REFERENCES

Papers in Computer Science:

1. S.-Y. Le, S.P. Jiang and W.X. Wu: Hydration of the nucleic acid bases. Acta Biochemica et Biophysica Sinica (in Chinese), 13: 433--440, 1981.

2. S.P. Jiang, S.-Y. Le, and W.X. Wu: Interactions of $Na^{+}$ with the bases, base pair and duplexes (AT.GC, AT.CG) of the DNA. Acta Biochimica et Biophysica Sinica} (in Chinese), 13: 485--494, 1981.

3. W.X. Wu, S.P. Jiang and S.-Y. Le: An improved intermolecular interaction potential energy method. Acta Biochimica et Biophysica Sinica (in Chinese), 13: 495--502, 1981.

4. S.P. Jiang and S.-Y. Le: Computer simulation of canonical ensemble of dilute solution Monte-Carlo calculation of thermodynamic quantity of solution of adenine bases. J. Molecular Science (Fenzi Kexue Xuebao, in Chinese), 1: 35--42, 1981.

5. S.-Y. Le et al.: Monte-Carlo simulation of the nucleic acid base (cytosine) Hydration. KeXue TongBao (in English), 27: 1218--, 1982.

6. S.-Y. Le et al.: Recognition and interaction between codon and anticodon. J. Molecular Science (Fenzi Kexue Xuebao, in Chinese), 2: 87--96, 1982.

7. S.P. Jiang and S.-Y. Le: Applications of computer in molecular biology. Nature (in chinese), 6: 7--8, 1982.

8. S.P. Jiang and S.-Y. Le: Microcomputer programs for nucleic acid sequences handling. Progress in Biochemistry and Biophysics} (in Chinese), 45: 71--, 1982.

9. S.P. Jiang, W.X. Wu, S.-Y. Le et al.: Conformation and electronic structure of cyclic 3',5'-nucleotides. Journal of Molecular Science; Fenzi Kexue Xuebao (in English), 2: 49--54, 1982.

10. S.-Y. Le, S.P. Jiang and Ji-Ping Jia: Analyses of nucleic acid sequence data on Microcomputer. Progress in Biochemistry and Biophysics (in Chinese), 49: 64--65, 1983.

11. S.P. Jiang, W.X. Wu and S.-Y. Le et al.: Dimer stacking conformation of cyclic GMP. Journal of Structural Chemistry} (in Chinese), 2: 163--, 1983.

12. S.-Y. Le and S.P. Jiang: Storage and editing of nucleic acid sequence data by computer. KeXue TongBao (in English), 29: 1243--1246, 1984.

13. S.-Y. Le and S.P. Jiang: Study of the hydration of complementary base G-C, A-T in B-DNA molecule. Journal of Structural Chemistry (in Chinese), 2: 57--61, 1983.

14. S.P. Jiang, S.-Y. Le, et al.: Computer application for Molecular Biology in China. Life Chemistry (in Chinese), 3(2), 21--24, 1983.

15. S.-Y. Le and S.P. Jiang: Prediction for folding structure of the maximum base pairs of single-stranded RNA (DNA). KeXue TongBao (in English), 29: 1679--1684, 1984.

16. S.-Y. Le and S.P. Jiang: Prediction of restriction endonuclease recognition sites in DNA molecules. Acta Biochimica et Biophysica Sinica (in Chinese), 16: 159--164, 1984.

17. S.-Y. Le and S.P. Jiang: Management of nucleic sequence data by TRS-80(1) microcomputer. Acta Biochimica et Biophysica Sinica (in Chinese), 16: 363--369, 1984.

18. S.-Y. Le and S.P. Jiang: Computer manipulation for the assembly of DNA sequences. Acta Biochimica et Biophysica Sinica} (in Chinese), 16: 425--431, 1984.

19. S.-Y. Le, et al.: Secondary structure of 5.8s ribosomal RNA. Acta Biochimica et Biophysica Sinica (in Chinese), 17: 549--556, 1985.

