Journal Publications (*: corresponding author)

  1. K.-T. Chen, C.-J. Chen, H.-T. Shen, C.-L. Liu, S.-H. Huang and C.L. Lu*, Multi-CAR: a tool of contig scaffolding using multiple references, BMC Bioinformatics, 17 (2016) 469.
  2. T. T. Ta, C.-Y. Lin and C.L. Lu*, An efficient algorithm for computing non-overlapping inversion and transposition distance, Information Processing Letters, 116 (2016) 744-749.
  3. C.-H. Yang, C.-T. Shih, K.-T. Chen, P.-H. Lee, P.-H. Tsai, J.-C. Lin, C.-Y. Yen, T.-Y. Lin and C.L. Lu*, iPARTS2: an improved tool for pairwise alignment of RNA tertiary structures, version 2, Nucleic Acids Research, 44 (2016) W328-332.
  4. K.-T. Chen, C.-L. Li, H.-T. Chiu and C.L. Lu*, An efficient algorithm for one-sided block ordering problem under block-interchange distance, Theoretical Computer Science, 609 (2016) 296-305.
  5. C.L. Lu*, An efficient algorithm for contig ordering problem under algebraic rearrangement distance, Journal of Computational Biology, 22 (2015) 975-987.
  6. C.S. Ou, C.L. Lu and R.C.T. Lee*, A systematical and parallel approach to solve problems involving special properties of bit-vectors, Computer Journal, 58 (2015) 1112-1121.
  7. C.L. Lu*, K.-T. Chen, S.-Y. Huang and H.-T. Chiu, CAR: contig assembly of prokaryotic draft genomes using rearrangements, BMC Bioinformatics, 15 (2014) 381.
  8. C.-L. Li, K.-T. Chen and C.L. Lu*, Assembling contigs in draft genomes using reversals and block-interchanges, BMC Bioinformatics, 14 (2013) S9.
  9. C.W. Lu, C.L. Lu and R.C.T. Lee*, A new filtration method and a hybrid strategy for approximate string matching, Theoretical Computer Science, 481 (2013) 9-17.
  10. K.-H. Huang, K.-T. Chen and C.L. Lu*, Sorting permutations by cut-circularize-linearize-and-paste operations, BMC Genomics, 12 (2011) S26.
  11. Y.-C. Liu, C.-H. Yang, K.-T. Chen, J.-R. Wang, M.-L. Cheng, J.-C. Chung, H.-T. Chiu and C.L. Lu*, R3D-BLAST: a search tool for similar RNA 3D substructures, Nucleic Acids Research, 39 (2011) W45-49.
  12. Y.-L. Huang, C.-C. Huang, C.Y. Tang and C.L. Lu*, SoRT2: a tool for sorting genomes and reconstructing phylogenetic trees by reversals, generalized transpositions and translocations, Nucleic Acids Research, 38 (2010) W221-227.
  13. C.-W. Wang, K.-T. Chen and C.L. Lu*, iPARTS: an improved tool of pairwise alignment of RNA tertiary structures, Nucleic Acids Research, 38 (2010) W340-347.
  14. Y.-L. Huang, C.-C. Huang, C.Y. Tang and C.L. Lu*, An improved algorithm for sorting by block-interchanges based on permutation groups, Information Processing Letters, 110 (2010) 345-350.
  15. C.-H. Cheng, C.-H. Yang, H.-T. Chiu and C.L. Lu*, Reconstructing genome trees of prokaryotes using overlapping genes, BMC Bioinformatics, 11 (2010) 102.
  16. Y.-L. Huang and C.L. Lu*, Sorting by reversals, generalized transpositions and translocations using permutation groups, Journal of Computational Biology, 17 (2010) 685-705.
  17. C.-E. Lai, M.-Y. Tsai, Y.-C. Liu, C.-W. Wang, K.-T. Chen and C.L. Lu*, FASTR3D: a fast and accurate search tool for similar RNA 3D structures, Nucleic Acids Research, 37 (2009) W287-295.
  18. H.-H. Su, C.L. Lu and C.Y. Tang*, An improved algorithm for finding a length-constrained maximum-density subtree in a tree, Information Processing Letters, 109 (2008) 161-164.
  19. Y.-F. Chang, Y.-L. Huang and C.L. Lu*, SARSA: a web tool for structural alignment of RNA using a structural alphabet, Nucleic Acids Research, 36 (2008) W19-24.
