研究主題 (Research Topics)
我們是一個演算法與生物資訊的實驗室，
研究興趣在於演算法的設計與分析
(包括了生物資訊演算法、圖論演算法與組合最佳化演算法等)
和生物資訊軟體工具的開發與應用。
目前我們實驗室的研究課題有序列的比對、基因體的重組、演化樹的重建、RNA/Protein 結構的預測、比較與搜尋等等。
- 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)
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MuSiC-ME:
A memory-efficient tool for multiple sequence alignment with constraints
(Bioinformatics, 21:20-30, 2005)
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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:
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ROBIN:
A tool for genome rearrangement of block-interchanges
(Bioinformatics, 21:2780-2782, 2005; Journal of Computational Biology, 12:102-112, 2005)
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FFBI:
A tool of circular genome rearrangement by fusions, fissions and block-interchanges
(BMC Bioinformatics, 7:295, 2006)
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SPRING:
Sorting permutation by reversals and block-interchanges
(Nucleic Acids Research, 34:W696-699, 2006)
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OGtree:
A tool for creating genome trees of prokaryotes based on overlapping genes
(Nucleic Acids Research, 36:W475-480, 2008)
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OGtree2.0:
A tool for genome trees of prokaryotes based on overlapping genes
(BMC Bioinformatics, 11:102, 2010)
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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:
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HPknotter:
A heuristic approach for detecting RNA H-type pseudoknots
(Bioinformatics, 21:3501-3508, 2005)
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PRooF:
A tool for detecting programmed ribosomal frameshifting (InCoB 2007)
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SARSA:
A web tool for structural alignment of RNA using a structural alphabet
(Nucleic Acids Research, 36:W19-24, 2008)
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FASTR3D:
A fast and accurate search tool for similar RNA 3D structures
(Nucleic Acids Research, 37:W287-295, 2009)
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iPARTS: An improved tool of pairwise alignment of RNA tertiary structures
(Nucleic Acids Research, 38:W340-347, 2010)
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R3D-BLAST:
A search tool for similar RNA 3D substructures
(Nucleic Acids Research, 39:W45-49, 2011)