20. S.-Y. Le, et al.: Relationship between secondary structure of the control region of mRNA initiation and translation efficiency. Acta Biochimica et Biophysica Sinica (in Chinese), 17: 664--672, 1985.

21. S.-Y. Le, et al.: Structural features of the nucleotide sequences of promoter sites recognized by E.coli RNA polymerase. Acta Biochimica et Biophysica Sinica (in Chinese), 17: 722--728, 1985.

22. S.-Y. Le and S.P. Jiang: Prediction of secondary structure for macromolecule RNAs. Acta Biophysica Sinica (in Chinese), 2: 78--84, 1986.

23. S.-W. Qian, S.-Y. Le, A.-B. Zhang and Z.-P. Li: The Programs for the Nucleic Acid Data Treatment on APPLE II Microcomputer. Chinese Biochemical Journal (in Chinese), 2: 75--82, 1986.

24. S.-Y. Le and S.P. Jiang: The folding and dynamic process of RNA. Acta Biophysica Sinica (in Chinese), 3: 227--231, 1987.

25. S.-Y. Le, K. Currey, R. Nussinov and Jacob V. Maizel: Studies of frequently recurring substructures in human alpha-like globe mRNA precursors. Computers and Biomedical Research, 20: 563--582, 1987.

26. S.-Y. Le, J.-H. Chen, K.M. Currey and Jacob V. Maizel: A program for predicting significant RNA secondary structures. Computer Applications in the Biosciences, 4: 153--159, 1988.

27. S.-Y. Le, J.-H. Chen, M.J. Braun, M.A. Gonda and Jacob V. Maizel: Stability of RNA stem-loop structure and distribution of non-random structure in the human immunodeficiency virus (HIV-1) Nucl. Acids Res., 16: 5153--5168, 1988.

28. S.-Y. Le, J.-H. Chen, R. Nussinov and Jacob V. Maizel: An improved secondary structure computation method and its application to intervening sequences in the human alpha-like globin mRNA precursors. Computer Applications in the Biosciences, 4: 337--344, 1988.

29. M.H. Malim, J. Hauber, S.-Y. Le, Jacob V. Maizel and B.R. Cullen:
The HIV-1 rev trans-activator acts through a structured target sequence to activate nuclear export of unspliced viral mRNA. Nature, 338: 254--257, 1989.

30. S.-Y. Le and Jacob V. Maizel: A method for assessing the statistical significance of RNA folding. J. of Theoretical Biology, 138: 495--510, 1989.

31. S.-Y. Le, J.-H. Chen, D. Chatterjee and Jacob V. Maizel, Jr.: Sequence divergence and open regions of RNA secondary structures in the envelope regions of the seventeen human immunodeficiency virus isolates. Nucleic Acids Research, 17: 3275--3288, 1989.

32. S.-Y. Le, J. Owens, R. Nussinov, J.-H. Chen, B. Shapiro and Jacob V. Maizel: RNA secondary structures: comparison and determination of frequently recurring substructures, Computer Applications in the Biosciences, 5: 205--210, 1989.

33. S.-Y. Le, J.-H. Chen and Jacob V. Maizel: Thermodynamic stability and statistical significance of potential stem-loop structures situated at the frameshift sites of retroviruses, Nuc. Acids Res. 17: 6143--6152, 1989.

34. S.-Y. Le, R. Nussinov and Jacob V. Maizel: Tree graphs of RNA secondary structures and their comparison, Computers and Biomedical Research, 22: 461--473, 1989.

35. S.M. Hanly, L.T. Rimsky, M.H. Malim, J.H. Kim, J. Hauber, S.-Y. Le, J.V. Maizel, B.R. Cullen and W.C. Greene: Comparison of the HTLV-1 Rex and HIV-1 Rev trans-regulatory proteins and their RNA response elements, Genes and Development, 3: 1534--1544, 1989.

