Selected Recent Papers:
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
S.-Y. Le and M. Zuker:
Common structures of 5' noncoding RNA in enteroviruses and rhinoviruses:
Thermodynamaical stability and statistical significance, J Mol. Biol.
216: 729--741, 1990.
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.
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.
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.
1. 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.
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.
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.
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.
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.
S.-Y. Le, N. Sonenberg, and J.V. Maizel Jr.,:
Unusual folding regions and ribosome landing pad within hepatitis C virus
and pestivirus RNAs. Gene 1995; 154:137-143.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
G. Collins, S.-Y. Le, and K. Zhang:
A new algorithm for computing similarity between RNA structures.
Information Sciences 139: 59-77, 2001.
S.-Y. Le, W-m. Liu, and J.V. Maizel, Jr.:
A data mining approach
to discover unusual folding regions in genome sequences.
Knowledge-Based Systems 15: 243-250, 2002.
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.
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.
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.
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.
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.
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.
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, CSB2004, IEEE Computer Society Press, Los Alamitos, CA.
USA.
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.
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, ISSN 1742-4690.
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.
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.
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.
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)
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.
Yeung, M. L., Bennasser, Y., Le, S-Y., and Jeang, K-T.: siRNA, miRNA and HIV:
Promises and challenges. Cell Res. 15: 935-946, 2005.
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.
Yeung, M. L., Bennasser, Y., Le, S-Y., and Jeang, K-T.: RNA interference and HIV-1.
Adv. Pharmacol. 55: 427-438, 2007.
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.
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