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Publications during 2019

1. C.L. Quan, F. Gao (2019). Quantitative analysis and assessment of base composition asymmetry and gene orientation bias in bacterial genomes. FEBS Letters, 10.1002/1873-3468.13374.[PubMed]

Publications during 2018

1. H. Luo, F. Gao as co-first author in BIG Data Center Members (2018). Database Resources of the BIG Data Center in 2018. Nucleic Acids Res, 46(Database issue):D14–D20.[PubMed]

2. H. Luo, C.L. Quan, C. Peng, F. Gao (2018). Recent development of Ori-Finder system and DoriC database for microbial replication origins. Briefings in Bioinformatics, 10.1093/bib/bbx174.[PubMed]

3. Z.K. Yang, F. Gao (2018). The systematic analysis of ultraconserved genomic regions in the budding yeast. Bioinformatics, 34(3):361-366.[PubMed]

4. F. Gao (2018). Recent developments of software and database in microbial genomics and functional genomics. Briefings in Bioinformatics, 10.1093/bib/bby013.[PubMed]

5. Z.K. Yang, H. Luo, Y. Zhang, B. Wang, F. Gao (2018). Recombinational DSBs-intersected genes converge on specific disease- and adaptability-related pathways. Bioinformatics, 10.1093/bioinformatics/bty376

6. H. Luo, F. Gao (2018). DoriC 10.0: an updated database of replication origins in prokaryotic genomes including chromosomes and plasmids. Nucleic Acids Research, 10.1093/nar/gky1014

Publications during 2017

1. W. Wei#, F. Gao#, M.Z. Du, H.L. Hua, J. Wang, F.B. Guo (2017). Zisland Explorer: detect genomic islands by combining homogeneity and heterogeneity properties. Brief Bioinform, 18(3):357-366.[PubMed]

2. G. Zhang, F. Gao (2017). Quantitative analysis of correlation between AT and GC biases among bacterial genomes. PLoS One, 12(2): e0171408.[PubMed]

3. Y. Lin, F.Z. Zhang, K. Xue, Y.Z. Gao, F.B. Guo (2017). Identifying bacterial essential genes based on a feature-integrated method. IEEE/ACM Trans Comput Biol Bioinform, 10.1109/TCBB.2017.2669968.[PubMed]

4. N. Jia, M.Z. Ding, Y. Zou, F. Gao, Y.J. Yuan (2017). Comparative genomics and metabolomics analyses of the adaptation mechanism in Ketogulonicigenium vulgare-Bacillus thuringiensis consortium. Sci Rep, 7:46759.[PubMed]

5. Xie, Z.X., Li, B.Z., Mitchell, L.A., Wu, Y., Qi, X., Jin, Z., Jia, B., Wang, X., Zeng, B.X., Liu, H.M., Wu, X.L., Feng, Q., Zhang, W.Z., Liu, W., Ding, M.Z., Li, X., Zhao, G.R., Qiao, J.J., Cheng, J.S., Zhao, M., Kuang, Z., Wang, X., Martin, J.A., Stracquadanio, G., Yang, K., Bai, X., Zhao, J., Hu, M.L., Lin, Q.H., Zhang, W.Q., Shen, M.H., Chen, S., Su, W., Wang, E.X., Guo, R., Zhai, F., Guo, X.J., Du, H.X., Zhu, J.Q., Song, T.Q., Dai, J.J., Li, F.F., Jiang, G.Z., Han, S.L., Liu, S.Y., Yu, Z.C., Yang, X.N., Chen, K., Hu, C., Li, D.S., Jia, N., Liu, Y., Wang, L.T., Wang, S., Wei, X.T., Fu, M.Q., Qu, L.M., Xin, S.Y., Liu, T., Tian, K.R., Li, X.N., Zhang, J.H., Song, L.X., Liu, J.G., Lv, J.F., Xu, H., Tao, R., Wang, Y., Zhang, T.T., Deng, Y.X., Wang, Y.R., Li, T., Ye, G.X., Xu, X.R., Xia, Z.B., Zhang, W., Yang, S.L., Liu, Y.L., Ding, W.Q., Liu, Z.N., Zhu, J.Q., Liu, N.Z., Walker, R., Luo, Y., Wang, Y., Shen, Y., Yang, H., Cai, Y., Ma, P.S., Zhang, C.T., Bader, J.S., Boeke, J.D., and Yuan, Y.J. (2017). "Perfect" designer chromosome V and behavior of a ring derivative. Science, 355(6329).[PubMed]

