Stochastic modelling of telomere length regulation in ageing research

Research output

Research output per year 2013 2014 2019 2020 2021 2022 2024

• 75 Article
• 7 Conference Paper
• 3 Review Article

Research output per year

Research output per year

Search results

• 2024

  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
  10 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
  43 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
  8 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
  12 Citations (Scopus)

• PScL-2LSAESM: bioimage-based prediction of protein subcellular localization by integrating heterogeneous features with the two-level SAE-SM and mean ensemble method

  Ullah, M., Hadi, F., Song, J. & Yu, D.-J., 1 Jan 2023, In: Bioinformatics. 39, 1, 8 p., btac727.

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

  Open Access
  2 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
  8 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
  9 Citations (Scopus)

• VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants

  Ge, F., Li, C., Iqbal, S., Muhammad, A., Li, F., Thafar, M. A., Yan, Z., Worachartcheewan, A., Xu, X., Song, J. & Yu, D.-J., 19 Jan 2023, In: Briefings in Bioinformatics. 24, 1, p. 1-16 16 p.

  Research output: Contribution to journal › Article › Research › peer-review
  15 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
  21 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)

• 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
  45 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)

• Positive-unlabeled learning in bioinformatics and computational biology: A brief review

  Li, F., Dong, S., Leier, A., Han, M., Guo, X., Xu, J., Wang, X., Pan, S., Jia, C., Zhang, Y., Webb, G., Coin, L. J. M., Li, C. & Song, J., Jan 2022, In: Briefings in Bioinformatics. 23, 1, 13 p., bbab461.

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

• PreAcrs: a machine learning framework for identifying anti-CRISPR proteins

  Zhu, L., Wang, X., Li, F. & Song, J., Dec 2022, In: BMC Bioinformatics. 23, 1, 21 p., 444.

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

  Open Access
  9 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
  18 Citations (Scopus)
• 2021

  Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features

  Zhu, Y.-H., Hu, J., Ge, F., Li, F., Song, J., Zhang, Y. & Yu, D.-J., 20 May 2021, In: Briefings in Bioinformatics. 22, 3, 14 p., bbaa076.

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

• Computational prediction and interpretation of both general and specific types of promoters in Escherichia coli by exploiting a stacked ensemble-learning framework

  Li, F., Chen, J., Ge, Z., Wen, Y., Yue, Y., Hayashida, M., Baggag, A., Bensmail, H. & Song, J., 1 Mar 2021, In: Briefings in Bioinformatics. 22, 2, p. 2126-2140 15 p.

  Research output: Contribution to journal › Article › Research › peer-review
  59 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
  11 Citations (Scopus)

• DeepTorrent: a deep learning-based approach for predicting DNA N4-methylcytosine sites

  Liu, Q., Chen, J., Wang, Y., Li, S., Jia, C., Song, J. & Li, F., 1 Jul 2021, In: Briefings in Bioinformatics. 22, 3, 14 p., bbaa124.

  Research output: Contribution to journal › Article › Research › peer-review
  100 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)

• 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.-Z., 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
  182 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
  12 Citations (Scopus)

• Large-scale comparative review and assessment of computational methods for anti-cancer peptide identification

  Liang, X., Li, F., Chen, J., Li, J., Wu, H., Li, S., Song, J. & Liu, Q., Jul 2021, In: Briefings in Bioinformatics. 22, 4, p. 1-17 17 p.

  Research output: Contribution to journal › Article › Research › peer-review
  59 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)

• MutTMPredictor: Robust and accurate cascade XGBoost classifier for prediction of mutations in transmembrane proteins

  Ge, F., Zhu, Y. H., Xu, J., Muhammad, A., Song, J. & Yu, D. J., Jan 2021, In: Computational and Structural Biotechnology Journal. 19, p. 6400-6416 17 p.

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

  Open Access
  25 Citations (Scopus)

• nhKcr: a new bioinformatics tool for predicting crotonylation sites on human nonhistone proteins based on deep learning

  Chen, Y. Z., Wang, Z. Z., Wang, Y., Ying, G., Chen, Z. & Song, J., Nov 2021, In: Briefings in Bioinformatics. 22, 6, p. 1-13 13 p.

