Research Topics
We are interested in the design and analysis of algorithms, including bioinformatics
algorithms, combinatorial optimization algorithms and graph algorithms, and the
development and applications of bioinformatics software tools. Current research
topics in our lab include
sequence alignment,
genome rearrangement,
evolutionary tree prediction,
RNA/Protein structural prediction, comparison and search, etc.
- Lab tools for multiple sequence alignment with constraints:
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MuSiC:
A Tool for Multiple Sequence Alignment with Constraints
(Bioinformatics, 20:2309-2311, 2004;
Discrete Applied Mathematics, 155:2471-2486, 2007)
-
MuSiC-ME:
A Memory-Efficient Tool for Multiple Sequence Alignment with Constraints
(Bioinformatics, 21:20-30, 2005)
-
RE-MuSiC:
A Tool for Multiple Sequence Alignment with Regular Expression Constraints
(Nucleic Acids Research, 35:W639-644, 2007;
Information Processing Letters, 103:240-246, 2007)
- Lab tools for genome rearrangement and evolutionary tree prediction:
-
ROBIN:
A Tool for Genome Rearrangement of Block-Interchanges
(Bioinformatics, 21:2780-2782, 2005; Journal of Computational Biology, 12:102-112, 2005)
-
FFBI:
A Tool of Circular Genome Rearrangement by Fusions, Fissions and Block-Interchanges
(BMC Bioinformatics, 7:295, 2006)
-
SPRING:
Sorting Permutation by Reversals and block-INterchanGes
(Nucleic Acids Research, 34:W696-699, 2006)
-
OGtree:
A Tool for Creating Genome Trees of Prokaryotes Based on Overlapping Genes
(Nucleic Acids Research, 36:W475-480, 2008)
-
OGtree2.0:
A Tool for Genome Trees of Prokaryotes Based on Overlapping Genes
(BMC Bioinformatics, 11:102, 2010)
-
SoRT2:
a tool for sorting genomes and reconstructing phylogenetic
trees by reversals, generalized transpositions and translocations
(Nucleic Acids Research, 38:W221-227, 2010;
Journal of Computational Biology, 17:685-705, 2010).
- Lab tools for RNA structural prediction, comparison and search: