Yanglab:Publications

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Selected Articles

2019

1. 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. 2019 Dec 17. doi: 10.1002/jcc.26132.
2. Zheng S, Rao J, Zhang Z, Xu J, Yuedong Yang*. Predicting Retrosynthetic Reactions Using Self-Corrected Transformer Neural Networks. J Chem Inf Model. 2019 Dec 24. doi: 10.1021/acs.jcim.9b00949.
3. 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. 2019 Dec 20. doi: 10.1021/acs.jcim.9b00438.
4. 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.
5. 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.

Previous

1. 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 (Citations>200).
2. G Taherzadeh, Y Zhou, AW Liew, Yuedong Yang*. Structure-based prediction of protein-peptide binding regions using Random Forest. Bioinformatics 2017 btx614 .
3. 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.
4. 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.
5. 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=7.3; Google Citations>200; ESI Highly Cited)
6. Yuedong Yang, Zhou Y. Specific interactions for ab initio folding of protein terminal regions with secondary structures. Proteins. 2008 Aug;72(2):793-803. (Citations>200)
7. 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, bbw129 (IF=5.2, ESI Highly Cited)
8. 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.(# co-first author; IF=11.9).
9. M. Atack#, Yuedong Yang#, Kate L. Seib, Yaoqi Zhou, Michael P. Jennings*. A survey of Type III restriction-modification systems reveals numerous, novel epigenetic regulators controlling phase variable regulons; phasevarions. Nucleic Acid Res 2018. (IF=10.2)
10. 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.
11. 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.