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

• PScL-HDeep: image-based prediction of protein subcellular location in human tissue using ensemble learning of handcrafted and deep learned features with two-layer feature selection

  Ullah, M., Han, K., Hadi, F., Xu, J., Song, J. & Yu, D. J., 5 Nov 2021, In: Briefings in Bioinformatics. 22, 6, 17 p.

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

• Systematic evaluation of machine learning methods for identifying human-pathogen protein-protein interactions

  Chen, H., Li, F., Wang, L., Jin, Y., Chi, C.-H., Kurgan, L., Song, J. & Shen, J., 27 May 2021, In: Briefings in Bioinformatics. 22, 3, 21 p., bbaa068.

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

• Using Particle Swarm Optimization Algorithm to Calibrate the Term Structure Model

  Zhou, Y., Liu, S., Tian, T., He, Q. & Ge, X., 2021, In: Mathematical Problems in Engineering. 2021, 11 p., 8893940.

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

  Open Access
  3 Citations (Scopus)

• Why can deep convolutional neural networks improve protein fold recognition? A visual explanation by interpretation

  Liu, Y., Zhu, Y. H., Song, X., Song, J. & Yu, D. J., Sept 2021, In: Briefings in Bioinformatics. 22, 5, p. 1-14 14 p.

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

  A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction

  Mei, S., Li, F., Leier, A., Marquez-Lago, T. T., Giam, K., Croft, N. P., Akutsu, T., Smith, A. I., Li, J., Rossjohn, J., Purcell, A. W. & Song, J., Jul 2020, In: Briefings in Bioinformatics. 21, 4, p. 1119-1135 17 p., bbz051.

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

• 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
  125 Citations (Scopus)

• Comparative analysis and prediction of quorum-sensing peptides using feature representation learning and machine learning algorithms

  Wei, L., Hu, J., Li, F., Song, J., Su, R. & Zou, Q., Jan 2020, In: Briefings in Bioinformatics. 21, 1, p. 106-119 14 p.

  Research output: Contribution to journal › Article › Research › peer-review
  109 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)

• DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites

  Li, F., Chen, J., Leier, A., Marquez-Lago, T., Liu, Q., Wang, Y., Revote, J., Smith, A. I., Akutsu, T., Webb, G. I., Kurgan, L. & Song, J., 15 Feb 2020, In: Bioinformatics. 36, 4, p. 1057-1065 9 p.

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

• Inference of model parameters using particle filter algorithm and Copula distributions

  Deng, Z., Zhang, X. & Tian, T., Jul 2020, In: IEEE/ACM Transactions on Computational Biology and Bioinformatics. 17, 4, p. 1231-1240 10 p.

  Research output: Contribution to journal › Article › Research › peer-review
  9 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
  50 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
  74 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
  44 Citations (Scopus)

• Pippin: A random forest-based method for identifying presynaptic and postsynaptic neurotoxins

  Li, P., Zhang, H., Zhao, X., Jia, C., Li, F. & Song, J., 5 May 2020, In: Journal of Bioinformatics and Computational Biology. 18, 2, 21 p., 2050008.

  Research output: Contribution to journal › Article › Research › peer-review
  1 Citation (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
  75 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)

• Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework

  Zhang, Y., Xie, R., Wang, J., Leier, A., Marquez-Lago, T. T., Akutsu, T., Webb, G. I., Chou, K.-C. & Song, J., Nov 2019, In: Briefings in Bioinformatics. 20, 6, p. 2185-2199 15 p.

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

• Large-scale comparative assessment of computational predictors for lysine post-translational modification sites

  Chen, Z., Liu, X., Li, F., Li, C., Marquez-Lago, T., Leier, A., Akutsu, T., Webb, G. I., Xu, D., Smith, A. I., Li, L., Chou, K. C. & Song, J., Nov 2019, In: Briefings in Bioinformatics. 20, 6, p. 2267-2290 24 p., bby089.

  Research output: Contribution to journal › Article › Research › peer-review
  93 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
  105 Citations (Scopus)