Dr Pengyao Ping

Research Staff Level B
Medicine & Health
Centre for Big Data Research in Health

Pengyao is a Research Fellow at the Centre for Big Data Research in Health, UNSW Sydney. He holds a PhD in Analytics from the University of Technology Sydney (UTS) and has multidisciplinary research experience in computational biology, statistical genetics, bioinformatics, biomedical data science, machine learning, and artificial intelligence (AI) for healthcare.

His research focuses on developing and applying computational, statistical, machine-learning, and deep-learning methods to integrate complex biomedical and digital health data and improve understanding of disease risk, clinical outcomes, and treatment effects. His experience spans genomics, proteomics, multi-omics, polygenic risk analysis, and predictive modelling using large-scale health data. He has analysed longitudinal electronic health records (EHRs), genomic data, and proteomic data from resources including the All of Us Research Program and UK Biobank to investigate associations among genetic factors, circulating proteins, clinical characteristics, medication use, and mental health.

His current research focuses on cardiovascular risk prediction and treatment evaluation across populations with and without type 2 diabetes and mental health conditions. This work uses routinely collected EHRs and longitudinal health information to develop and assess approaches for identifying risk and understanding how treatment effects may vary between individuals. His broader interests include AI for clinical and biomedical research, natural language processing (NLP) of clinical notes, model interpretability, and translating data-driven methods into useful clinical decision-support tools. He also develops scalable computational methods for bioinformatics, including graph-based approaches to biological sequence analysis.

Through his interdisciplinary research integrating complex biological and clinical data, Dr Ping aims to advance precision medicine and translate data-driven discoveries into meaningful outcomes with real-world impact in disease prediction, prevention, and care.