  20. L.-W. Jiang, K.-L. Lin and C.L. Lu*, OGtree: a tool for creating genome trees of prokaryotes based on overlapping genes, Nucleic Acids Research, 36 (2008) W475-480.
  21. Y.S. Chung, C.L. Lu and C.Y. Tang*, Constrained sequence alignment: a general model and the hardness results, Discrete Applied Mathematics, 155 (2007) 2471-2486.
  22. Y.S. Chung, W.H. Lee, C.Y. Tang and C.L. Lu*, RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints, Nucleic Acids Research, 35 (2007) W639-644.
  23. Y.S. Chung, C.L. Lu and C.Y. Tang*, Efficient algorithms for regular expression constrained sequence alignment, Information Processing Letters, 103 (2007) 240-246.
  24. C.L. Lu*, Y.-L. Huang, T.C. Wang and H.-T. Chiu, Analysis of circular genome rearrangement by fusions, fissions and block-interchanges, BMC Bioinformatics, 7 (2006) 295.
  25. Y.C. Lin, C.L. Lu*, Y.-C. Liu and C.Y. Tang, SPRING: a tool for the analysis of genome rearrangement using reversals and block-interchanges, Nucleic Acids Research, 34 (2006) W696-699.
  26. C.-H. Huang, C.L. Lu* and H.-T. Chiu, A heuristic approach for detecting RNA H-type pseudoknots, Bioinformatics, 21 (2005) 3501-3508.
  27. Q. Wu, C.L. Lu* and R.C.T. Lee, The approximability of the weighted hamiltonian path completion problem on a tree, Theoretical Computer Science, 341 (2005) 385-397.
  28. C.L. Lu*, T.C. Wang, Y.C. Lin and C.Y. Tang, ROBIN: a tool for genome rearrangement of block-interchanges, Bioinformatics, 21 (2005) 2780-2782.
  29. C.L. Lu* and Y.P. Huang, A memory-efficient algorithm for multiple sequence alignment with constraints, Bioinformatics, 21 (2005) 20-30.
  30. Y.C. Lin, C.L. Lu*, H.-Y. Chang and C.Y. Tang, An efficient algorithm for sorting by block-interchanges and its application to the evolution of vibrio species, Journal of Computational Biology, 12 (205) 102-112.
  31. Y.-T. Chen, H.-Y. Chang, C.L. Lu and H.-L. Peng*, Evolutionary analysis of the two-component systems in Pseudomonas Aeruginosa PAO1, Journal of Molecular Evolution, 59 (2004) 725-737.
  32. Y.T. Tsai, Y.P. Huang, C.T. Yu and C.L. Lu*, MuSiC: a tool for multiple sequence alignment with constraints, Bioinformatics, 20 (2004) 2309-2311.
  33. C.Y. Tang*, C.L. Lu, M.D.T. Chang, Y.T. Tsai, Y.J. Sun, K.M. Chao, J.M. Chang, Y.H. Chiou, C.M. Wu, H.T. Chang and W.I. Chou, Constrained multiple sequence alignment tool development and its application to RNase family alignment, Journal of Bioinformatics and Computational Biology, 1 (2003) 267-287.
  34. C.L. Lu, C.Y. Tang* and R.C.T. Lee, The full Steiner tree problem, Theoretical Computer Science, 306 (2003) 55-67.
  35. C.L. Lu, S.-L. Peng and C.Y. Tang*, Efficient minus and signed domination in graphs, Theoretical Computer Science, 301 (2003) 381-397.
  36. C.L. Lu, M.T. Ko and C.Y. Tang*, Perfect edge domination and efficient edge domination in graphs, Discrete Applied Mathematics, 119 (2002) 227-250.
  37. C.L. Lu and C.Y. Tang*, Weighted efficient domination problem on some perfect graphs, Discrete Applied Mathematics, 117 (2002) 163-182.
  38. C.L. Lu and C.Y. Tang*, Solving the weighted efficient edge domination problem on bipartite permutation graphs, Discrete Applied Mathematics, 87 (1998) 203-211.
  39. C.L. Lu and C.Y. Tang*, A linear-time algorithm for the weighted feedback vertex problem on interval graphs, Information Processing Letters, 61 (1997) 107-111.

Book Chapters

  1. C.L. Lu*, Sorting by transpositions and reversals (approximate ratio 1.5), in: M.-Y. Kao ed., Encyclopedia of Algorithms, 2nd edition, Springer (ISBN: 978-1-4939-2864-4), 2016, pp. 2022-2026.
