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Selected Publications:
 See My Google Scholar for the full publication list (Totally >140 articles; Cited>6000; H-index=38).
Published on Nature Machine Intelligence, Nucleic Acids Res(4, IF=17), Brief in Bioinfo(5, IF=11.6), Bioinformatics(>10, IF=6.9), etc.
(First authors from collaboration groups are labelled Italic )
The related source codes and packages on Github

    Preprints

  1. Zheng S, Tao Zeng, Chengtao Li, Binghong Chen, Connor W. Coley, Yuedong Yang*, Ruibo Wu*. BioNavi-NP: Biosynthesis Navigator for Natural Products. arxiv 2105.13121.


    2. 2022

  2. [STAR2] Rao J, Zheng S, Mai S, Yuedong Yang*.Communicative Subgraph Representation Learning for Multi-Relational Inductive Drug-Gene Interaction Prediction. IJCAI 2022 (accepted).
  3. Zeng Y, Wei Z, Zhong F, Pan Z, Lu Y, Yuedong Yang*. A Parameter-free Deep Embedded Clustering Method for Single-cell RNA-seq Data. Brief Bioinfo 2022 (accepted)
  4. Wang X, Zhou X, Rao J, Zhang Z, and Yuedong Yang. Imputing DNA Methylation by Transferred Learning Based Neural Network. J Comput Sci Tech 2022; 37(2):320.
  5. Zhang H, Xiu X, Yuedong Yang*, Y Yang*, H Zhao*. Identification of putative causal relationships between type 2 diabetes and biomarkers in East Asians by Mendelian randomization. Am J Epidem 2022.
  6. [STAR1] Wang P, Zheng S, Jiang Y, Li C, Liu J, Wen C, Atanas P, Qian D*, Chen H*, Yuedong Yang*. Structure-aware multi-modal deep learning for drug-protein interactions prediction. J Chem Inf Model 2022; 62(5):1308–1317.
  7. [STAR2] Chen K, Zhao H, Yuedong Yang*. Capturing large genomic contexts for accurately predicting enhancer-promoter interactions. Brief in Bioinfo 2022; bbab577 .
  8. [STAR2] Yuan Q, Chen S, Rao J, Zheng S, Zhao H, Yuedong Yang*. AlphaFold2-aware protein-DNA binding site prediction using graph transformer. Brief in Bioinfo 2022; bbab564 .
  9. [STAR2] Zeng Y, Zhou X, Pan Z, Lu Y*, Yuedong Yang*. A Robust and Scalable Graph Neural Network for Accurate Single Cell Classification. Brief in Bioinfo 2022; bbab570.