6. Wu, Y., Li, B.Z., Zhao, M., Mitchell, L.A., Xie, Z.X., Lin, Q.H., Wang, X., Xiao, W.H., Wang, Y., Zhou, X., Liu, H., Li, X., Ding, M.Z., Liu, D., Zhang, L., Liu, B.L., Wu, X.L., Li, F.F., Dong, X.T., Jia, B., Zhang, W.Z., Jiang, G.Z., Liu, Y., Bai, X., Song, T.Q., Chen, Y., Zhou, S.J., Zhu, R.Y., Gao, F., Kuang, Z., Wang, X., Shen, M., Yang, K., Stracquadanio, G., Richardson, S.M., Lin, Y., Wang, L., Walker, R., Luo, Y., Ma, P.S., Yang, H., Cai, Y., Dai, J., Bader, J.S., Boeke, J.D., and Yuan, Y.J. (2017). Bug mapping and fitness testing of chemically synthesized chromosome X. Science, 355(6329).[PubMed]

7. N. Jia, M.Z. Ding, H. Luo, F. Gao, Y.J. Yuan (2017). Complete genome sequencing and antibiotics biosynthesis pathways analysis of Streptomyces lydicus 103. Sci Rep, 7:44786.[PubMed]

8. F.B. Guo, C. Dong, H.L. Hua, S. Liu, H. Luo, H.W. Zhang, Y.T. Jin, K.Y. Zhang (2017). Accurate prediction of human essential genes using only nucleotide composition and association information. Bioinformatics, 33(12):1758-1764.[PubMed]

9. C. Peng, Y. Lin, H. Luo, F. Gao (2017). A Comprehensive Overview of Online Resources to Identify and Predict Bacterial Essential Genes. Front Microbiol, 8:2331.[PubMed]

Publications during 2016

1. F. Gao, ed. (2016). DNA Replication Origins in Microbial Genomes. Lausanne: Frontiers Media, ISBN: 978-2-88919-779-8

2. N. Jia, M.Z. Ding, J. Du, C.H. Pan, G. Tian, J.D. Lang, J.H. Fang, F. Gao, Y.J. Yuan (2016). Insights into mutualism mechanism and versatile metabolism of Ketogulonicigenium vulgare Hbe602 based on comparative genomics and metabolomics studies. Sci Rep, 6:23068.[PubMed]

3. N. Jia, M.Z. Ding, F. Gao, Y.J. Yuan (2016). Comparative genomics analysis of the companion mechanisms of Bacillus thuringiensis Bc601 and Bacillus endophyticus Hbe603 in bacterial consortium. Sci Rep, 6:28794.[PubMed]

4. F. Gao (2016). Editorial: DNA Replication Origins in Microbial Genomes. Front Microbiol, 6: 1545.[PubMed]

5. N. Jia, M.Z. Ding, Y.Z. Du, S. Feng, F. Gao, Y.J. Yuan (2016). Complete Genome Sequence of the Industrial Bacterium Ketogulonicigenium vulgare SKV. Genome Announc, 4(6), e01426-16.[PubMed]

Publications during 2015

1. F. Gao, H. Luo, C.T. Zhang, R. Zhang (2015). Book chapter: "Gene Essentiality Analysis Based on DEG 10, an Updated Database of Essential Genes.". Methods in Molecular Biology, 1279:219-33.[PubMed]

2. C. Peng, H. Luo, X. Zhang, F. Gao (2015). Recent advances in the genome-wide study of DNA replication origins in yeast. Front Microbiol, 6:117.[PubMed]

3. C.T. Zhang (2015). Editorial: Z-curve Applications in Genome Analysis. Curr Genomics, 15(2):77.[PubMed]

4. F. Gao (2015). Bacteria may have multiple replication origins. Front Microbiol, 6, 324.[PubMed]

5. C. Zhang, H. Luo, F. Gao, C.T. Zhang, R. Zhang (2015). A reduction in both visceral and subcutaneous fats contributes to increased adiponectin by lifestyle intervention in the Diabetes Prevention Program. Acta Diabetol, 52(3):625-8.[PubMed]

6. F. Gao, H. Luo, Z. Fu, C. T. Zhang, R. Zhang (2015). Exome sequencing identifies novel ApoB loss-of-function mutations causing hypobetalipoproteinemia in type 1 diabetes. Acta Diabetol, 52(3), 531-537.[PubMed]

7. C. Zhang, F. Gao, H. Luo, C.T. Zhang, R. Zhang (2015). Differential response in levels of high-density lipoprotein cholesterol to one-year metformin treatment in prediabetic patients by race/ethnicity. Cardiovasc Diabetol, 14:79.[PubMed]

