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Development of novel sophisticated algorithms in RNA folding, analyses
of RNA structures and discovery of ncRNAs, RNA motifs and RNA functional
elements.
a) Develop computing algorithms for predicting common RNA structures
from a set of related RNA sequences by integrating RNA folding,
phylogenetical analysis, RNA structural comparison, and various algorithms
such as dynamic programming and genetic algorithms.
b) Develop sophisticated search tools for detecting homologous structured
RNAs in genomic sequences based on the detailed information of sequence and
higher-ordered RNA structure. Such novel algorithm will completely differ
from other currently used search algorithms because it takes structural
constraints of the query RNA in detail, including each base-pairs in the RNA
structure and each nucleotide in the single strands. Also, the homologous
structured RNAs in genomes are strictly inferred from a robust statistical
distribution of a quantitative measure, maximal similarity score that was
computed by the comparison of structure morphology.
c) Develop novel algorithms for finding local well-ordered structures
that are both the thermodynamic stable and uniquely
folded in genomic sequences. The unusual well-ordered structures are expected
to be correlated with important functions.
d) Develop computing protocols for discoveries of unknown FSR, ncRNA and
conserved RNA structural motif.
e) Develop computing protocols for finding potential targets of regulating
RNAs in genomes.
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Data mining of RNA functional elements in RNA sequences.
a) We emphasize our research on RNA-based gene regulation,
post-transcriptional gene regulation and prediction of functional RNA structures
and dsRNAs.
b) Determination of the common RNA structure for functional RNA molecules
and ncRNAs.
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Nanoparticle study of RNA building block.
To enhance the therapeutic treatment of cancer, it is important to develop
multifunctional, targeted RNA nanoparticles capable to bypassing biological
barries to deliver the therapeutic agents directly to cancer cells. It is
our goal to discover RNA building blocks that can be used in bottom-up
assembly in nanotechnology.
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Provide flexible and powerful computational tools and advice to NIH
investigators on various topics associated with RNA folding and RNA
structural analysis.
We will establish valuable resource for computation of RNA structure
with facilitating the use of the resource by NIH scientists. Through our
examples of successful collaborative projects it demonstrates that the
combination of bench scientists and computational approaches with perfectly
designed experiments yields fruitful results. We seek for collaborations,
especially, with bench scientists.