  2. C.L. Lu* and C.Y. Tang, Sorting genomes by rearrangements and its application to phylogeny reconstruction, in: Genomics III - Methods, Techniques and Applications, iConcept Press (ISBN: 978-1-922227-416), 2014, pp. 229-224.
  3. C.L. Lu*, Sorting by transpositions and reversals (approximate ratio 1.5), in: M.-Y. Kao ed., Encyclopedia of Algorithms, Springer (ISBN: 978-0-387-30770-1), 2008, pp. 863-866.
  4. C.L. Lu*, Y.C. Lin, Y.-L. Huang and C.Y. Tang, Analysis of genome rearrangement by block-interchanges, in: N. Bergman ed., Methods in Molecular Biology, vol. 396 (Comparative Genomics, Volume 2), Humana Press (ISBN: 978-1-934115-37-4), 2007, pp. 121-134.

Conference Publications

  1. K.-T. Chen, C.-J. Chen, H.-T. Shen, C.-L. Liu, S.-H. Huang and C.L. Lu*, Multi-CAR: a tool of contig scaffolding using multiple references, in: Proceedings of the 27th International Conference on Genome Informatics (GIW 2016), 2016.
  2. C.-H. Yang, C.-T. Shih, K.-T. Chen, P.-H. Lee, P.-H. Tsai, J.-C. Lin, C.-Y. Yen, T.-Y. Lin and C.L. Lu*, iPARTS2: an improved tool for pairwise alignment of RNA tertiary structures, version 2, in: Proceedings of the 27th International Conference on Genome Informatics (GIW 2016), highlight paper, 2016.
  3. T.T. Ta, C.-Y. Lin and C.L. Lu*, An efficient algorithm for computing non-overlapping inversion and transposition distance, in: Proceedings of the 32th Workshop on Combinatorial Mathematics and Computational Theory (ALGO 2015), 2015, pp. 55-61.
  4. S.-W. Chou, C.-H. Yang, K.-T. Chen and C.L. Lu*, Prefix block-interchanges on binary strings, in: Proceedings of the 2014 International Computer Symposium (ICS 2014), Frontiers in Artificial Intelligence and Applications, IOS Press, vol. 274, 2014, pp. 1960-1969.
  5. S.-Y. Huang, C.-H. Yang, T.T. Ta, C.L. Lu*, Approximate string matching problem under non-overlapping inversion distance, in: Proceedings of the 2014 International Computer Symposium (ICS 2014), Frontiers in Artificial Intelligence and Applications, IOS Press, vol. 274, 2014, pp. 40-48.
  6. C.W. Lu, C.L. Lu and R.C.T. Lee*, Improved exact string matching algorithms based upon selective matching order and branch and bound approach, in: Proceedings of the 31th Workshop on Combinatorial Mathematics and Computational Theory (ALGO 2014), 2014, pp. 19-28.
  7. K.-T. Chen, C.-L. Li, C.-H. Yang and C.L. Lu*, An efficient algorithm for one-sided block ordering problem with block-interchange distance, in: D.-Z. Du and G. Zhang eds., Proceedings of the 19th Annual International Computing and Combinatorics Conference (COCOON 2013), Lecture Notes in Computer Science, Springer-Verlag, vol. 7936, 2013, pp. 409-420.
  8. C.S. Ou, C.L. Lu and R.C.T. Lee*, Solving the subcircuit extraction problem by using bit-parallel filtering algorithm, in: Proceedings of the 30th Workshop on Combinatorial Mathematics and Computational Theory (ALGO 2013), 2013, pp. 116-123.
  9. C.-L. Li, K.-T. Chen and C.L. Lu*, Assembling contigs in draft genomes using reversals and block-interchanges, in: Proceedings of the Third Annual RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-seq 2013), 2013.
  10. C.W. Lu, C.L. Lu and R.C.T. Lee*, A new filtration method and a hybrid strategy for approximate string matching, in: Proceedings of the 2012 International Computer Symposium (ICS 2012), Advances in Intelligent Systems and Applications, Springer-Verlag, vol. 1, 2012, pp. 143-155.
  11. K.-H. Huang, K.-T. Chen and C.L. Lu*, Sorting permutations by cut-circularize-linearize-and-paste operations, in: Proceedings of the 10th International Conference on Bioinformatics and 1st International Society for Computational Biology Asia Joint Conference (InCoB/ISCB-Asia 2011), 2011.
  12. K.-H. Huang, K.-T. Chen and C.L. Lu*, Sorting by cut-circularize-linearize-and-paste operations, in: Proceedings of the 28th Workshop on Combinatorial Mathematics and Computational Theory (ALGO 2011), 2011, pp. 81-89.