8. Z.G. Hua, Y. Lin, Y.Z. Yuan, D.C. Yang, W. Wei, F.B. Guo (2015). ZCURVE 3.0: identify prokaryotic genes with higher accuracy as well as automatically and accurately select essential genes. Nucleic Acids Res, 43(W1):W85-90.[PubMed]

9. X. Zhang,C. Peng, G. Zhang, F. Gao (2015). Comparative analysis of essential genes in prokaryotic genomic islands. Sci Rep, 5:12561.[PubMed]

10. N. Jia, J. Du, M. Z. Ding, F. Gao, Y. J. Yuan (2015). Genome Sequence of Bacillus endophyticus and Analysis of Its Companion Mechanism in the Ketogulonigenium vulgare-Bacillus Strain Consortium. PLoS One, 6;10(8):e0135104.[PubMed]

11. C. Peng, F. Gao (2015). Protein localization analysis of essential genes in prokaryotes. Sci Rep, 4:6001.[PubMed]

12. H. Luo, F. Fao, Y. Lin (2015). Evolutionary conservation analysis between the essential and nonessential genes in bacterial genomes. Sc. Rep, 5, 13210.[PubMed]

13. H. Huang, C.C. Song, Z. Yang, Y. Dong, Y. Hu, F. Gao (2015). Identification of the replication origins from Cyanothece ATCC 51142 and their interactions with the DnaA protein: from in silico to in vitro studies. Front Microbiol, 6, 1370.[PubMed]

Publications during 2014

1. H. Luo, Y. Lin, F. Gao, C.T. Zhang, R. Zhang (2014). DEG 10, an update of the Database of Essential Genes that includes both protein-coding genes and non-coding genomic elements. Nucleic Acids Res, 42(Database issue):D574-80.[PubMed]

2. R. Zhang, C.T. Zhang (2014). A Brief Review: The Z-curve Theory and its Application in Genome Analysis. Curr Genomics, 15(2):78-94.[PubMed]

3. F.B. Guo, Y. Lin, L.L. Chen (2014). Recognition of Protein-coding Genes Based on Z-curve Algorithms. Curr Genomics, 15(2):95-103.[PubMed]

4. F. Gao (2014). Recent Advances in the Identification of Replication Origins Based on the Z-curve Method. Curr Genomics, 15(2), 104-112.[PubMed]

5. R. Zhang, H.Y. Ou, F. Gao, H. Luo (2014). Identification of Horizontally-transferred Genomic Islands and Genome Segmentation Points by Using the GC Profile Method. Curr Genomics, 15(2):113-21.[PubMed]

6. H. Huang, Y. Dong, Z.L. Yang, H. Luo, X. Zhang, F. Gao (2014). Complete Sequence of pABTJ2, a Plasmid from A. baumannii MDR-TJ, Carrying Many Phage-like Elements. Genomics Proteomics Bioinformatics, 12(4):172-7.[PubMed]

7. H. Luo, C.T. Zhang, F. Gao (2014). Ori-Finder 2, an integrated tool to predict replication origins in the archaeal genomes. Front Microbiol, 5:482.[PubMed]

Publications during 2013

1. F. Gao, H. Luo, C.T. Zhang (2013). DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes. Nucleic Acids Res, 41(Database issue):D90-3.[PubMed]

2. C.T. Zhang (2013). A novel triangle mapping technique to study the h-index based citation distribution. Sci Rep, 3:1023.[PubMed]

3. C.T. Zhang (2013). The h'-index, effectively improving the h-index based on the citation distribution. PLoS One, 8(4):e59912.[PubMed]

4. Z.G. Yang, C.T. Zhang (2013). A proposal for a novel impact factor as an alternative to the JCR impact factor. Sci Rep, 3:3410.[PubMed]

5. B.L. Hao, C.T Zhang, Y.X. Li, H. Li, L.P. Wei, M. Kanehisa, L.H Lai, R.S Chen, N. Rajewsky, M.Q. Zhang, J.D. Han, R. Jiang, X.G. Zhang, Y.D Li (2013). Advanced topics in bioinformatics and computational biology. Basics of Bioinformatics, 369-95

Publications during 2012

1. F. Gao#, Y. Lin#, R.R. Zhang (2012). RNA-DNA differences are rarer in proto-oncogenes than in tumor suppressor genes. Sci Rep, 2:245.[PubMed]

2. F. Gao, H. Luo, C.T. Zhang (2012). DeOri: a database of eukaryotic DNA replication origins. Bioinformatics, 28(11):1551-2.[PubMed]