    10. 2021

  10. Huang Z, Li L, Zhang X, Song Y, Chen J, Zhao H, Chong Y*, Wu H, Yuedong Yang*, Shen J*, Zha Y*. A coarse-refine segmentation network for COVID-19 CT images. IET Image Processing 2021; 16(2):333-343.
  11. Zheng S, Z Lei, H Ai, H Chen, D Deng*, Yuedong Yang*. Deep Scaffold Hopping with Multi-modal Transformer Neural Networks. J Cheminfo 2021; 13:87.
  12. Zhang Z, Chai H, Yi Wang, Pan Z, Yuedong Yang*. Cancer survival prognosis with Deep Bayesian Perturbation Cox Network. Comput Biol Med 2021 .
  13. [STAR1] Yuan S, Yuedong Yang*, Hu R*. The Unfolding Multiomics Landscapes of HBV (Hepatitis B Virus)-Host Interactions. J Hepatology 2021 (IF=25).
  14. [STAR2] Yuan Q, Chen J, Zhao H, Zhou Y*, Yuedong Yang*. Structure-aware protein-protein interaction site prediction using deep graph convolutional network. Bioinformatics 2021; btab643.
  15. Chai H, Xia L, Zhang L, Yang J, Zhang Z, Qian X, Yuedong Yang*, Pan W*. An adaptive transfer-learning based deep Cox neural network for hepatocellular carcinoma prognosis prediction. Front Oncology 2021.
  16. Liu W#, Chen L#, Chen Ken#, Wu J#, Peng R, Tang Y, Chen J, Yuedong Yang*, P Li*, Z Huang*. Identification of novel single nucleotide variants with potential of mediating malfunction of microRNA in congenital heart disease. Front Cardiovasc Med 2021.
  17. Chai H, Zhang Z, Wang Y, Yuedong Yang*. Predicting bladder cancer prognosis by integrating multi-omics data through a transfer learning-based Cox proportional hazards network. CCF Trans HPC 2021 .
  18. Z Sun, S Zheng, H Zhao, Niu Z, Lu Y, Pan Y, Yuedong Yang*. To improve the predictions of binding residues with DNA, RNA, carbohydrate, and peptide via multiple-task deep neural networks. IEEE TCBB 2021; TCBB.2021.3118916 .
  19. [STAR2] Zhang H, Xiu X, Xue A, Yuedong Yang*, Y Yang*, H Zhao*. The putative causal effect of type 2 diabetes in risk of cataract: a Mendelian randomization study in East Asian. Int J Epidemiol 2021; 50(6):2024-2037.(IF=7.7).
  20. [STAR1] Zhou X, Chai H, Zeng Y, Zhao H, Yuedong Yang*. scAdapt: Virtual adversarial domain adaptation network for single cell RNA-seq data classification across platforms and species. Brief in Bioinfo 2021, bbab281 & RECOMB 2021 (Bioinformatics Top conference)[PDF].
  21. [STAR1] Chai H, Zhou X, Zhang Z, Rao J, Zhao H, Yuedong Yang*. Integrating multi-omics data with deep learning for predicting cancer prognosis. Comput Biol Med 2021; 134:104481 [PDF].
  22. [STAR2] Rao J, Zhou X, Lu Y, Zhao H, Yuedong Yang*. Imputing Single-cell RNA-seq data by combining Graph Convolution and Autoencoder Neural Networks. iScience 2021; 24(5):102393; [PDF].
  23. Zheng F, Li L, Zhang X, Song Y, Huang Z, Chong Y, Chen Z, Zhu H, Wu J, Chen W, Lu Y, Yuedong Yang*, Zha Y*, Zhao H*, Shen J*. Accurately Discriminating COVID-19 from Viral and Bacterial Pneumonia According to CT Images Via Deep Learning. Interdiscip Sci-Comput Life Sci. 2021 Feb 27:1–13. [PDF] .
  24. Wang J, Zheng S, Chen J, Yuedong Yang*. Meta Learning for Low Resource Molecular Optimization. J Chem Inf Model 2021; [PDF].
  25. [STAR1] Song Y, Zheng S, Li L, Zhang X, Zhang X, Huang Z, Chen J, Zhao H, Jie Y, Wang R, Chong Y*, Shen J*, Zha Y*, Yuedong Yang*. Deep learning Enables Accurate Diagnosis of Novel Coronavirus (COVID-19) with CT images. IEEE TCBB 2021;18(6):2775-2780. [PDF].
  26. [STAR1] Chen J, Zheng S, Zhao H, Yuedong Yang*. Structure-aware Protein Solubility Prediction From Sequence Through Graph Convolutional Network And Predicted Contact Map. J Cheminfo 2021; 13(1):7 [PDF].
    27. Peer Reviewed Conference Articles
  27. [STAR2] Chen J#, Zheng S#, Yuedong Yang*. Learning Attributed Graph Representation with Communicative Message Passing Transformer. IJCAI 2021 arxiv (AI Top conference, CCF-A, Acceptance rate=13.9%) [PDF].
  28. Mai S#, Zheng S#, Yuedong Yang*, Hu H*. Communicative Message Passing for Inductive Relation Reasoning. AAAI 2021(AI Top conference, CCF-A, acceptance=21%) arxiv 2012.08911.
  29. Huang Z, H Chai, R Wang, H Wang, Yuedong Yang*, H Wu*. Integration of Patch Features through Self-Supervised Learning and Transformer for Survival Analysis on Whole Slide Images. MICCAI 2021 (Medical Image Top Conference) [PDF] .
  30. Zhang P, Zheng S, Chen J, Zhou Y*, and Yuedong Yang*. DeepANIS: Predicting antibody paratope from concatenated CDR sequences by integrating bidirectional long-short-term memory and transformer neural networks. BIBM 2021(Acceptance rate=19.6%. CCF-B).
  31. [STAR1] Chen S, Zhang S, Li X, Liu Y, and Yuedong Yang*. SEGEM: a Fast and Accurate Automatic Protein Backbone Structure Modeling Method for Cryo-EM. BIBM 2021.
  32. Y Wang, Z Zhang, H Chai, and Yuedong Yang*. Multi-omics Cancer Prognosis Analysis Based on Graph Convolution Network. BIBM 2021.
  33. H Zhang, J Wei, Z Liu, X Liu, Y Chong, Y Lu, H Zhao, and Yuedong Yang*. DGAT-onco: A differential analysis method to detect oncogenes by integrating functional information of mutations. BIBM 2021; bioRxiv.