  13. C.S. Ou, C.L. Lu and R.C.T. Lee*, A bit-parallel approach to solve approximation string matching problem for unlimited pattern length, in: 4th Annual Meeting of Asian Association for Algorithms and Computation (AAAC 2011), 2011.
  14. K.-T. Chen, C.-W. Wang and C.L. Lu*, An improved tool of pairwise alignment of RNA tertiary structures, in: 9th International Conference on Bioinformatics (InCoB 2010), 2010.
  15. C.-H. Yang, C.-H. Cheng, H.-T. Chiu and C.L. Lu*, OGtree2: A tool for reconstructing genome trees of prokaryotes using overlapping genes, in: 9th International Conference on Bioinformatics (InCoB 2010), 2010.
  16. K.-H. Chen, G.-S. Huang, C.L. Lu and R.C.T. Lee*, A multidimensional divide-and-conquer algorithm for assigning secondary structures in proteins, in: Proceedings of the 26th Workshop on Combinatorial Mathematics and Computational Theory (ALGO 2009), 2009, pp. 1-8.
  17. Y.-L. Huang, C.-C.Huang, C.Y. Tang, and C.L. Lu*, An improved algorithm for sorting by block-interchanges based on permutation groups, in: Proceedings of the 26th Workshop on Combinatorial Mathematics and Computational Theory (ALGO 2009), 2009, pp. 9-14.
  18. H.-H. Su, C.L. Lu and C.Y. Tang*, An improved algorithm for finding a length-constrained maximum-density subtree in a tree, in: Proceedings of the 25th Workshop on Combinatorial Mathematics and Computational Theory (ALGO 2008), 2008, pp. 146-150.
  19. Y.-L. Huang, C.-J. Wu, H.-T. Chiu, C.Y. Tang and C.L. Lu*, A bioinformatics approach to improving prediction of programmed ribosomal frameshifting, in: S. Ranganathan ed., Proceedings of the Sixth International Conference on Bioinformatics (InCoB 2007), 2007.
  20. Y.S. Chung, C.L. Lu and C.Y. Tang*, Efficient algorithms for regular expression constrained sequence alignment, in: M. Lewenstein and G. Valiente eds., Proceedings of the 17th Annual Symposium on Combinatorial Pattern Matching (CPM 2006), Lecture Notes in Computer Science, Springer-Verlag, vol. 4009, 2006, pp. 389-400.
  21. K.H. Chen, C.S. Tsai, B.M.T. Lin, C.Y. Tang, C.L. Lu, R.C.T. Lee*, The application of multidimensional scaling to the protein structure alignment problem, in: Proceedings of the 22nd Workshop on Combinatorial Mathematics and Computational Theory (ALGO 2005), 2005, pp. 97-106.
  22. T. Kloks, C.M. Lee, J. Liu, C.L. Lu and S.-L. Peng*, Descrying induced interval graphs, in: Proceedings of the 2003 European Conference on Combinatorics, Graph Theory and Applications (Eurocomb 2003), 2003, pp. 234-239.
  23. Y.H. Chen, C.L. Lu and C.Y. Tang*, On the full and bottleneck full Steiner tree problems, in: T. Warnow and B. Zhu eds., Proceedings of the Ninth Annual International Computing and Combinatorics Conference (COCOON 2003), Lecture Notes in Computer Science, Springer-Verlag, vol. 2697, 2003, pp. 122-129.
  24. C.Y. Tang*, C.L. Lu, M.D.T. Chang, Y.T. Tsai, Y.J. Sun, K.M. Chao, J.M. Chang, Y.H. Chiou, C.M. Wu, H.T. Chang and W.I. Chou, Constrained multiple sequence alignment tool development and its application to RNase family alignment, in: V. Markstein and P. Markstein eds., Proceedings of the First IEEE Computer Society Bioinformatics Conference (CSB 2002), 2002, pp. 127-137.
  25. C.L. Lu, C.Y. Tang* and R.C.T. Lee, The full Steiner tree problem in phylogeny, in: O.H. Ibarra and L. Zhang eds., Proceedings of the Eighth Annual International Computing and Combinatorics Conference (COCOON 2002), Lecture Notes in Computer Science, Springer-Verlag, vol. 2387, 2002, pp. 107-116.
