Jiangning Song

Research output

Research output per year 2004 2016 2018 2020 2021 2022 2023 2024

• 239 Article
• 17 Conference Paper
• 10 Review Article
• 7 Chapter (Book)
• 10 More
  • 4 Editorial
  • 3 Comment / Debate
  • 2 Letter
  • 1 Other contribution

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
• 2023

  An informatic workflow for the enhanced annotation of excretory/secretory proteins of Haemonchus contortus

  Zheng, Y., Young, N. D., Song, J., Chang, B. C. H. & Gasser, R. B., Jan 2023, In: Computational and Structural Biotechnology Journal. 21, p. 2696-2704 9 p.

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

  Open Access

  File
  1 Citation (Scopus)

• Association between air pollution and telomere length: A study of 471,808 UK Biobank participants

  Wu, Y., Gasevic, D., Wen, B., Yu, P., Xu, R., Zhou, G., Zhang, Y., Song, J., Liu, H., Li, S. & Guo, Y., 21 Sept 2023, In: The Innovation Medicine. 1, 2, 10 p., 100017.

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

  Open Access

  File

• Association between long-term exposure to wildfire-related PM_2.5 and mortality: A longitudinal analysis of the UK Biobank

  Gao, Y., Huang, W., Xu, R., Gasevic, D., Liu, Y., Yu, W., Yu, P., Yue, X., Zhou, G., Zhang, Y., Liu, H., Song, J., Guo, Y. & Li, S., 5 Sept 2023, In: Journal of Hazardous Materials. 457, 7 p., 131779.

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

  Open Access

• ATTIC is an integrated approach for predicting A-to-I RNA editing sites in three species

  Chen, R., Li, F., Guo, X., Bi, Y., Li, C., Pan, S., Coin, L. J. M. & Song, J., 1 May 2023, In: Briefings in Bioinformatics. 24, 3, 15 p., bbad170.

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

• Causal effects of air pollution on mental health among Adults——An exploration of susceptible populations and the role of physical activity based on a longitudinal nationwide cohort in China

  Ju, K., Lu, L., Wang, W., Chen, T., Yang, C., Zhang, E., Xu, Z., Li, S., Song, J., Pan, J. & Guo, Y., 15 Jan 2023, In: Environmental Research. 217, 12 p., 114761.

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

• COPPER: an ensemble deep-learning approach for identifying exclusive virus-derived small interfering RNAs in plants

  Bu, Y., Jia, C., Guo, X., Li, F. & Song, J., May 2023, In: Briefings in Functional Genomics. 22, 3, p. 274-280 7 p.

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

• DeepAIR: A deep learning framework for effective integration of sequence and 3D structure to enable adaptive immune receptor analysis

  Zhao, Y., He, B., Xu, F., Li, C., Xu, Z., Su, X., He, H., Huang, Y., Rossjohn, J., Song, J. & Yao, J., Aug 2023, In: Science Advances. 9, 32, 18 p., eabo512.

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

  Open Access

• Deep domain adversarial neural network for the deconvolution of cell type mixtures in tissue proteome profiling

  Wang, F., Yang, F., Huang, L., Li, W., Song, J., Gasser, R. B., Aebersold, R., Wang, G. & Yao, J., 19 Oct 2023, (Accepted/In press) In: Nature Machine Intelligence. 14 p.

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

• DeepSecE: A Deep-Learning-Based Framework for Multiclass Prediction of Secreted Proteins in Gram-Negative Bacteria

  Zhang, Y., Guan, J., Li, C., Wang, Z., Deng, Z., Gasser, R. B., Song, J. & Ou, H-Y., 25 Oct 2023, In: Research. 6, 15 p., 0258.

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

  Open Access

• Designing Effective Predictors of Protein Post-Translational Modifications Using iLearnPlus

  Chen, Z., Li, F., Wang, X., Wang, Y., Kurgan, L. & Song, J., 2023, Machine Learning in Bioinformatics of Protein Sequences: Algorithms, Databases and Resources for Modern Protein Bioinformatics. Kurgan, L. (ed.). 1st ed. Singapore: World Scientific Publishing, p. 309-328 20 p.

