生物信息学, 机器学习/深度学习,优化算法





2017.5至今,中山大学数据科学和计算机学院, 教授,中山大学百人计划引进人才





2006.9-2011.3, 美国印第安纳大学信息学院&药学院,博士后

  1. Novel antimicrobial target discovery by an integrated approach. Australian Research Council Linkage (LP150100137), 2015-2017 (co-PI, AUD $241,564)
  2. Developing species-specific, structure-targeting peptides as a novel class of antibiotics. Australian NHMRC Project (1121629), 2017-2019. (co-PI, AUD $607,967)


BMC Bioinformatics (IF=2.4) 编委

Biomed Research Int, 客座编辑 (2015)

程序委员会委员:PRICAI-13, IFIP-9


. 期刊论文 (2011年之后)

  1. 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 Apr 18. doi: 10.1093/bioinformatics/btx218. (IF=5.8; Accepted on Mar 2017.)
  2. 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.
  3. 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 2017 (Accepted on Nov 2016; IF=8.4)
  4. Yuedong Yang, X Li, H Zhao, J Zhan, J Wang, and Y Zhou. Genome-scale characterization of RNA ertiary structures and their functional impact by RNA solvent accessibility prediction. RNA 2017. 23(1), 14-22 (IF=4.3)
  5. 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. (IF=5.8)
  6. T Wang, Yuedong Yang, Y Zhou, and H Gong. LRFragLib: an effective algorithm to identify fragments for de novo protein structure prediction. Bioinformatics 2017. 33 (5): 677-684. (IF=5.8)
  7. Zhang X, Li M, Lin H, Rao X, Feng W, Yuedong Yang, Mort M, Cooper DN, Wang Y, Wang Y, Wells C, Zhou Y, Liu Y. regSNPs-splicing: a tool for prioritizing synonymous single-nucleotide substitution. Hum Genet. 2017 Apr 8. doi: 10.1007/s00439-017-1783-x.  (Accepted on Mar).
  8. Carraro M, Minervini G, Giollo M, Bromberg Y, Capriotti E, Casadio R, Dunbrack R, Elefanti L, Fariselli P, Ferrari C, Gough J, Katsonis P, Leonardi E, Lichtarge O, Menin C, Martelli PL, Niroula A, Pal LR, Repo S, Scaini MC, Vihinen M, Wei Q, Xu Q, Yuedong Yang, Yin Y, Zaucha J, Zhao H, Zhou Y, Brenner SE, Moult J, Tosatto SCE. Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI. Hum Mutat. 2017 Apr 25. doi: 10.1002/humu.23235.  (Accepted on Apr).
  9. H Cao, D Wei, Yuedong Yang, Y Shang, G Li, Y Zhou, Q Ma, Y Xu. Systems-level understanding of ethanol-induced stresses and adaptation in E. coli. Scientific Reports 2017. 7, 44150.
  10. Li M, Feng W, Zhang X, Yuedong Yang, Wang K, Mort M, Cooper DN, Wang Y, Zhou Y, Liu Y. ExonImpact: Prioritizing Pathogenic Alternative Splicing Events. Hum Mutat. 2017; 38 (1), 16-24. (IF=5.1)
  11. 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. (IF=3.7)
  12. 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. (IF=5.8)
  13. DI Stanisic, J Gerrard, J Fink, PM Griffin, XQ Liu, L Sundac, S Sekuloski, IB Rodriguez, J Pingnet, Yuedong Yang, Y Zhou, KR Trenholme, CYT Wang, H Hackett, J Chan, C Langer, E Hanssen, SL Hoffman, JG Beeson, JS McCarthy, MF Good. Infectivity of Plasmodium falciparum in malaria-naïve individuals is related to knob expression and cyto-adherence of the parasite. Infection and Immunity 2016; 84 (9), 2689-2696. (IF=3.6).
  14. W Zhang, M Yang, Yuedong Yang, J Zhan, X Zhao, Y Zhou. Optimal secretion of alkali-tolerant xylanase in Bacillus subtilis by signal peptide screening. Applied Microbiology and Biotechnology 2016. 100(20):8745-56. DOI:  10.1007/s00253-016-7615-4. (IF=3.3)
  15. 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. (IF=5.1; *Corresponding authors)
  16. G Ni, S Chen, Yuedong Yang, S Cummins, J Zhan, Z Li, B Zhu, K Mounsey, S Walton, M Wei, Y Wang, Y Zhou, T Wang, X Liu. Investigation of the Possibility of Using Peptides with a Helical Repeating Pattern of Hydrophobic and Hydrophilic Residues to Inhibit IL-10. Plos One 2016. 11 (4), e0153939.