    34. 2020

  34. [STAR2] Zheng S#, Rao J#, Song Y, Zhang J, Xiao X, Fang EF, Yuedong Yang*, Niu Z*. PharmKG: A Dedicated Knowledge Graph Benchmark for Biomedical Data Mining. Brief in Bioinfo 2020 (IF=9.0); doi:10.1093/bib/bbaa344; [PDF].
  35. [STAR1] Lv X, Z Chen, Y Lu*, and Yuedong Yang*. An End-to-end Oxford Nanopore Basecaller Using Convolution-augmented Transformer. BIBM 2020:337-342(Bioinformatics top conference, acceptance=19.4%) bioRxiv 2020.11.09.374165 [PDF].
  36. [STAR1] Zeng Y, Zhou X, Rao J, Lu Y*, Yuedong Yang*. Accurately Clustering Single-cell RNA-seq data by Capturing Structural Relations between Cells through Graph Convolutional Network. BIBM 2020;519-522 bioRxiv 2020.09.02.278804 .
  37. Zheng S, Zhang J, Rao J, Xiao X, Menpes-Smith W, JY Chen, Yuedong Yang* and Z Niu*. Biomedical Knowledge Graph of COVID-19: Construction and Applications. SIGKDD 2020 (BioKDD workshop).
  38. [STAR2] Song Y# , S Zheng# , Z Niu , Z Fu , Y Lu and Yuedong Yang*. Communicative Representation Learning on Attributed Molecular Graphs. IJCAI 2020 (AI Top conference, DOI: 10.24963/ijcai.2020/388, CCF-A, Acceptance rate=12.6%) [PDF].
  39. Zhou X, H Chai, H Zhao, CH Luo*, Yuedong Yang*. Imputing missing RNA-seq data from DNA methylation by using transfer learning based neural network. Gigascience 2020 (IF=6.0; doi:10.1093/gigascience/giaa076) [PDF].
  40. [STAR2] Ke Y, Rao J, Zhao H, Lu Y, Xiao N*, Yuedong Yang*. Accurate Prediction of Genome-wide RNA Secondary Structure Profile Based on Extreme Gradient Boosting. Bioinformatics. 2020 May 28: 36(17):4576-82. doi: 10.1093/bioinformatics/btaa534 [PDF].
  41. Lv X, Chen J, Lu Y, Chen Z, Xiao N*, Yuedong Yang*. Accurately Predicting Mutation-Caused Stability Changes from Protein Sequences Using Extreme Gradient Boosting. J Chem Inf Model. 2020 Apr 27;60(4):2388-2395. doi: 10.1021/acs.jcim.0c00064 [PDF].
  42. [STAR1] Cai Y, Li X, Sun Z, Lu Y, Zhao H, Hanson J, Paliwal K, Litfin T, Zhou Y*, Yuedong Yang*. SPOT-Fold: Fragment-Free Protein Structure Prediction Guided by Predicted Backbone Structure and Contact Map. J Comput Chem. 2020 Mar 30;41(8):745-750. doi: 10.1002/jcc.26132 [PDF].
  43. [STAR1] Zheng S, Rao J, Zhang Z, Xu J*, Yuedong Yang*. Predicting Retrosynthetic Reactions Using Self-Corrected Transformer Neural Networks. J Chem Inf Model. 2020 Jan 27;60(1):47-55. doi: 10.1021/acs.jcim.9b00949 [PDF].
  44. [STAR2] Zheng S#, Y Li#, S Chen, J Xu* and Yuedong Yang*. Predicting Drug Protein Interaction using Quasi-Visual Question Answering System. Nature Machine Intelligence 2020;2(1):134-140 [PDF].
  45. [STAR1] Chen S, Sun Z, Lin L, Liu Z, Liu X, Chong Y, Lu Y, Zhao H*, Yuedong Yang*. To Improve Protein Sequence Profile Prediction through Image Captioning on Pairwise Residue Distance Map. J Chem Inf Model. 2020 Jan 27;60(1):391-399. doi: 10.1021/acs.jcim.9b00438 [PDF].