3. Z.G. Yang, F. Gao, C.T. Zhang (2012). Comparison of journal self-citation rates between some Chinese and non-Chinese international journals. PLoS ONE, 7(11):e49001.[PubMed]

4. H. Huang, Z.L. Yang, X.M. Wu, Y. Wang, Y.J. Liu, H. Luo, X. Lv, Y.R. Gan, S.D. Song, F. Gao (2012). Complete genome sequence of Acinetobacter baumannii MDR-TJ and insights into its mechanism of antibiotic resistance. J Antimicrob Chemother, 67, 2825-2832.[PubMed]

Publications before 2012

1. F. Gao, Y. Wang, Y.J. Liu, X.M. Wu, X. Lv, Y.R. Gan, S.D. Song, H. Huang (2011). Genome sequence of Acinetobacter baumannii MDR-TJ. J Bacteriol, 193(9):2365-6.[PubMed]

2. F. Gao, R. Zhang (2011). Enzymes are enriched in bacterial essential genes. PLoS One, 6(6):e21683.[PubMed]

3. Y. Lin, R. Zhang (2011). Putative essential and core-essential genes in Mycoplasma genomes. Sci Rep, 1:53.[PubMed]

4. Y. Lin, F. Gao, C.T. Zhang (2010). Functionality of essential genes drives gene strand-bias in bacterial genomes. Biochem Biophys Res Commun, 396(2):472-6.[PubMed]

5. R. Zhang, Y. Lin (2009). DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. Nucleic Acids Res, 37(Database issue):D455-8.[PubMed]

6. C.T. Zhang (2009). A proposal for calculating weighted citations based on author rank. EMBO Rep, 10(5):416-7.[PubMed]

7. C.T. Zhang (2009). The e-index, complementing the h-index for excess citations. PLoS One, 4(5):e5429.[PubMed]

8. C.T. Zhang (2009). Relationship of the h-index, g-index, and e-index. J Am Soc Inf Sci Tech, 61(3), 625-8

9. C.T. Zhang, R. Zhang (2008). Gene essentiality analysis based on DEG, a database of essential genes. Methods Mol Biol, 416:391-400.[PubMed]

10. R. Zhang, Y. Lin, C.T. Zhang (2008). Greglist, a database listing potential G-quadruplex regulated genes. Nucleic Acids Res, 36(Database issue):D372-6.[PubMed]

11. R. Zhang, C.T. Zhang (2008). Accurate localization of the integration sites of two genomic islands at single-nucleotide resolution in the genome of Bacillus cereus ATCC 10987. Comp Funct Genomics, 451930.[PubMed]

12. F. Gao, C.T. Zhang (2008). Ori-Finder: a web-based system for finding oriCs in unannotated bacterial genomes. BMC Bioinformatics, 9:79.[PubMed]

13. W.X. Zheng, C.T. Zhang (2008). Biological Implications of Isochore Boundaries in the Human Genome. J Biomol Struct Dyn, 25(4):327-36.[PubMed]

14. F. Gao, C.T. Zhang (2008). Origins of replication in Sorangium cellulosum and Microcystis aeruginosa. DNA Res, 15(3):169-71.[PubMed]

15. F. Gao, C.T. Zhang (2008). Prediction of replication time zones at single nucleotide resolution in the human genome. FEBS Lett, 582(16):2441-4.[PubMed]

16. W.X. Zheng, C.T. Zhang (2008). Ultraconserved Elements Between the Genomes of the Plants Arabidopsis thaliana and Rice. J Biomol Struct Dyn, 26(1):1-8.[PubMed]

17. F. Gao, C.T. Zhang (2008). Origins of replication in Cyanothece 51142. Proc Natl Acad Sci U S A, 105(52):E125.[PubMed]

18. F. Gao, C.T. Zhang (2007). DoriC: a database of oriC regions in bacterial genomes. Bioinformatics, 23(14):1866-7.[PubMed]

19. F. B. Guo, C.T. Zhang (2006). ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes. BMC Bioinformatics, 7:9.[PubMed]

20. R. Zhang, C.T. Zhang (2006). The impact of comparative genomics on infectious disease research. Microbes Infect, 8(6):1613-22.[PubMed]

21. F. Gao, C.T. Zhang (2006). Isochore structures in the chicken genome. FEBS J, 273(8):1637-48.[PubMed]

22. F. Gao, C.T. Zhang (2006). GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences. Nucleic Acids Res, 34(Web Server issue):W686-91.[PubMed]

23. R. Zhang, C.T. Zhang (2005). Identification of replication origins in archaeal genomes based on the Z-curve method. Archaea, 1(5):335-46.[PubMed]