Location
Level 5, HTH Building, 55 Botany Street, Randwick NSW 2031
  • Journal articles | 2025
    Lan T; Su S; Ping P; Li J, 2025, 'Novel Design for Multi-Epitope Vaccines of COVID-19 and Critical In silico Assessment Steps', Current Bioinformatics, 20, pp. 878 - 889, http://dx.doi.org/10.2174/0115748936303461240827061629
    Journal articles | 2025
    Ping P; Lan T; Su S; Liu W; Li J, 2025, 'How error correction affects polymerase chain reaction deduplication: A survey based on unique molecular identifier datasets of short reads', Quantitative Biology, 13, http://dx.doi.org/10.1002/qub2.99
    Journal articles | 2025
    Ping P; Li J, 2025, 'Construction of edit-distance graphs for large sets of short reads through minimizer-bucketing', Bioinformatics Advances, 5, http://dx.doi.org/10.1093/bioadv/vbaf081
    Journal articles | 2025
    Ping P; Su S; Cai X; Lan T; Zhang X; Peng H; Pan Y; Liu W; Li J, 2025, 'Noise2read: Accurately Rectify Millions of Erroneous Short Reads Through Graph Learning on Edit Distances', Genomics Proteomics & Bioinformatics, pp. qzaf120, http://dx.doi.org/10.1093/gpbjnl/qzaf120
    Journal articles | 2025
    Su S; Ni Z; Lan T; Ping P; Tang J; Yu Z; Hutvagner G; Li J, 2025, 'Predicting viral host codon fitness and path shifting through tree-based learning on codon usage biases and genomic characteristics', Scientific Reports, 15, http://dx.doi.org/10.1038/s41598-025-91469-z
    Journal articles | 2024
    Lan T; Su S; Ping P; Hutvagner G; Liu T; Pan Y; Li J, 2024, 'Generating mutants of monotone affinity towards stronger protein complexes through adversarial learning', Nature Machine Intelligence, 6, pp. 315 - 325, http://dx.doi.org/10.1038/s42256-024-00803-z
    Journal articles | 2023
    Cai X; Lan T; Ping P; Oliver B; Li J, 2023, 'Intra-Host Co-Existing Strains of SARS-CoV-2 Reference Genome Uncovered by Exhaustive Computational Search', Viruses, 15, http://dx.doi.org/10.3390/v15051065
    Journal articles | 2022
    Wang L; Tan Y; Yang X; Kuang L; Ping P, 2022, 'Review on predicting pairwise relationships between human microbes, drugs and diseases: from biological data to computational models', Briefings in Bioinformatics, 23, http://dx.doi.org/10.1093/bib/bbac080
    Journal articles | 2021
    Zhang X; Ping P; Hutvagner G; Blumenstein M; Li J, 2021, 'Aberration-corrected ultrafine analysis of miRNA reads at single-base resolution: a k-mer lattice approach', Nucleic Acids Research, 49, pp. E106, http://dx.doi.org/10.1093/nar/gkab610
    Journal articles | 2019
    Ping P; Wang L; Kuang L; Ye S; Iqbal MFB; Pei T, 2019, 'A novel method for LncRNA-disease association prediction based on an lncRNA-disease association network', IEEE ACM Transactions on Computational Biology and Bioinformatics, 16, pp. 688 - 693, http://dx.doi.org/10.1109/TCBB.2018.2827373
    Journal articles | 2019
    Xuan Z; Feng X; Yu J; Ping P; Zhao H; Zhu X; Wang L, 2019, 'A Novel Method for Predicting Disease-Associated LncRNA-MiRNA Pairs Based on the Higher-Order Orthogonal Iteration', Computational and Mathematical Methods in Medicine, 2019, http://dx.doi.org/10.1155/2019/7614850
    Journal articles | 2018
    Wang L; Ping P; Kuang L; Ye S; Lqbal FMB; Pei T, 2018, 'A novel approach based on bipartite network to predict human microbe-disease associations', Current Bioinformatics, 13, pp. 141 - 148, http://dx.doi.org/10.2174/1574893612666170911143601
    Journal articles | 2018
    Yu J; Ping P; Wang L; Kuang L; Li X; Wu Z, 2018, 'A novel probability model for lncRNA–disease association prediction based on the naïve bayesian classifier', Genes, 9, http://dx.doi.org/10.3390/genes9070345
    Journal articles | 2018
    Zhao H; Kuang L; Wang L; Ping P; Xuan Z; Pei T; Wu Z, 2018, 'Prediction of microRNA-disease associations based on distance correlation set', BMC Bioinformatics, 19, http://dx.doi.org/10.1186/s12859-018-2146-x
    Journal articles | 2018
    Zhou S; Xuan Z; Wang L; Ping P; Pei T, 2018, 'A Novel Model for Predicting Associations between Diseases and LncRNA-miRNA Pairs Based on a Newly Constructed Bipartite Network', Computational and Mathematical Methods in Medicine, 2018, http://dx.doi.org/10.1155/2018/6789089
    Journal articles | 2017
    Ping P; Zhu X; Wang L, 2017, 'SIMILARITIES/DISSIMILARITIES ANALYSIS of PROTEIN SEQUENCES BASED on PCA-FFT', Journal of Biological Systems, 25, pp. 29 - 45, http://dx.doi.org/10.1142/S0218339017500024
    Journal articles | 2017
    Zhu X; Ping P; Qiu Y; Wang L, 2017, 'Similarities/dissimilarities analysis of protein sequences based on the appearance model', Journal of Computational and Theoretical Nanoscience, 14, pp. 1449 - 1460, http://dx.doi.org/10.1166/jctn.2017.5684
  • Conference Papers | 2017
    Qiu Y; Wang L; Ping P; Pei T, 2017, 'Method for predicting hot spot residues at protein-protein interface based on the extreme learning machine', in 2017 3rd IEEE International Conference on Computer and Communications Iccc 2017, pp. 2689 - 2698, http://dx.doi.org/10.1109/CompComm.2017.8323022
    Preprints |
    Ping P; Lan T; Su S; Liu W; Li J, How Error Correction Affects PCR Deduplication: A Survey Based on UMI Datasets of Short Reads, http://dx.doi.org/10.1101/2024.05.30.596723
    Preprints |
    Ping P; Su S; Cai X; Lan T; Zhang X; Peng H; Pan Y; Liu W; Li J, Turn ‘noise’ to signal: accurately rectify millions of erroneous short reads through graph learning on edit distances, http://dx.doi.org/10.1101/2024.04.05.588226
    Preprints |
    Su S; Ni Z; Lan T; Ping P; Tang J; Yu Z; Hutvagner G; Li J, Predicting viral host codon fitness and path shifting through tree-based learning on codon usage biases and genomic characteristics, http://dx.doi.org/10.21203/rs.3.rs-4408141/v1

  • Google Cloud Research Grant | March 2026–March 2027 | USD $5,000
    Integrative Genomic Analysis of Psychotropic Medication Treatment and Mental Health Phenotypes in the All of Us Cohort (Award No. GCP19980904).
  • UK Biobank–Amazon Web Services Platform Credits | October 2025–October 2026 | GBP £1,000.