By Dr Pengyao Ping

Journal articles

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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