24. R. Zhang, C.T. Zhang (2005). Genomic islands in the Corynebacterium efficiens genome. Appl Environ Microbiol, 71(6):3126-30.[PubMed]

25. W.X. Zheng, L.L. Chen, H.Y. Ou, F. Gao, C.T. Zhang (2005). Coronavirus phylogeny based on a geometric approach. Mol Phylogenet Evol, 36(2):224-32.[PubMed]

26. C. T. Zhang, F. Gao and R. Zhang (2005). Segmentation algorithm for DNA sequences. Phys Rev E, 72(4 Pt 1):041917.[PubMed]

27. R. Zhang, H.Y. Ou, C.T. Zhang (2004). DEG: a database of essential genes. Nucleic Acids Res, 32(Database issue):D271-2.[PubMed]

28. C.T. Zhang, R. Zhang (2004). Isochore structures in the mouse genome. Genomics, 83(3):384-94.[PubMed]

29. H.Y. Ou, F.B. Guo, C.T. Zhang (2004). GS-Finder: a program to find bacterial gene start sites with a self-training method. Int J Biochem Cell Biol, 36(3):535-44.[PubMed]

30. R. Zhang, C.T. Zhang (2004). A systematic method to identify genomic islands and its applications in analyzing the genomes of Corynebacterium glutamicum and Vibrio vulnificus CMCP6 chromosome I. Bioinformatics, 20(5):612-22.[PubMed]

31. F. Gao, C.T. Zhang (2004). Comparison of various algorithms for recognizing short coding sequences of human genes. Bioinformatics, 20(5):673-81.[PubMed]

32. C.T. Zhang, R. Zhang (2004). A nucleotide composition constraint of genome sequences. Comput Biol Chem, 28(2):149-53.[PubMed]

33. R. Zhang, C.T. Zhang (2004). Identification of replication origins in the genome of the methanogenic archaeon, Methanocaldococcus jannaschii. Extremophiles, 8(3):253-8.[PubMed]

34. R. Zhang, C.T. Zhang (2004). Isochore structures in the genome of the plant Arabidopsis thaliana. J Mol Evol, 59(2):227-38.[PubMed]

35. C.T. Zhang, R. Zhang (2004). Genomic islands in Rhodopseudomonas palustris. Nat Biotechnol, 22(9):1078-9.[PubMed]

36. F.B. Guo, J. Wang, C.T. Zhang (2004). Gene recognition based on nucleotide distribution of ORFs in a hyper-thermophilic crenarchaeon, Aeropyrum pernix K1. DNA Res, 11(6):361-70.[PubMed]

37. F.B. Guo, H.Y. Ou, CT Zhang (2003). ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes. Nucleic Acids Res, 31(6):1780-9.[PubMed]

38. H.Y. Ou, F.B. Guo, C.T. Zhang (2003). Analysis of nucleotide distribution in the genome of Streptomyces coelicolor A3 (2) using the Z curve method. FEBS Lett, 540(1-3):188-94.[PubMed]

39. R. Zhang, C.T. Zhang (2003). Multiple replication origins of the archaeon Halobacterium species NRC-1. Biochem Biophys Res Commun, 302(4):728-34.[PubMed]

40. C.T. Zhang, R. Zhang, H.Y. Ou (2003). The Z curve database: a graphic representation of genome sequences. Bioinformatics, 19(5):593-9.[PubMed]

41. L.L. Chen, C.T. Zhang (2003). Seven GC-rich microbial genomes adopt similar codon usage patterns regardless of their phylogenetic lineages. Biochem Biophys Res Commun, 306(1):310-7.[PubMed]

42. L.L. Chen, H.Y. Ou, R. Zhang, C.T. Zhang (2003). ZCURVE_CoV: a new system to recognize protein coding genes in coronavirus genomes, and its applications in analyzing SARS-CoV genomes. Biochem Biophys Res Commun, 307(2):382-8.[PubMed]

43. C.T. Zhang, R. Zhang (2003). Q9, a content-balancing accuracy index to evaluate algorithms of protein secondary structure prediction. Int J Biochem Cell Biol, 35(8):1256-62.[PubMed]

44. L.L. Chen, C.T. Zhang (2003). Gene recognition from questionable ORFs in bacterial and archaeal genomes. J Biomol Struct Dyn, 21(1):99-109.[PubMed]

45. F. Gao, H.Y. Ou, L.L. Chen, W.X. Zheng, C.T. Zhang (2003). Prediction of proteinase cleavage sites in polyproteins of coronaviruses and its applications in analyzing SARS‐CoV genomes. FEBS Lett, 553(3):451-6.[PubMed]

