chen, Z., Zhao, P., Li, F., Marquez-Lago, T. T., Leier, A., Revote, J., Zhu, Y., Powell, D. R., Akutsu, T., Webb, G. I., Chou, K-C., Smith, A. I., Daly, R. J., Li, J. & Song, J., 21 May 2020, In: Briefings in Bioinformatics. 21, 3, p. 1047-1057 11 p.

  Research output: Contribution to journal › Article › Research › peer-review
  325 Citations (Scopus)

• Inspector: a lysine succinylation predictor based on edited nearest-neighbor undersampling and adaptive synthetic oversampling

  Zhu, Y., Jia, C., Li, F. & Song, J., 15 Mar 2020, In: Analytical Biochemistry. 593, 10 p., 113592.

  Research output: Contribution to journal › Article › Research › peer-review
  49 Citations (Scopus)

• PASSION: an ensemble neural network approach for identifying the binding sites of RBPs on circRNAs

  Jia, C., Bi, Y., Chen, J., Leier, A., Li, F. & Song, J., 1 Aug 2020, In: Bioinformatics. 36, 15, p. 4276-4282 7 p.

  Research output: Contribution to journal › Article › Research › peer-review
  73 Citations (Scopus)

• PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins

  Zhang, Y., Yu, S., Xie, R., Li, J., Leier, A., Marquez-Lago, T. T., Akutsu, T., Smith, A. I., Ge, Z., Wang, J., Lithgow, T. & Song, J., 1 Feb 2020, In: Bioinformatics. 36, 3, p. 704-712 9 p.

  Research output: Contribution to journal › Article › Research › peer-review
  43 Citations (Scopus)

• PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact

  Li, F., Fan, C., Marquez-Lago, T. T., Leier, A., Revote, J., Jia, C., Zhu, Y., Smith, A. I., Webb, G. I., Liu, Q., Wei, L., Li, J. & Song, J., 21 May 2020, In: Briefings in Bioinformatics. 21, 3, p. 1069-1079 11 p.

  Research output: Contribution to journal › Article › Research › peer-review
  34 Citations (Scopus)

• Procleave: Predicting protease-specific substrate cleavage sites by combining sequence and structural information

  Li, F., Leier, A., Liu, Q., Wang, Y., Xiang, D., Akutsu, T., Webb, G. I., Smith, A. I., Marquez-Lago, T., Li, J. & Song, J., Feb 2020, In: Genomics Proteomics and Bioinformatics. 18, 1, p. 52-64 13 p.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access

  File
  73 Citations (Scopus)

• PROSPECT: A web server for predicting protein histidine phosphorylation sites

  Chen, Z., Zhao, P., Li, F., Leier, A., Marquez-Lago, T. T., Webb, G. I., Baggag, A., Bensmail, H. & Song, J., 2020, In: Journal of Bioinformatics and Computational Biology. 18, 3, 17 p., 2050018.

  Research output: Contribution to journal › Article › Research › peer-review
  24 Citations (Scopus)
• 2019

  Bastion3: A two-layer ensemble predictor of type III secreted effectors

  Wang, J., Li, J., Yang, B., Xie, R., Marquez-Lago, T. T., Leier, A., Hayashida, M., Akutsu, T., Zhang, Y., Chou, K-C., Selkrig, J., Zhou, T., Song, J. & Lithgow, T., 1 Jun 2019, In: Bioinformatics. 35, 12, p. 2017-2028 12 p., bty914.

  Research output: Contribution to journal › Article › Research › peer-review
  69 Citations (Scopus)

• Deep learning with evolutionary and genomic profiles for identifying cancer subtypes

  Lin, C. Y., Ruan, P., Li, R., Yang, J. M., See, S., Song, J. & Akutsu, T., 27 Jun 2019, In: Journal of Bioinformatics and Computational Biology. 17, 3, 15 p., 1940005.

  Research output: Contribution to journal › Article › Research › peer-review
  14 Citations (Scopus)

• MULTiPly: a novel multi-layer predictor for discovering general and specific types of promoters

  Zhang, M., Li, F., Marquez-Lago, T. T., Leier, A., Fan, C., Kwoh, C. K., Chou, K-C., Song, J. & Jia, C., 1 Sept 2019, In: Bioinformatics. 35, 17, p. 2957-2965 9 p., btz016.

  Research output: Contribution to journal › Article › Research › peer-review
  104 Citations (Scopus)

• Positive-unlabelled learning of glycosylation sites in the human proteome

  Li, F., Zhang, Y., Purcell, A. W., Webb, G. I., Chou, K-C., Lithgow, T., Li, C. & Song, J., 6 Mar 2019, In: BMC Bioinformatics. 20, 1, 17 p., 112.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access

  File
  68 Citations (Scopus)
• 2018

  Genome-scale metabolic modeling of responses to polymyxins in Pseudomonas aeruginosa

  Zhu, Y., Czauderna, T., Zhao, J., Klapperstueck, M., Mahamad Maifiah, M. H. B., Han, M-L., Lu, J., Sommer, B., Velkov, T., Lithgow, T., Song, J., Schreiber, F. & Li, J., 1 Apr 2018, In: GigaScience. 7, 4, 18 p., giy021.

  Research output: Contribution to journal › Article › Research › peer-review

  Open Access

  File
  41 Citations (Scopus)