    46. 2019

  46. Chen K, Lu Y, Zhao H, Yuedong Yang*. Predicting the change of exon splicing caused by genetic variant using support vector regression. Hum Mutat. 2019 Sep;40(9):1235-1242. doi: 10.1002/humu.23785 [PDF].
  47. [STAR1] Chen P, Ke Y, Lu Y, Du Y, Li J, Yan H, Zhao H, Zhou Y, Yuedong Yang*. DLIGAND2: an improved knowledge-based energy function for protein-ligand interactions using the distance-scaled, finite, ideal-gas reference state. J Cheminform 2019 Aug 7;11(1):52 [PDF].

    48. 2018 & before

  48. [STAR1] Atack JM#, Yuedong Yang#, Seib KL, Zhou Y, Jennings MP. A survey of Type III restriction-modification systems reveals numerous, novel epigenetic regulators controlling phase-variable regulons; phasevarions. Nucleic Acids Res. 2018 Apr 20;46(7):3532-3542. [PDF].
  49. Hanson J, Paliwal K, Litfin T, Yuedong Yang*, Zhou Y*. Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks. Bioinformatics. 2018 Dec 1;34(23):4039-4045.
  50. [STAR2] Taherzadeh G, Y Zhou, AW Liew, Yuedong Yang*. Structure-based prediction of protein-peptide binding regions using Random Forest. Bioinformatics 2018 Feb 1;34(3):477-484.
  51. J Gao, Yuedong Yang*, Y Zhou*. Grid-based prediction of torsion angle probabilities of protein backbone and its application to discrimination of protein intrinsic disorder regions and selection of model. BMC bioinformatics 2018;19 (1), 29.
  52. [STAR1] Zhao H*, Yuedong Yang*, Y. Lu, M. Mort, D. N. Cooper, and Y. Zhou*. Quantitative mapping of genetic similarity in human heritable diseases by shared mutations. Human Mutation 2018. Hum Mutat. 2018 Feb;39(2):292-301.
  53. [STAR2] Yuedong Yang , J Gao, J Wang, R Heffernan, J Hanson, K Paliwal, and Y Zhou. Sixty-five years of long march in protein secondary structure prediction: the final stretch? Brief in Bioinfo 2018 May 1;19(3):482-494. (ESI highly cited). [ PDF ]
  54. Guruge I, G Taherzadeh, J Zhan, Y Zhou*, Yuedong Yang*. B‐factor profile prediction for RNA flexibility using support vector machines. J Comput Chem 2018;39(8), 407-411 .
  55. H Zhao*, DR Nyholt, YH Yang, J Wang, Yuedong Yang*. Improving the detection of pathways in genome-wide association studies by combined effects of SNPs from Linkage Disequilibrium blocks. Scientific Rep 2017. 7,3512.
  56. [STAR1] Heffernan R, Yuedong Yang*, Paliwal K, Zhou Y*. Capturing Non-Local Interactions by Long Short Term Memory Bidirectional Recurrent Neural Networks for Improving Prediction of Protein Secondary Structure, Backbone Angles, Contact Numbers, and Solvent Accessibility. Bioinformatics. 2017 Sep 15;33(18):2842-2849. (ESI highly cited)
  57. T Litfin, Y Zhou*, Yuedong Yang*. SPOT-Ligand 2: Improving structure-based virtual screening by binding-homology search on an expanded structural template library. Bioinformatics 2017 Apr 15;33(8):1238-1240.
  58. [STAR2] Yuedong Yang, X Li, H Zhao, J Zhan, J Wang, and Y Zhou. Genome-scale characterization of RNA tertiary structures and their functional impact by RNA solvent accessibility prediction. RNA 2017. 23(1), 14-22.