46. C.T. Zhang, R. Zhang (2003). An isochore map of the human genome based on the Z curve method. Gene, 317(1-2):127-35.[PubMed]

47. S.Y. Wen, C.T. Zhang (2003). Identification of isochore boundaries in the human genome using the technique of wavelet multiresolution analysis. Biochem Biophys Res Commun, 311(1):215-22.[PubMed]

48. R. Zhang, C.T. Zhang (2003). Identification of genomic islands in the genome of Bacillus cereus by comparative analysis with Bacillus anthracis. Physiol Genomics, 16(1):19-23.[PubMed]

49. C.T. Zhang, J. Wang, R. Zhang (2002). Using a Euclid distance discriminant method to find protein coding genes in the yeast genome. Comput Chem, 26(3):195-206.[PubMed]

50. Y.H. Wang, C.T. Zhang, P.X. Dong (2002). Recognizing shorter coding regions of human genes based on the statistics of stop codons. Biopolymers, 63(3):207-16.[PubMed]

51. Z.P. Feng, C.T. Zhang (2002). A graphic representation of protein sequence and predicting the subcellular locations of prokaryotic proteins. Int J Biochem Cell Biol, 34(3):298-307.[PubMed]

52. C.T. Zhang, R. Zhang (2002). Evaluation of gene-finding algorithms by a content-balancing accuracy index. J Biomol Struct Dyn, 19(6):1045-52.[PubMed]

53. R. Zhang, C.T. Zhang (2002). Single replication origin of the archaeon Methanosarcina mazei revealed by the Z curve method. Biochem Biophys Res Commun, 297(2):396-400.[PubMed]

54. Z.D. Zhang, Z.R. Sun, C.T. Zhang (2001). A new approach to predict the helix/strand content of globular proteins. J Theor Biol, 208(1):65-78.[PubMed]

55. Z.P. Feng, C.T. Zhang (2001). Prediction of the subcellular location of prokaryotic proteins based on the hydrophobicity index of amino acids. Int J Biol Macromol, 28(3):255-61.[PubMed]

56. C.T. Zhang, R. Zhang (2001). A refined accuracy index to evaluate algorithms of protein secondary structure prediction. Proteins, 43(4):520-2.[PubMed]

57. J. Wang, C.T. Zhang (2001). Analysis of the codon usage pattern in the Vibrio cholerae genome. J Biomol Struct Dyn, 18(6):872-80.[PubMed]

58. J. Wang, C.T. Zhang (2001). Identification of protein‐coding genes in the genome of Vibrio cholerae with more than 98% accuracy using occurrence frequencies of single nucleotides. Eur J Biochem, 268(15):4261-8.[PubMed]

59. C.T. Zhang, J. Wang, R. Zhang (2001). A novel method to calculate the G+ C content of genomic DNA sequences. J Biomol Struct Dyn, 19(2):333-41.[PubMed]

60. Z.P. Feng, C.T. Zhang (2000). Prediction of membrane protein types based on the hydrophobic index of amino acids. J Protein Chem, 19(4):269-75.[PubMed]

61. C.T. Zhang, R. Zhang (2000). S curve, a graphic representation of protein secondary structure sequence and its applications. Biopolymers, 53(7):539-49.[PubMed]

62. C.T. Zhang, J. Wang (2000). Recognition of protein coding genes in the yeast genome at better than 95% accuracy based on the Z curve. Nucleic Acids Res, 28(14):2804-14.[PubMed]

63. C.T. Zhang, R. Zhang (1999). Skewed distribution of protein secondary structure contents over the conformational triangle. Protein Eng, 12(10):807-10.[PubMed]

64. W.S. Bu, Z.P. Feng, Z.D. Zhang, C.T. Zhang (1999). Prediction of protein (domain) structural classes based on amino‐acid index. Eur J Biochem, 266(3):1043-9.[PubMed]

65. C.T. Zhang, R. Zhang (1999). A quadratic discriminant analysis of protein structure classification based on the Helix/Strand content. J Theor Biol, 201(3):189-99.[PubMed]

66. C.T. Zhang, Z.S. Lin, Z.D. Zhang, M. Yan (1998). Prediction of the helix/strand content of globular proteins based on their primary sequences.. Protein Eng, 11(11):971-9.[PubMed]

67. M. Yan, Z.S. Lin, C.T. Zhang (1998). A new fourier transform approach for protein coding measure based on the format of the Z curve.. Bioinformatics, 14(8):685-90.[PubMed]