36. M.H. Malim, S. Bohnlein, R. Fenrick, S.-Y. Le, J.V. Maizel and B.R. Cullen:
Functional comparison of the Rev trans-activators encoded by different primate immunodeficiency virus species, Proc. Natl. Acad. Sci. USA, 86: 8222--8226, 1989.

37. R. Fenrick, M.H. Malim, J. Hauber, S.-Y. Le}, J.V. Maizel and B.R. Cullen:
Functional analysis of the Tat trans-activator of the human immunodeficiency virus type 2, J. of Virology 63: 5006--5012, 1989.

38. S.-Y. Le, M.H. Malim, B.R. Cullen and J.V. Maizel: A highly conserved RNA folding region adjacent to the cleavage site of OMP/TMP in the envelope gene of primate immunodeficiency viruses, Nucl Acids Res, 18: 1613--1623, 1990.

39. J.-H. Chen, S.-Y. Le, B. Shapiro, K.M. Currey and J.V. Maizel: A computational procedure for assessing the significance of RNA secondary structure, Computer Applications in the Biosciences, 6: 7--18, 1990.

40. S.-Y. Le, J.-H. Chen and Jacob V. Maizel: Efficient searches for unusual folding regions in RNA sequences, Structure & Methods, V1: Human Genome Initiative & DNA Recombination (R.H. & M.H. Sarma eds), pp. 127--136, Adenine Press 1990.

41. Ruth Nussinov, B. Shapiro, S.-Y. Le and Jacob V. Maizel, Jr.: Speeding up the dynamic algorithm for planar RNA folding, Mathematical Biosciences, 100: 33--47, 1990.

42. S.-Y. Le, R. Nussinov and Jacob V. Maizel: Studies of local stability in histone, U-snRNA and globin precursor mRNAs around transcription termination sites. Computers Math. Applic. 20: No. 4--6, pp. 49--56, 1990.

43. L.S. Tiley, P.H. Brown, S.-Y. Le, J.V. Maizel, J.E. Clements and B.R. Cullen:
Visna virus encodes a post-transcriptional regulator of viral structural gene expression, Proc. Natl. Acad. Sci. USA, 87: 7497--7501, 1990.

44. S.-Y. Le and M. Zuker: Common structures of 5' noncoding RNA in enteroviruses and rhinoviruses: Thermodynamaical stability and statistical significance, Journal of Molecular Biology, 216: 729--741, 1990.

45. S.-Y. Le, J.-H. Chen and Jacob V. Maizel: Detection of unusual RNA folding regions in HIV and SIV sequences, Computer Applications in the Biosciences, 7: 51--55, 1991.

46. S.-Y. Le and M. Zuker: Predicting common foldings of homologous RNAs, Journal of Biomolecular Structure & Dynamics, 8: 1027--1044, 1991.

47. R. Nicholson, J. Pelletier, S.-Y. Le and N. Sonenberg:
Structural and functional analysis of the ribosome landing pad of polioviruses: in vivo translation studies. J. of Virology, 65: 5886--5894, 1991.

48. S.-Y. Le, B. Shapiro, J.-H. Chen, R. Nussinov and Jacob V. Maizel: RNA pseudoknots downstream of the frameshift sites of retroviruses: Genetic Analysis: Techniques and Application, 8: 191--205, 1991.

49. J.-H. Chen, S.-Y. Le, and Jacob V. Maizel: A procedure for RNA pseudoknot prediction. Computer Applications in the Biosciences, 8: 243--248, 1992.

50. S.-Y. Le, J.-H. Chen, N. Sonenberg, and Jacob V. Maizel: Conserved tertiary structure elements in the 5' untranslated region of human enteroviruses and rhinoviruses. Virology, 191: 858--866, 1992.

51. S.-Y. Le, J.-H. Chen, and Jacob V. Maizel: Identification of unusual RNA folding patterns encoded by bacteriophage T4 gene 60. Gene, 124: 21--28, 1993.

52. S.-Y. Le, J.-H. Chen, and Jacob V. Maizel:
Prediction of alternative RNA secondary structures based on fluctuating thermodynamic parameters. Nucl Acids Res, 21: 2173--2178, 1993.