  59. [STAR1]Hanson J*, Yuedong Yang*, K Paliwal, and Y Zhou*. Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks. Bioinformatics 2017. 33 (5): 685-692.(ESI highly cited) .
  60. Yuedong Yang, R Heffernan, K Paliwal, J Lyons, A Dehzangi, A Sharma, J Wang, A Satter, Y Zhou*. SPIDER2: A Package to Predict Secondary Structure, Accessible Surface Area, and Main-Chain Torsional Angles by Deep Neural Networks. Prediction of Protein Secondary Structure, 2017; 55-63 (Book chapter, cited:110).
  61. Gao J, Yuedong Yang*, Y Zhou*. Predicting the errors of predicted local backbone angles and nonlocal solvent-accessibilities of proteins by deep neural networks. Bioinformatics 2016. 32 (24): 3768-3773.
  62. Zhao H, D Fan, D Nyholt, Yuedong Yang*. Enrichment of SNPs in functional categories reveals genes affecting complex traits. Human Mutation 2016 Aug;37(8):820-6.
  63. [STAR1] Heffernan R, K. Paliwal, J. Lyons, A. Dehzangi, A. Sharma, J. Wang, A. Sattar, Y. Zhou* and Yuedong Yang*. Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins. Bioinformatics 2016; 32(6):843-9.
  64. G Taherzadeh, Y Zhou, AW Liew, Yuedong Yang*. Sequence-based Prediction of Protein-Carbohydrate Binding Sites Using Support Vector Machines. J Chem Inf Model 2016; 56(10), 2115-2122.
  65. [STAR2] Yuedong Yang, J Zhan, Y Zhou. SPOT-Ligand: Fast and effective structure-based virtual screening by binding homology search according to ligand and receptor similarity. J Comp Chem 2016 Jul 5;37(18):1734-9.
  66. Yuedong Yang* and Y Zhou*. Effective ab initio protein conformational sampling based on predicted torsion angles. J Comp Chem 2016; 37(11):976-80. .
  67. [STAR2]Heffernan R, K. Paliwal, J. Lyons, A. Dehzangi, A. Sharma, J. Wang, A. Sattar, Yuedong Yang* and Y. Zhou*. Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning. Scientific Reports 2015; 5:11476 (Cited:240; ESI Highly cited).
  68. Lyons J, A. Dehzangi*, R. Heffernan, Yuedong Yang*, Y. Zhou, A. Sharma, J. Wang, K. Paliwal*. Advancing the accuracy of protein fold recognition by utilizing profiles from hidden markov models. IEEE T Nanobioscience 2015, 14(7), 761-772.
  69. Zhao H, Yuedong Yang*, M Itzsteinc, Y Zhou*. Carbohydrate-binding protein identification by coupling structural similarity search with binding affinity prediction. J Comput Chem. 2014 Nov 15;35(30):2177-83. doi: 10.1002/jcc.23730. (Cover Article).
  70. [STAR2] J Lyons, A Dehzangi, R Heffernan, A Sharmaa, K Paliwal, A Sattar, Y Zhou*, Yuedong Yang*. Predicting backbone Calpha angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network. J Comput Chem. 2014; 35(28):2040-6. doi: 10.1002/jcc.23718.
  71. Zhao H, W Wang, Yaoqi Zhou*, and Yuedong Yang*. Predicting DNA-Binding Proteins and Binding Residues by Complex Structure Prediction and Application to Human Proteome. Plos One 2014; 9(5), e96694.
  72. Zhao H#, Yuedong Yang#, Janga SC, Kao CC, Zhou Y. Prediction and validation of the unexplored RNA-binding protein atlas of the human proteome. Proteins. 2014 Apr;82(4):640-7.