68. C.T. Zhang, R. Zhang (1998). A new criterion to classify globular proteins based on their secondary structure contents. Bioinformatics, 14(10):857-865.[PubMed]

69. K.C. Chou, W.M. Liu, G.M. Maggiora, C.T. Zhang (1998). Prediction and classification of domain structural classes. Proteins, 31(1):97-103.[PubMed]

70. C.T. Zhang, Z.S. Lin, M. Yan, R. Zhang (1998). A novel approach to distinguish between intron-containing and intronless genes based on the format of Z curves. J Theor Biol, 192(4):467-73.[PubMed]

71. C.T. Zhang, Z.D. Zhang, Z.M. He (1998). Prediction of the secondary structure contents of globular proteins based on three structural classes. J Protein Chem, 17(3):261-72.[PubMed]

72. C.T. Zhang, R. Zhang (1998). A new quantitative criterion to distinguish between α/β and α+ β proteins (domains). FEBS Lett, 440(1-2):153-7.[PubMed]

73. C.T. Zhang, K.C. Chou (1997). Prediction of β-turns in proteins by 1-4 and 2-3 correlation model. Biopolymers, 41(6), 673-702

74. K.C. Chou, C.T. Zhang, G.M. Maggiora (1997). Disposition of amphiphilic helices in heteropolar environments. Proteins, 28(1):99-108.[PubMed]

75. C.T. Zhang (1997). Relations of the numbers of protein sequences, families and folds. Protein Eng, 10(7):757-61.[PubMed]

76. C.T. Zhang (1997). A symmetrical theory of DNA sequences and its applications. J Theor Biol, 187(3):297-306.[PubMed]

77. K.C. Chou, C.T. Zhang, D.W. Elrod (1996). Do “antisense proteins” exist?. J Protein Chem, 15(1):59-61.[PubMed]

78. C.T. Zhang, K.C. Chou (1996). Beat motion in DNA double helix and a mechanism of energy exchange between its two strands with microwave frequency. Chemical physics, 206(3), 271-277

79. Z.R. Sun, C.T. Zhang, F.H. Wu, L.W. Peng (1996). A vector projection method for predicting supersecondary motifs. J Protein Chem, 15(8):721-9.[PubMed]

80. C.T. Zhang, Z. Zhang, Z. He (1996). Prediction of the secondary structure content of globular proteins based on structural classes. J Protein Chem, 15(8):775-86.[PubMed]

81. K.C. Chou, C.T. Zhang (1995). Prediction of protein structural classes. Crit Rev Biochem Mol Biol, 30(4):275-349.[PubMed]

82. C.T. Zhang (1995). Diagrammatic representation of base composition in DNA sequences. Visualizing Biological Information, 84-95

83. K.C. Chou, C.T. Zhang, F.J. Kézdy, R.A. Poorman (1995). A vector projection method for predicting the specificity of GalNAc‐transferase. Proteins, 21(2), 118-126.[PubMed]

84. C.T. Zhang, K.C. Chou (1995). The nonlinear stretching model of hydrogen bonds and local self-fluctuation of base rotation in DNA. Chemical Physics, 191(1-3), 17-23

85. C.T. Zhang, K.C. Chou (1995). Monte Carlo simulation studies on the prediction of protein folding types from amino acid composition. II. Correlative effect. J Protein Chem, 14(4):251-8.[PubMed]

86. C.T. Zhang, K.C. Chou, G.M. Maggiora (1995). Predicting protein structural classes from amino acid composition: application of fuzzy clustering. Protein Eng, 8(5):425-35.[PubMed]

87. C.T. Zhang, K.C. Chou (1995). An eigenvalue-eigenvector approach to predicting protein folding types. J Protein Chem, 14(5):309-26.[PubMed]

88. C.T. Zhang, K.C. Chou (1995). An analysis of protein folding type prediction by seed-propagated sampling and jackknife test. J Protein Chem, 14(7):583-93.[PubMed]

89. K.C. Chou, C.T. Zhang, G.M. Maggiora (1994). Solitary wave dynamics as a mechanism for explaining the internal motion during microtubule growth. Biopolymers, 34(1):143-53.[PubMed]

90. C.T. Zhang, K.C. Chou (1994). An alternate-subsite-coupled model for predicting HIV protease cleavage sites in proteins. Protein Eng, 7(1):65-73.[PubMed]

91. R. Zhang, C.T. Zhang (1994). Z curves, an intutive tool for visualizing and analyzing the DNA sequences. J Biomol Struct Dyn, 11(4):767-82.[PubMed]

92. B. Mao, K.C. Chou, C.T. Zhang (1994). Protein folding classes: a geometric interpretation of the amino acid composition of globular proteins. Protein Eng, 7(3):319-30.[PubMed]

