Research Topics
We are an Algorithm and Bioinformatics lab with interest
in the design and analysis of algorithms, including bioinformatics
algorithms, graph algorithms and combinatorial optimization algorithms, and the
development and applications of bioinformatics software tools. Current research
topics in our lab include
sequence alignment,
genome rearrangement,
evolutionary tree reconstruction,
contig scaffolding,
RNA/Protein structural prediction, comparison and search, etc.
- Lab tools for multiple sequence alignment with constraints:
-
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 reconstruction:
-
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:
-
HPknotter:
A heuristic approach for detecting RNA H-type pseudoknots
(Bioinformatics, 21:3501-3508, 2005)
-
PRooF:
A tool for detecting programmed ribosomal frameshifting (InCoB 2007)
-
SARSA:
A web tool for structural alignment of RNA using a structural alphabet
(Nucleic Acids Research, 36:W19-24, 2008)
-
FASTR3D:
A fast and accurate search tool for similar RNA 3D structures
(Nucleic Acids Research, 37:W287-295, 2009)
-
iPARTS: An improved tool of pairwise alignment of RNA tertiary structures
(Nucleic Acids Research, 38:W340-347, 2010)
-
iPARTS2: An improved tool for pairwise alignment of RNA tertiary structures, version 2
(Nucleic Acids Research, 44:W328-332, 2016)
-
R3D-BLAST:
A search tool for similar RNA 3D substructures
(Nucleic Acids Research, 39:W45-49, 2011)
-
R3D-BLAST2: An improved search tool for similar RNA 3D substructures (BMC Bioinformatics 18:574, 2017)
- Lab tools for scaffolding contigs:
-
CAR:
contig assembly of prokaryotic draft genomes using rearrangements
(BMC Bioinformatics, 15:381, 2014)
-
Multi-CAR:
a tool of contig scaffolding using multiple references
(BMC Bioinformatics, 17:469, 2016)
-
CSAR:
a contig scaffolding tool using algebraic rearrangements
(Bioinformatics, 34:109-111, 2018)
-
Multi-CSAR:
a multiple reference-based contig scaffolder using algebraic rearrangements
(BMC Systems Biology, 12:139, 2018)
-
CSAR-web:
a web server of contig scaffolding using algebraic rearrangements
(Nucleic Acids Research, 46:55-59, 2018)