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Selected Publications. See Google Scholar for the full publication list (Totally >100 articles; Cited>4000; H-index=34)

    Preprints

  1. S Zheng, Z Lei, H Ai, H Chen, D Deng*, Yuedong Yang*. Deep Scaffold Hopping with Multi-modal Transformer Neural Networks. chemRxiv 13011767
  2. Zhe Sun, Shuangjia Zheng, Huiying Zhao, Zhangming Niu, Yutong Lu, Yi Pan, Yuedong Yang*. To improve the predictions of binding residues with DNA, RNA, carbohydrate, and peptide via multiple-task deep neural networks. bioRxiv 2020.02.11.943571
  3. Haoyang Zhang, Junkang Wei, Zifeng Liu, Xun Liu, Yutian Chong, Yutong Lu, Huiying Zhao, Yuedong Yang*. DGAT-onco: A powerful method to detect oncogenes by integrating differential mutational analysis and functional impacts of somatic mutations bioRxiv 2020.02.15.947085

    2021

  4. Jianwen Chen#, Shuangjia#, Yuedong Yang*. Learning Attributed Graph Representation with Communicative Message Passing Transformer. IJCAI 2021 (acceptance rate=13.9%).
  5. Hua Chai, Xiang Zhou, Zhongyue Zhang, Jiahua Rao, Huiying Zhao, Yuedong Yang*. Integrating multi-omics data with deep learning for predicting cancer prognosis. Comput Biol Med (accepted).
  6. Jiahua Rao, Xiang Zhou, Yutong Lu, Huiying Zhao, Yuedong Yang*. Imputing Single-cell RNA-seq data by combining Graph Convolution and Autoencoder Neural Networks. iScience 2021;24(5):102393
  7. 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.
  8. Wang J, Zheng S, Chen J, Yuedong Yang*. Meta Learning for Low Resource Molecular Optimization. J Chem Inf Model 2021; doi:10.1021/acs.jcim.0c01416.
  9. 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 TCBB; DOI: 10.1109/TCBB.2021.3065361
  10. 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 Feb 8;13(1):7 .
  11. Zhou X, Chai H, Zeng Y, Zhao H, Luo C*,Yuedong Yang*. scAdapt: Virtual adversarial domain adaptation network for single cell RNA-seq data classification across platforms and species. biorxiv RECOMB 2021 (Bioinformatics Top conference, In press).
  12. 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.


  13. 2020

  14. 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.
  15. Xuan Lv, Zhiguang Chen, Yutong Lu*, and Yuedong Yang*. An End-to-end Oxford Nanopore Basecaller Using Convolution-augmented Transformer. BIBM 2020 (Bioinformatics top conference, acceptance=19.4%) bioRxiv 2020.11.09.374165.
  16. Yuansong Zeng, Xiang Zhou, Jiahua Rao, Yutong Lu*, Yuedong Yang*. Accurately Clustering Single-cell RNA-seq data by Capturing Structural Relations between Cells through Graph Convolutional Network. BIBM 2020 (accepted) bioRxiv 2020.09.02.278804 .
  17. 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).
  18. Ying Song# , Shuangjia Zheng# , Zhangming Niu , Zhang-hua Fu , Yutong 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%).
  19. Xiang Zhou, Hua Chai, Huiying Zhao, Ching-Hsing 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).
  20. 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 .
  21. 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 .
  22. 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.
  23. 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 .
  24. 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.
  25. 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.

  26. 2019

  27. 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.
  28. 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. doi: 10.1186/s13321-019-0373-4.

  29. 2018 & before

  30. 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. doi: 10.1093/nar/gky192. PMID: 29554328.
  31. 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. doi: 10.1093/bioinformatics/bty481. PMID: 29931279.
  32. G Taherzadeh, 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.
  33. 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.
  34. H. Zhao*, 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.
  35. 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 Bioinformatics 2018 May 1;19(3):482-494. (ESI highly cited)
  36. I Guruge, 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
  37. 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.
  38. 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
  39. 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.
  40. 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 .
  41. J Hanson*, 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)
  42. Y 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)
  43. J Gao, 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.
  44. H Zhao, 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.
  45. R. Heffernan, 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.
  46. 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.
  47. 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.
  48. Yuedong Yang* and Y Zhou*. Effective ab initio protein conformational sampling based on predicted torsion angles. J Comp Chem 2016; 37(11):976-80.
  49. R. Heffernan, 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)
  50. J. Lyons, 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.
  51. H Zhao, 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)
  52. 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.
  53. H Zhao, 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.
  54. 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.
  55. 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.
  56. 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)
  57. 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.
  58. 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
  59. 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).
  60. 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)
  61. 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)
  62. 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.
  63. 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.
  64. 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.
  65. 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.
  66. 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))
  67. 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)
  68. 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.
  69. 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.