  17. T. Hoque, Yuedong Yang, A. Mishra and Yaoqi Zhou. sDFIRE: Sequence‐specific statistical energy function for protein structure prediction by decoy selections. J Comp Chem 2016 May 5;37(12):1119-24. (IF=3.6)
  18. J. Yu, Z. Cao, Yuedong Yang, C. Wang, Z. Su, Y. Zhao, J. Wang and Y. Zhou. Natural protein sequences are more intrinsically disordered than random sequences. Cellular and Molecular Life Sciences 2016 Aug;73(15):2949-57. (IF=5.8)
  19. G. Taherzadeh, Yuedong Yang, T. Zhang, A. W. Liew and Y. Zhou. Sequence-based prediction of protein-peptide binding sites using Support Vector Machine. J Comp Chem 2016 May 15;37(13):1223-9. (IF=3.6)
  20. P Brown, Yuedong Yang, Yaoqi Zhou, Wayne Pullan. A heuristic for the time constrained asymmetric linear sum assignment problem. J Comb Optim 2017. 33:551-566. (IF=1.1)
  21. 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. (IF=3.6)
  22. Yuedong Yang* and Y Zhou*. Effective ab initio protein conformational sampling based on predicted torsion angles. J Comp Chem 2016; 37(11):976-80. (IF=3.6)
  23. 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. (IF=5.0; *Corresponding authors)
  24. P Brown, W Pullan, Yuedong Yang, Y Zhou. Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic. Bioinformatics 2016; 32(3):370-7. (IF=5.0).
  25. 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. (IF=2.3; *Co-corresponding authors).
  26. 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  (*co-corresponding authors; IF=5.6)
  27. Lukas Folkman, Yuedong Yang, Zhixiu Li, Bela Stantic, Abdul Sattar, Matthew Mort, David N Cooper, Yunlong Liu, Yaoqi Zhou. DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels. Bioinformatics 2015. 31 (10): 1599-1606. (IF=5.3)
  28. H Zhao, Yuedong Yang*, M von 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, *co-corresponding authors; IF=3.8)
  29. James Lyons, Abdollah Dehzangi, Rhys Heffernan, Alok Sharmaa, Kuldip Paliwal, Abdul Sattar, Yaoqi 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. (IF=3.8; *Corresponding authors).
  30. Z Li, Yuedong Yang, E Faraggi, J Zhan, and Y Zhou. Direct prediction of profiles of sequences compatible with a protein structure by neural networks with fragment-based local and energy-based non-local profiles. Proteins. 2014 Oct;82(10):2565-73. doi: 10.1002/prot.24620. (IF=3.3)
  31. 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. (*co-corresponding authors; IF=3.5)
  32. 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. doi: 10.1002/prot.24441. (# co-first author; IF=3.3)
  33. Wang J, Yuedong Yang, Cao Z, Li Z, Zhao H, and Yaoqi Zhou*. The role of semi-disorder in temperature adaption of bacterial FlgM proteins. Biophy J. 2013 Dec 3;105(11):2598-605. (IF=4.0)
  34. Zhou BR, Feng H, Kato H, Dai L, Yuedong Yang, Zhou Y, Bai Y. Structural insights into the histone H1-nucleosome complex. PNAS 2013 Nov 26;110(48):19390-5. (IF=9.8)
  35. 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. (# co-first author; IF=3.2)
  36. Zhao H#, Yuedong Yang#, Hai Lin, Xinjun Zhang, Matthew Mort, David N. Cooper, Yunlong Liu*, and Yaoqi Zhou*. Discriminating disease-causing from neutral non-frame shifting micro-INDELs by support vector machines with integrated sequence- and structure­- based features. Genome Biology. 2013 Mar 13;14(3):R23.(# co-first author; IF=11.3)
  37. Zhixiu Li, Yuedong Yang, Jian Zhan, Liang Dai and Yaoqi Zhou. Energy Functions in De Novo Protein Design: Current Challenges and Future Prospects. Annu Rev Biophys. 2013 Feb 28; 42(1). (IF=15.4)
  38. 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. (IF=3.3)
  39. 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 (# co-first author; IF=2.8).