93. C.T. Zhang, Y. Zhan (1994). Analysis on the distribution of bases in 1487 human protein coding sequences. J Theor Biol, 167(2):161-6.[PubMed]

94. C.T. Zhang, K.C. Chou (1994). A graphic approach to analyzing codon usage in 1562 Escherichia coli protein coding sequences. J Mol Biol, 238(1):1-8.[PubMed]

95. K.C. Chou, C.T. Zhang (1994). Predicting protein folding types by distance functions that make allowances for amino acid interactions. J Biol Chem, 269(35):22014-20.[PubMed]

96. J.J. Chou, C.T. Zhang (1993). A joint prediction of the folding types of 1490 human proteins from their genetic codons. J Theor Biol, 161(2):251-62.[PubMed]

97. K.C. Chou, C.T. Zhang (1993). A new approach to predicting protein folding types. J Protein Chem, 12(2):169-78.[PubMed]

98. C.T. Zhang, K.C. Chou (1993). Graphic analysis of codon usage strategy in 1490 human proteins. J Protein Chem, 12(3):329-35.[PubMed]

99. K.C. Chou, C.T. Zhang, F.J. Kézdy (1993). A vector projection approach to predicting HIV protease cleavage sites in proteins. Proteins, 16(2):195-204.[PubMed]

100. K.C. Chou, C.T. Zhang (1993). Studies on the specificity of HIV protease: an application of Markov chain theory. J Protein Chem, 12(6):709-24.[PubMed]

101. C.T. Zhang, K.C. Chou (1992). Monte Carlo simulation studies on the prediction of protein folding types from amino acid composition. Biophys J, 63(6):1523-9.[PubMed]

102. C.T. Zhang, K.C. Chou (1992). An optimization approach to predicting protein structural class from amino acid composition. Protein Sci, 1(3), 401-408.[PubMed]

103. K.C. Chou, C.T. Zhang (1992). A correlation‐coefficient method to predicting protein‐structural classes from amino acid compositions. Eur J Biochem, 207(2):429-3.[PubMed]

104. K.C. Chou, C.T. Zhang (1992). Diagrammatization of codon usage in 339 human immunodeficiency virus proteins and its biological implication. AIDS Res Hum Retroviruses, 8(12):1967-76.[PubMed]

105. W.G. Han, C.T. Zhang (1991). A theory of non-linear stretch vibrations of hydrogen bonds. Journal of Physics: Condensed Matter, 3(1), 27

106. G.F. Zhou, C.T. Zhang (1991). A short review on the nonlinear motion in DNA. Physica Scripta, 43(3), 347-352

107. C.T. Zhang, R. Zhang (1991). Diagrammatic representation of the distribution of DNA bases and its applications. Int J Biol Macromol, 13(1):45-9.[PubMed]

108. C.T. Zhang, Z.X. Shang (1991). The study of stacking energy for natural DNA sequences. J Theor Biol, 149(2):257-63.[PubMed]

109. C.T. Zhang, R. Zhang (1991). Analysis of distribution of bases in the coding sequences by a digrammatic technique. Nucleic Acids Res, 19(22):6313-7.[PubMed]

110. C.T. Zhang (1990). Equations between frequencies of amino acids in organisms. J Theor Biol, 142(2):281-4.[PubMed]

111. C.T. Zhang (1990). Solitary-wave excitation of hydrogen-bond stretching in deoxyribonucleic acid. Journal of Physics, 8259-8268

112. C.T. Zhang, G.F. Zhou (1990). Analysis of patterns of twist angles in DNA double helix. Int J Biol Macromol, 12(4):226-32.[PubMed]

113. C.T. Zhang, G.T. Ying (1989). Upper limit for the variances of some helical parameters in DNA double helix. Int J Biol Macromol, 11(1):9-12.[PubMed]

114. C.T. Zhang, G.F. Zhou (1989). Analysis of sequences of twist angles in DNA double helix. Int J Biol Macromol, 11(3):165-8.[PubMed]

115. C.T. Zhang, Y.Q. Cen (1989). The study of DNA sequences by their sequences of twist angles. J Theor Biol, 138(4):457-65.[PubMed]

116. C.T. Zhang (1989). Harmonic and subharmonic resonances of microwave absorption in DNA. Phys Rev A Gen Phys, 40(4):2148-2153.[PubMed]

117. C.T. Zhang (1987). Soliton excitations in deoxyribonucleic acid (DNA) double helices. Phys Rev A Gen Phys, 35(2):886-891.[PubMed]

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