53. S.-Y. Le, J.-H. Chen, N. Sonenberg, and Jacob V. Maizel: Conserved tertiary structure elements in the 5' nontranslated region of cardiovirus, aphthovirus and hepatitis A virus RNAs. Nucl Acids Res, 21: 2445--2451, 1993.

54. S.-Y. Le, N. Sonenberg, and Jacob V. Maizel: Distinct structural elements and internal entry of ribosomes in mRNA3 encoded by infectious bronchitis virus. Virology, 198: 405--411, 1994.

55. S.-Y. Le, N. Pattabiraman, and Jacob V. Maizel:
RNA tertiary structure of the HIV RRE domain II containing non-Watson-Crick base pairs GG and GA: Molecular modeling studies. Nucl Acids Res, 22: 3966--3976, 1994.

56. S.-Y. Le, N. Sonenberg, and Jacob V. Maizel: Unusual folding regions and ribosome landing pad within hepatitis C virus and pestivirus RNAs. Gene, 154: 137--143, 1995.

57. S.-Y. Le, K. Zhang and Jacob V. Maizel:
A method for predicting common structures of homologous RNAs. Computers and Biomedical Research, 28: 53--66, 1995.

58. C. Wang, S.-Y. Le, N. Ali and A. Siddiqui: An RNA pseudoknot is an essential structural element of the internal ribosome entry site located within the hepatitis C virus 5' noncoding region. RNA 1: 526--537, 1995.

59. S.-Y. Le, A. Siddiqui and Jacob V. Maizel: A common structural core in the internal ribosome entry sites of picornavirus, hepatitis C virus, and pestivirus. Virus Genes, 12: 135--147, 1996.

60. S.-Y. Le, and Jacob V. Maizel:
A common RNA structural motif involved in the internal initiation of translation of cellular mRNAs. Nucl Acid Res, 25: 362--369, 1997.

61. J. Bernstein, O. Sella, S.-Y. Le and O. Elroy-Stein:
PDGF2/c-sis mRNA leader contains a differentiation-linked internal ribosomal entry site (D-IRES). J. Biol. Chem., 272: 9356--9362, 1997.

62. S.-Y. Le, and Jacob V. Maizel:
Evolution of a common structural core in the internal ribosome entry sites of picornavirus. Virus Genes, 16: 25--38, 1998.

63. V. Pramodh, N. Pattabiraman, S.-Y. Le and Jacob V. Maizel: A molecular modeling study of antibiotics-RNA interactions: Application to HIV-1 Rev response element. J. Mol. Structure (TheoChem), 423: 125-136, 1998.

64. G. Akiri, O. Elroy-Stein, D. Nahari, Y. Finkelstein, S.-Y. Le, and B.Z. Levi:
The 5' Untranslated region (5'UTR) of vascular endothelial growth factor (VEGF) contains an internal ribosome entry site (IRES) and promoter activity. Oncogene, 17: 227-236, 1998.

65. S.-Y. Le, Jih-H. Chen, N. Pattabiraman and Jacob V. Maizel, Jr.: Ion-RNA interactions in the RNA pseudoknot of a ribosomal frameshifting site: Molecilar modeling studies. J. Biomolecular Structure and Dynamics, 16: 1-11, 1998.

66. S.-Y. Le, W.-m. Liu, and Jacob V. Maizel, Jr.: Phylogenetic evidence for the improved RNA higher-order structure in internal ribosome entry sequences of HCV and pestiviruses. Virus Genes, 17: 279-295, 1998.

67. Jih-H. Chen, S.-Y. Le, B. Shapiro and Jacob V. Maizel, Jr.: Optimization of an RNA folding algorithm for parallel architectures. Parallel Computing, 24: 1617-1634, 1998.

68. Sella, O., G. Gerlitz, S.-Y. Le and Elroy-Stein, O.:
Differentiation-induced internal translation of c-sis mRNA: Analysis of the cis elements and their differentiation-linked binding to the hnRNP C protein. Mol. Cell Biol. 19:(8) 5429-5440, 1999.