  Research output: Chapter in Book/Report/Conference proceeding › Chapter (Book) › Research › peer-review

• Digerati – A multipath parallel hybrid deep learning framework for the identification of mycobacterial PE/PPE proteins

  Li, F., Guo, X., Bi, Y., Jia, R., Pitt, M. E., Pan, S., Li, S., Gasser, R. B., Coin, L. JM. & Song, J., Sept 2023, In: Computers in Biology and Medicine. 163, 11 p., 107155.

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

• Genetic algorithm-based feature selection with manifold learning for cancer classification using microarray data

  Wang, Z., Zhou, Y., Takagi, T., Song, J., Tian, Y. S. & Shibuya, T., 8 Apr 2023, In: BMC Bioinformatics. 24, 1, 22 p., 139.

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

  Open Access

• Genome-Wide Analysis of Haemonchus contortus Proteases and Protease Inhibitors Using Advanced Informatics Provides Insights into Parasite Biology and Host–Parasite Interactions

  Zheng, Y., Young, N. D., Song, J. & Gasser, R. B., Aug 2023, In: International Journal of Molecular Sciences. 24, 15, 18 p., 12320.

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

  Open Access

• Global estimates of daily ambient fine particulate matter concentrations and unequal spatiotemporal distribution of population exposure: a machine learning modelling study

  Yu, W., Ye, T., Zhang, Y., Xu, R., Lei, Y., Chen, Z., Yang, Z., Zhang, Y., Song, J., Yue, X., Li, S. & Guo, Y., Mar 2023, In: The Lancet Planetary Health. 7, 3, p. e209-e218 10 p.

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

  Open Access
  13 Citations (Scopus)

• 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
  3 Citations (Scopus)

• ICEberg 3.0: functional categorization and analysis of the integrative and conjugative elements in bacteria

  Wang, M., Liu, G., Liu, M., Tai, C., Deng, Z., Song, J. & Ou, H-Y., 23 Oct 2023, (Accepted/In press) In: Nucleic Acids Research. 6 p.

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

  Open Access

• Improving Cancer Survival Prediction via Graph Convolutional Neural Network Learning on Protein-Protein Interaction Networks

  Cai, H., Liao, Y., Zhu, L., Wang, Z. & Song, J., 2023, (Accepted/In press) In: IEEE Journal of Biomedical and Health Informatics. 10 p., 2023.3332640.

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

  Open Access

• Interpretable artificial intelligence model for accurate identification of medical conditions using immune repertoire

  Zhao, Y., He, B., Xu, Z., Zhang, Y., Zhao, X., Huang, Z. A., Yang, F., Wang, L., Duan, L., Song, J. & Yao, J., 19 Jan 2023, In: Briefings in Bioinformatics. 24, 1, 14 p., bbac555.

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

• 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., Nov 2023, (Accepted/In press) In: Bioinformatics. 8 p.

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

  Open Access

• MULGA, a unified multi-view graph autoencoder-based approach for identifying drug–protein interaction and drug repositioning

  Ma, J., Li, C., Zhang, Y., Wang, Z., Li, S., Guo, Y., Zhang, L., Liu, H., Gao, X. & Song, J., Sept 2023, In: Bioinformatics. 39, 9, 8 p., btad524.

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

  Open Access

• Multi-modality data-driven analysis of diagnosis and treatment of psoriatic arthritis

  Xu, J., Ou, J., Li, C., Zhu, Z., Li, J., Zhang, H., Chen, J., Yi, B., Zhu, W., Zhang, W., Zhang, G., Gao, Q., Kuang, Y., Song, J., Chen, X. & Liu, H., Dec 2023, In: npj Digital Medicine. 6, 1, 11 p., 13.

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

  Open Access

• PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships

  Pan, T., Li, C., Bi, Y., Wang, Z., Gasser, R. B., Purcell, A. W., Akutsu, T., Webb, G. I., Imoto, S. & Song, J., Mar 2023, In: Bioinformatics. 39, 3, 8 p., btad094.