  73. Zhao H#, Yuedong Yang#, Zhou Y. Prediction of RNA binding proteins comes of age from low resolution to high resolution. Mol Biosyst. 2013 Aug 27;9(10):2417-25.
  74. [STAR2] Zhao H#, Yuedong Yang#, Hai Lin, Xinjun Zhang, Matthew Mort, David N. Cooper, Yunlong Liu*, and Yaoqi Zhou*. DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels. Genome Biology. 2013 Mar 13;14(3):R23.(IF=14).
  75. [STAR1] Yuedong Yang, Zhan J, Zhao H, Zhou Y. A new size-independent score for pairwise protein structure alignment and its assessment by structure classification and nucleic-acid binding prediction. Proteins. 2012 Aug;80(8):2080-8.
  76. Lu T#, Yuedong Yang#, Yao B, Liu S, Zhou Y, Zhang C. Template-based structure prediction and classification of transcription factors in Arabidopsis thaliana. Protein Sci. 2012 Mar 30; 21(6):828-838.
  77. Zhao H#, Yuedong Yang#, Zhou Y. Highly accurate and high-resolution function prediction of RNA binding proteins by fold recognition and binding affinity prediction. RNA Biology. 2011 Nov 1;8(6).
  78. [STAR2] Yuedong Yang, Faraggi E, H Zhao, Zhou Y. Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of the query and corresponding native properties of templates. Bioinformatics 2011 Aug 1;27(15):2076-82. (ESI highly cited).
  79. [STAR2] Zhao H#, Yuedong Yang#, Zhou Y. Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets. Nucleic Acids Res. 2011 Apr;39(8):3017-25. (IF=11).
  80. Dai L#, Yuedong Yang#, Kim H and Zhou Y. Improving computational protein design by using structure-derived sequence profile. Proteins. 2010 Aug 1;78(10):2338-48.
  81. Zhao H#, Yuedong Yang#, Zhou Y. Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function. Bioinformatics. 2010 Aug 1;26(15):1857-63.
  82. [STAR1] Faraggi E#, Yuedong Yang#, Zhang S, Zhou Y. Predicting continuous local structure and the effect of its substitution for secondary structure in fragment-free protein structure prediction. Structure (Cell Press). 2009 Nov 11;17(11):1515-27.
  83. Xu B#, Yuedong Yang#, Liang H, Zhou Y. An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription factor binding profiles. Proteins. 2009 Aug 15;76(3):718-30.
  84. [STAR2] Yuedong Yang, Zhou Y. Specific interactions for ab initio folding of protein terminal regions with secondary structures. Proteins. 2008 Aug;72(2):793-803. (Cited: 210)).
  85. Yuedong Yang, Zhou Y. Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions. Protein Sci. 2008 Jul;17(7):1212-9. (Cited: 120).
  86. Yuedong Yang, Liu H. Genetic algorithms for protein conformation sampling and optimization in a discrete backbone dihedral angle space. J Comput Chem. 2006 Oct;27(13):1593-602.
  87. Ding H#, Yuedong Yang#, Zhang J, Wu J, Liu H, Shi Y. Structural basis for SUMO-E2 interaction revealed by a complex model using docking approach in combination with NMR data. Proteins. 2005 Dec 1;61(4):1050-8.
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