69. Jih-H. Chen, S.-Y. Le, and Jacob V. Maizel, Jr.:
Prediction of common secondary structures of RNAs: a genetic algorithm approach. Nucleic Acids Res 28:(4) 991-999, 2000.

70. A. Pozner, D. Goldenberg, V. Negreanu, S.-Y. Le, O. Elroy-Stein, D. Levanon, and Y. Groner:
Transcription-coupled translation control of AML1/RUNX1 is mediated by cap- and internal ribosome entry site-dependent mechanisms. Mol. Cell Biol. 20:(7) 2297-2307, 2000.

71. S. Chen, S.-Y. Le, D.L. Newton, J.V. Maizel, jr. and S.M. Rybak:
A gender-specific mRNA encoding a cytotoxic ribonuclease contains a 3' UTR of unusual length and structure. Nucleic Acids Res 28:(12) 2375-2382, 2000.

72. G. Collins, S.-Y. Le, and K. Zhang:
A new method for computing similarity between RNA structures. Proceedings of the 5th Joint Conference on Information Sciences, Atlantic City, NJ, vol. 2, pp. 761-765, 2000.

73. J. Yang, H. Bogerd, S.-Y. Le and B.R. Cullen:
The human endogenous retrovirus K Rev response element coincides with a conserved RNA folding region. RNA 6:1551-1564, 2000.

74. S.-Y. Le, W-m. Liu, J.-H Chen, and J.V. Maizel, Jr.:
Local thermodynamic stability scores are well represented by a noncentral student's t distribution. J. Theor. Biol. 210: 411-423, 2001.

75. J.V. Maizel, Jr. and S.-Y. Le: Computational discovery of important functional and structural features in mRNA sequences. Proceedings of the Atlantic Symposium on Computational Biology and Genome Information Systems & Technology. pp. 6-8, 2001.

76. S.-Y. Le, W-m. Liu, and J.V. Maizel, Jr.: Searching for gene regulatory elements related to the unusual folding regions in genome sequences. Proceedings of the 2001 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences. pp. 33-39, 2001.

77. G. Collins, S.-Y. Le, and K. Zhang:
A new algorithm for computing similarity between RNA structures. Information Sciences 139: 59-77, 2001.

78, S.-Y. Le, W-m. Liu, and J.V. Maizel, Jr.:
A data mining approach to discover unusual folding regions in genome sequences. Knowledged-Based Systems 15: 243-250, 2002.

79. S.-Y. Le, Jih-H. Chen, D. Konings and J.V. Maizel, Jr.: Local well-ordered folding sequences in ferritin and transferrin receptor mRNAs. Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences. CSREA Press, Las Vegas, Navada, USA, 2002, pp. 41-47.

80. S.-Y. Le and J.V. Maizel, Jr.:
Data mining of structural features in 5' untranslated regions of cellular mRNAs. Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences. CSREA Press, Las Vegas, Navada, USA, 2002, pp. 62-68.

81. Jih-H. Chen, S.-Y. Le, Bruce A. Shapiro, and J.V. Maizel, Jr.: A Theoretical approach for determining energy rules for tRNA. Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences. CSREA Press, Las Vegas, Navada, USA, 2002, pp. 69-74.

82. S.-Y. Le, K. Zhang and J.V. Maizel, Jr.:
RNA molecules with structure dependent functions are uniquely folded. Nucleic Acids Research, 30: 1-9, 2002.

83. S.-Y. Le, Jih-H. Chen, D. Konings and J.V. Maizel, Jr.:
Discovering well-ordered folding patterns in nucleotide sequences. Bioinformatics, 19: 354-361, 2003.

84. S.-Y. Le, Jih-H. Chen and J.V. Maizel, Jr.:
Statistical inference for well-ordered structures in nucleotide sequences. Prceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003, 190-196. IEEE Computer Society Press, Los Alamitos, CA. USA.