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

  Open Access
  1 Citation (Scopus)

• Polysaccharide-Targeting Lipid Nanoparticles to Kill Gram-Negative Bacteria

  Lai, X., Chow, S. H., Le Brun, A. P., Muir, B. W., Bergen, P. J., White, J., Yu, H. H., Wang, J., Danne, J., Jiang, J. H., Short, F. L., Han, M. L., Strugnell, R. A., Song, J., Cameron, N. R., Peleg, A. Y., Li, J. & Shen, H. H., Oct 2023, (Accepted/In press) In: Small. 13 p., 230502.

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

  Open Access

• Predicting Pseudouridine Sites with Porpoise

  Guo, X., Li, F. & Song, J., 2023, Computational Epigenomics and Epitranscriptomics. Oliveira, P. H. (ed.). New York NY USA: Springer, Vol. 2624. p. 139-151 13 p. (Methods in Molecular Biology).

  Research output: Chapter in Book/Report/Conference proceeding › Chapter (Book) › Other › peer-review

• 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

• Preterm birth and term low birth weight associated with wildfire-specific PM_2.5: A cohort study in New South Wales, Australia during 2016–2019

  Zhang, Y., Ye, T., Yu, P., Xu, R., Chen, G., Yu, W., Song, J., Guo, Y. & Li, S., Apr 2023, In: Environment International. 174, 9 p., 107879.

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

  Open Access
  2 Citations (Scopus)

• ProsperousPlus: a one-stop and comprehensive platform for accurate protease-specific substrate cleavage prediction and machine-learning model construction

  Li, F., Wang, C., Guo, X., Akutsu, T., Webb, G. I., Coin, L. J. M., Kurgan, L. & Song, J., Nov 2023, In: Briefings in Bioinformatics. 24, 6, 14 p., bbad372.

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

• 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
  1 Citation (Scopus)

• ResNetKhib: a novel cell type-specific tool for predicting lysine 2-hydroxyisobutylation sites via transfer learning

  Jia, X., Zhao, P., Li, F., Qin, Z., Ren, H., Li, J., Miao, C., Zhao, Q., Akutsu, T., Dou, G., Chen, Z. & Song, J., 19 Mar 2023, In: Briefings in Bioinformatics. 24, 2, 13 p., bbad063.

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

• Smad7 in the hippocampus contributes to memory impairment in aged mice after anesthesia and surgery

  Liu, C., Wu, J., Li, M., Gao, R., Zhang, X., Ye-Lehmann, S., Song, J., Zhu, T. & Chen, C., Dec 2023, In: Journal of Neuroinflammation. 20, 1, 18 p., 175.

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

  Open Access
  1 Citation (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

• SPDB: a comprehensive resource and knowledgebase for proteomic data at the single-cell resolution

  Wang, F., Liu, C., Li, J., Yang, F., Song, J., Zang, T., Yao, J. & Wang, G., Nov 2023, In: Nucleic Acids Research. 10 p., gkad1018.

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

  Open Access

• Surformer: An interpretable pattern-perceptive survival transformer for cancer survival prediction from histopathology whole slide images

  Wang, Z., Gao, Q., Yi, X., Zhang, X., Zhang, Y., Zhang, D., Lio`, P., Bain, C. A., Bassed, R., Li, S., Guo, Y., Imoto, S., Yao, J., Daly, R. J. & Song, J., Nov 2023, In: Computer Methods and Programs in Biomedicine. 241, 12 p., 107733.

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

  Open Access

• TADB 3.0: an updated database of bacterial toxin–antitoxin loci and associated mobile genetic elements

  Guan, J., Chen, Y., Goh, Y-X., Wang, M., Tai, C., Deng, Z., Song, J. & Ou, H-Y., 28 Oct 2023, (Accepted/In press) In: Nucleic Acids Research. 7 p., gkad962.

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

  Open Access

• Targeting tumor heterogeneity: multiplex-detection-based multiple instance learning for whole slide image classification

  Wang, Z., Bi, Y., Pan, T., Wang, X., Bain, C., Bassed, R., Imoto, S., Yao, J., Daly, R. J. & Song, J., 1 Mar 2023, In: Bioinformatics. 39, 3, 7 p., btad114.