  40. Faraggi E, Zhang T, Yuedong Yang, Kurgan L, Zhou Y. SPINE X: improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles. J Comput Chem. 2012 Jan 30;33(3):259-67. (IF=3.8)
  41. Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, Ko JS, Lee H, Seok C, Bourquard T, Bernauer J, Poupon A, Aze J, Soner S, Ovali SK, Ozbek P, Tal NB, Haliloglu T, Hwang H, Vreven T, Pierce BG, Weng Z, PÃl’rez-Cano L, Pons C, FernÃa˛ndez-Recio J, Jiang F, Yang F, Gong X, Cao L, Xu X, Liu B, Wang P, Li C, Wang C, Robert CH, Guharoy M, Liu S, Huang Y, Li L, Guo D, Chen Y, Xiao Y, London N, Itzhaki Z, Schueler-Furman O, Inbar Y, Potapov V, Cohen M, Schreiber G, Tsuchiya Y, Kanamori E, Standley DM, Nakamura H, Kinoshita K, Driggers CM, Hall RG, Morgan JL, Hsu VL, Zhan J, Yuedong Yang , Zhou Y, Kastritis PL, Bonvin AM, Zhang W, Camacho CJ, Kilambi KP, Sircar A, Gray JJ, Ohue M, Uchikoga N, Matsuzaki Y, Ishida T, Akiyama Y, Khashan R, Bush S, Fouches D, Tropsha A, Esquivel-Rodriguez J, Kihara D, Stranges PB, Jacak R, Kuhlman B, Huang SY, Zou X, Wodak SJ, Janin J, Baker D. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J Mol Biol. 2011 Nov 25;414(2):289-302. (IF=4.0)
  42. 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). (#co-first author; IF=5.4).
  43. 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. (IF=5.3; Citations=126; ESI highly cited).
  44. Zhao H#, Yuedong Yang#, Zhou Y. Structure-based prediction of RNA-binding domains andRNA-binding sites and application to structural genomics targets. Nucleic Acids Res. 2011 Apr;39(8):3017-25. (# co-first author; IF=9.2; Citations=59)
  45. Zhou Y, Duan Y, Yuedong Yang, Faraggi E, Lei H. Trends in template/fragment-free protein structure prediction. Theoretical Chemistry accounts. 2011 Jan;128(1):3-16. (IF=2.1)
  46. 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. (# co-first author; IF=3.3)
  47. 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. (# co-first author; IF=5.8)
  48. 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. (# co-first author; IF=6.8; Citations=65)
  49. 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. (# co-first author; (IF=3.3)
  50. Yuedong Yang, Zhou Y. Specific interactions for ab initio folding of protein terminal regions with secondary structures. Proteins. 2008 Aug;72(2):793-803. (IF=3.3; Citations=114)
  51. 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. (IF=2.8; Citations=98)
  52. 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. (IF=3.8)
  53. Cheng S, Yuedong Yang, Wang W, Liu H. Transition state ensemble for the folding of B domain of protein A: a comparison of distributed molecular dynamics simulations with experiments. J Phys Chem B. 2005 Dec 15;109(49):23645-54. (IF=3.4)
  54. 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. (# co-first author; IF=3.3)
  55. Zhou H, Xu Y, Yuedong Yang, Huang A, Wu J, Shi Y. Solution structure of AF-6 PDZ domain and its interaction with the C-terminal peptides from Neurexin and Bcr. J Biol Chem. 2005 Apr 8;280(14):13841-7. (IF=4.6)

. 著作章节:

  1. Yuedong Yang*, R. Heffernan, K. Paliwal, J. Lyons, A. Dehzangi, A. Sharma, J. Wang, A. Sattar, and Y. Zhou*. SPIDER2: a package to predict secondary structure, accessible surface area, and main-chain torsional angles. Methods in Molecular Biology 2017; Predicting Protein Secondary Structure 55-63.
  2. JF Yu, Yuedong Yang, X Sun, JH Wang. Sequence and Structure Analysis of Biological Molecules Based on Computational Methods. BioMed Res Int. 2015; 565328 (Editorial)
  3. Yuedong Yang, H. Zhao, J. Wang, and Y. Zhou. SPOT-Seq: Predicting protein-RNA complex structure and RNA-binding function by fold recognition and binding affinity prediction. Methods in Molecular Biology (Protein Structure Prediction). 119-130, 2014.