85. S.-Y. Le, J.V. Maizel, Jr. and K. Zhang: Predicting distinct fold-back structures and related microRNAs in genomic sequences. Prceedings of the JCIS 2003, Atlantic Symposium on Computational Biology and Genome Informatics. 933-937. 2003 JCIS/Association for Intelligent Machinery, Inc. Research Triangle Park, North Carolina, USA.

86. R. Kilav, O. Bell, S.-Y. Le, J. Silver and T. Naveh-Many:
The parathyroid hormone mRNA 3'-untranslated region AU-rich element is an unstructured functional element. The Journal of Biological Chemistry, 279: 2109-2116, 2004.

87. S. Cencig, C. Nanbru, S.-Y. Le, C. Gueydan, G. Huez, and V. Kruys:
Mapping and characterization of the minimal internal ribosome entry segment in the human c-myc mRNA 5' untranslated region. Oncogene, 23: 267-277, 2004.

88. S.-Y. Le, J.V. Maizel, Jr. and K. Zhang:
An algorithm for detecting homologues of known structured RNA in genomes. Proceedings of the 2004 IEEE Bioinformatics Conference, CSB 2004, 300-310. IEEE Computer Society Press, Los Alamitos, CA. USA.

89. S.-Y. Le and J.V. Maizel:
Computational discovery of distinct RNA elememts with functional structures in genomic sequences. Recent Research Developments in Molecular & Cellular Biology, 5: 63-77, 2004 ISBN: 81-7736-213-5.

90. Y. Bennasser, S.-Y. Le, M.L. Yeung and K.-T. Jeang:
HIV-1 encoded candidate micro-RNAs and their cellular targets. Retrovirology, 1:43, 2004, ISBN 1742-4690.

91. S.-Y. Le, J.V. Maizel, Jr. and K. Zhang:
Finding conserved well-ordered RNA structures in genomic sequences. International Journal on Computational Intelligence and Applications, 4: 417-430, 2004.

92. Y. Bennasser, S.-Y. Le, M. Benkirane and K.-T. Jeang:
Evidence that HIV-1 encodes an siRNA and a suppressor of RNA silencing. Immunity, 22: 607-619, 2005.

93. S.-Y. Le and J.V. Maizel, Jr.:
Finding double-stranded RNA structures in the 3'Untranslated Region of Eukaryotic mRNAs. Proceedings of the JCIS 2005, 6th International Symposium on Computational Biology and Genome Informatics (CBGI), Salt Lake City, Marriott City Center, Utah, USA, CBG-5: 1273-1277, 2005.

94. M. L. Yeung, Y. Bennasser, S.-Y. Le, and K.-T. Jeang:
siRNA, miRNA and HIV: promises and challenges. Cell Research, 15(11-12): 935-946, 2005.

95. Y. Bennasser, S.-Y. Le, M.L. Yeung and K.-T. Jeang: miRNAs in HIV-1 infection. in Book: Methods in Molecular Biology, vol. 342: 241-252, MicroRNA Protocols. Edited by S. Ying, Humana Press, Totowa, N.J. USA., 2006. (ISBN 1588295818)

96. H.Tanabe and S.-Y. Le: Prediction of structural homologs to functional RNAs involved in determination of life span of Paramecium tetraurelia. Jpn. J. Protozool, 39: 151-156, 2006.

97. Le, S-Y. and Maizel, J. V., Jr.: Data mining of imperfect double-stranded RNA in 3' untranslated regions of eukaryotic mRNAs. Biomol. Eng. 24(3): 351-359, 2007.

98. Yeung, M. L., Bennasser, Y., Le, S-Y., and Jeang, K-T.: RNA interference and HIV-1. Adv. Pharmacol. 55: 427-438, 2007.

99. Le, S-Y. and Chen, J-H.: Statistical Inference on Distinct RNA Stem-loops in Genomic Sequences. Lecture Notes in Bioinformatics, LNBI 4414: 314-327, 2007.