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

  Open Access
  2 Citations (Scopus)

• The evolutionary mechanism of non-carbapenemase carbapenem-resistant phenotypes in Klebsiella spp

  Rosas, N. C., Wilksch, J., Barber, J., Li, J., Wang, Y., Sun, Z., Rocker, A., Webb, C. T., Perlaza-Jiménez, L., Stubenrauch, C. J., Dhanasekaran, V., Song, J., Taiaroa, G., Davies, M., Strugnell, R. A., Bao, Q., Zhou, T., McDonald, M. J. & Lithgow, T., 6 Jul 2023, In: eLife. 12, 27 p., e83107.

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

  Open Access

• TIMER is a Siamese neural network-based framework for identifying both general and species-specific bacterial promoters

  Zhu, Y., Li, F., Guo, X., Wang, X., Coin, L. J. M., Webb, G. I., Song, J. & Jia, C., 20 Jul 2023, In: Briefings in Bioinformatics. 24, 4, p. 1-12 12 p.

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

• 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
  1 Citation (Scopus)

• Vision transformer-based weakly supervised histopathological image analysis of primary brain tumors

  Li, Z., Cong, Y., Chen, X., Qi, J., Sun, J., Yan, T., Yang, H., Liu, J., Lu, E., Wang, L., Li, J., Hu, H., Zhang, C., Yang, Q., Yao, J., Yao, P., Jiang, Q., Liu, W., Song, J., Carin, L., & 3 othersChen, Y., Zhao, S. & Gao, X., 20 Jan 2023, In: iScience. 26, 1, 28 p., 105872.

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

  Open Access
  7 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
  1 Citation (Scopus)
• 2022

  A multi-channel deep convolutional neural network for multi-classifying thyroid diseases

  Zhang, X., Lee, V. C. S., Rong, J., Lee, J. C., Song, J. & Liu, F., Sept 2022, In: Computers in Biology and Medicine. 148, 11 p., 105961.

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

• A polytherapy based approach to combat antimicrobial resistance using cubosomes

  Lai, X., Han, M-L., Ding, Y., Chow, S. H., Le Brun, A. P., Wu, C-M., Bergen, P. J., Jiang, J., Hsu, H-Y., Muir, B. W., White, J., Song, J., Li, J. & Shen, H-H., Dec 2022, In: Nature Communications. 13, 1, 12 p., 343.

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

  Open Access
  24 Citations (Scopus)

• A Regional Multiple Instance Learning Network for Whole Slide Image Segmentation

  Cai, H., Yi, W., Li, Y., Liao, W. & Song, J., 2022, Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine. Adjeroh, D., Long, Q., Shi, X., Guo, F., Hu, X., Aluru, S., Narasimhan, G., Wang, J., Kang, M., Mondal, A. M. & Liu, J. (eds.). Piscataway NJ USA: IEEE, Institute of Electrical and Electronics Engineers, p. 922-928 7 p. (Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022).

  Research output: Chapter in Book/Report/Conference proceeding › Conference Paper › Research › peer-review

• 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
  9 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
  1 Citation (Scopus)

• Cell graph neural networks enable the precise prediction of patient survival in gastric cancer

  Wang, Y., Wang, Y. G., Hu, C., Li, M., Fan, Y., Otter, N., Sam, I., Gou, H., Hu, Y., Kwok, T., Zalcberg, J., Boussioutas, A., Daly, R. J., Montúfar, G., Liò, P., Xu, D., Webb, G. I. & Song, J., 2022, In: npj Precision Oncology. 6, 1, 12 p., 45.

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

  Open Access
  9 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
  4 Citations (Scopus)

• Coassembled nitric oxide-releasing nanoparticles with potent antimicrobial efficacy against methicillin-resistant staphylococcus aureus (MRSA) strains

  Liu, Y., Chen, X., Lai, X., Dzuvor, C. K. O., Lyu, L., Chow, S. H., He, L., Yu, L., Wang, Y., Song, J., Hsu, H-Y., Lin, T-W., Chan, P. W. H. & Shen, H-H., 24 Aug 2022, In: ACS Applied Materials & Interfaces. 14, 33, p. 37369–37379 11 p.

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

• Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction

  Zhang, M., Jia, C., Li, F., Li, C., Zhu, Y., Akutsu, T., Webb, G., Zou, Q., Coin, L. J. M. & Song, J., Mar 2022, In: Briefings in Bioinformatics. 23, 2, 25 p., bbab551.

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