Latest update: April.2, 2013

-- Refereed Journal Articles --

1. Qi Dai*, Yan Li, Xiaoqing Liu, Yuhua Yao, Yunjie Cao, Pingan He. Comparison study on statistical features of predicted secondary structures for protein structural class prediction: From content to position. BMC Bioinformatics, 2013, 14: 152.

1. Qi Dai*, Xiaoqing Liu, Yuhua Yao, Fukun Zhao. Using Markov model to improve word normalization algorithm for biological sequence comparison. Amino Acids, 2012, DOI 10.1007/s00726-011-0906-2.

2. Qi Dai*, Xiaodong Guo, Lihua Li. Sequence comparison via polar coordinates representation and curve tree. Journal of Theoretical Biology, 2012, 292: 78-85.

3. Qi Dai*, Lihua Li, Xiaoqing Liu, Yuhua Yao, Fukun Zhao, Michael Zhang. Integrating Overlapping Structures and Background Information of Words Significantly Improves Biological Sequence Comparison. PLOS one, 2011. 6(11): e26779.

4. Qi Dai*, Wu Li, Lihua Li. Improving protein structural class prediction using novel combined sequence information and predicted secondary structural features. Journal of Computational Chemistry, 2011, 32: 3393-3398.

5. Qi Dai*, Xiaoqing Liu, Yuhua Yao, Fukun Zhao. Numerical characteristics of word frequencies and their application to dissimilarity measure for sequence comparison. Journal of Theoretical Biology, 2011, 276(1): 174-180.

6. Xiaoqing Liu, Qi Dai*, Lihua Li, Zerong He. An efficient binomial model-based measure for sequence comparison and its application. J Biomol Struct Dyn, 2011, 28(5):833-843.

7. Xiaoqing Liu, Qi Dai*, Lihua Li, Zhilong Xiu. Resistant mechanism against nelfinavir of subtype C human immunodeficiency virus type 1 proteases. Journal of Molecular Structure, 2011, 986: 30-38.

8. Qi Dai*, Xiaoqing Liu, Lihua Li, Yuhua Yao, Bin Han, Lei Zhu. Using Gaussian Model to Improve Biological Sequence Comparison. Journal of Computational Chemistry, 2010, 31: 351-361.

9. Shuyan Ding, Qi Dai, Hongmei Liu, Tianming Wang. A simple feature representation vector for phylogenetic analysis of DNA sequences, Journal of Theoretical Biology, 2010, 265(4):618-623.

10. Yuhua Yao*, Qi Dai, Ling Li, Xu-Ying Nan, Ping-An He, Yao-Zhou Zhang. Similarity/dissimilarity studies of protein sequences based on a new 2D graphical representation. Journal of Computational Chemistry, 2010, 31(5): 1045-1052.

11. Qi Dai*, Yanchun Yang, Tianming Wang. Markov model plus k-word distributions: A synergy that produces novel statistical measures for sequence comparison, Bioinformatics, 2008, doi: 10.1093/bioinformatics/btn436.

12. Qi Dai*, Tianming Wang. Comparison study on k-word statistical measures for protein: from sequence to 'sequence space'. BMC Bioinformatics, 2008, revised.

13. Qi Dai*, Tianming Wang. Use of linear regression model to compare RNA secondary structures, Journal of Theoretical Biology, 2008, 253(4):854-60

14. Qi Dai*, Tianming Wang. Use of statistical measures for analyzing RNA secondary structures, Journal of Computational Chemistry, 2008, 29: 1292-1305.

15. Yuhua Yao, Qi Dai, Xu-Ying Nan, Ping-An He, Zuo-Ming Nie, Song-Ping Zhou, Yao-Zhou Zhang. Analysis of similarity/dissimilarity of DNA sequences based on a class of 2D graphical representation , Journal of Computational Chemistry, 2008, 29: 1632-1639.

16. Yuhua Yao, Qi Dai, Chun Li, Ping-An He, Xu-Ying Nan, Yao-Zhou Zhang. Analysis of similarity/dissimilarity of DNA sequences based on a class of 2D graphical representation , Proteins: Structure, Function, and Bioinformatics, 2008, 10.1002/prot.22110.

17. Qi Dai*, Xiaoqing Liu, Tianming Wang. C(i,j) matrix: A better numerical characterization for graphical representations of biological sequences, Journal of Theoretical Biology, 2007, 247: 103-109.

18. Qi Dai*, Xiaoqing Liu, Tianming Wang, Vukicevic, Damir. Linear regression model of DNA sequences and its application, Journal of Computational Chemistry, 2007, 28: 1434-1445.

19. Qi Dai*, Xiaoqing Liu, Tianming Wang. Analysis of protein sequences and their secondary structures based on transition matrices. Journal of Molecular Structure-THEOCHEM, 2007, 803: 115-122.

20. Qi Dai*, Xiaoqing Liu, Tianming Wang. Numerical characterization of DNA sequences based on the k-step Markov chain transition probability . Journal of Computational Chemistry, 2006, 27: 1830-1842.

21. Qi Dai*, Xiaoqing Liu, Tianming Wang. A novel 2D graphical representation of DNA sequences and its application. Journal of Molecular Graphics & Modelling, 2006, 25: 340-344.

22. Xiaoqing Liu, Qi Dai, Zhilong Xiu, Tianming Wang, PNN-curve: A new 2D graphical representation of DNA sequences and its application. Journal of Theoretical Biology, 2006, 243: 555-561.