  26. C.Y. Tang*, C.L. Lu, M.D.T. Chang, Y.J. Sun, Y.T. Tsai, J.M. Chang, Y.H. Chiou, C.M. Wu, H.T. Chang, W.I. Chou and S.C. Chiang, Constrained sequence alignment tool development and its application to RNase family alignment, in: F. Valafar ed., Proceedings of the 2002 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS 2002), 2002, pp. 365-370.
  27. C.L. Lu, Z.Y. Su and C.Y. Tang*, A new measure of edit distance between labeled trees, in: J. Wang ed., Proceedings of the Seventh Annual International Computing and Combinatorics Conference (COCOON 2001), Lecture Notes in Computer Science, Springer-Verlag, vol. 2108, 2001, pp. 338-348.
  28. C.L. Lu, S.-L. Peng and C.Y. Tang*, Efficient minus and signed domination in graphs, in: D.T. Lee and S.H. Teng eds., Proceedings of the Eleventh Annual International Symposium on Algorithms and Computation (ISAAC 2000), Lecture Notes in Computer Science, Springer-Verlag, vol. 1969, 2000, pp. 241-253.
  29. Q. Wu, C.L. Lu and R.C.T. Lee*, An approximate algorithm for the weighted Hamiltonian path completion problem on a tree, in: D.T. Lee and S.H. Teng eds., Proceedings of the Eleventh Annual International Symposium on Algorithms and Computation (ISAAC 2000), Lecture Notes in Computer Science, Springer-Verlag, vol. 1969, 2000, pp. 156-167.
  30. Y.D. Liang, C.L. Lu and C.Y. Tang*, Efficient domination on permutation graphs and trapezoid graphs, in: T. Jiang and D.T. Lee eds., Proceedings of the Third Annual International Computing and Combinatorics Conference (COCOON 1997), Lecture Notes in Computer Science, Springer-Verlag, vol. 1276, 1997, pp. 232-241.
  31. C.L. Lu and C.Y. Tang*, On the Complexity of Efficient Minus Domination, in: Proceedings of the 14th Workshop on Combinatorial Mathematics and Computation Theory (ALGO 1997), 1997, pp. 45-48.
  32. C.L. Lu and C.Y. Tang*, On the complexity of the perfect edge domination problem, in: Proceedings of International Conference on Algorithms (joint with International Computer Symposium ICS 1996), 1996, pp. 64-71.
  33. C.L. Lu and C.Y. Tang*, Solving the weighted efficient edge domination problem on bipartite permutation graphs, in: Proceedings of the 13th Workshop on Combinatorial Mathematics and Computation Theory (ALGO 1996), 1996, pp. 118-124.
  34. C.L. Lu and C.Y. Tang*, The complexity of the efficient edge domination problem, in: Proceedings of the 12th Workshop on Combinatorial Mathematics and Computation Theory (ALGO 1996), 1996, pp. 145-149.
  35. C.L. Lu and C.Y. Tang*, A linear time algorithm for the weighted feedback vertex problem on interval graphs, in: Proceedings of the 11th Workshop on Combinatorial Mathematics and Computation Theory (ALGO 1995), 1995, pp. 80-83.
  36. M.S. Chang* and C.L. Lu, Efficient algorithms for the weighted k-domination problem and its variants on interval and circular-arc graphs, in: Proceedings of the 7th Workshop on on Discrete Mathematics and Theory of Computation (ALGO 1993), 1993.
  37. M.S. Chang*, F.H. Wang, S.-L. Peng and C.L. Lu, Irredundance of weighted interval graphs, in: Proceedings of the 6th Workshop on on Discrete Mathematics and Theory of Computation (ALGO 1992), 1992.

Posters

  1. K-T Chen, H-T Chiu and C.L. Lu*, CAR: contig assembly of prokaryotic draft genomes using rearrangements, in: 1st joint conference between International Conference on Genome Informatics and International Conference on Bioinformatics (GIW/InCoB 2015), Odaiba, Tokyo, 2015.
  2. C.L. Lu*, C-L Li, K-T Chen, C-H Yang, W-Y Tsai and H-T Chiu, An efficient algorithm for ordering partially assembled genomes using block-interchanges, in: 23rd International Conference on Genome Informatics (GIW 2012), Tainan, Taiwan, 2012.
  3. C.L. Lu*, C-L Lee, W-Y Tsai and H-T Chiu, Ordering partially assembled genomes using block-interchanges, in: 11th International Conference on Bioinformatics (InCoB 2012), Bangkok, Thailand, 2012.
  4. C.-E. Lai, M.-Y. Tsai, Y.-C. Liu, C.-W. Wang, K.-T. Chen and C.L. Lu*, FASTR3D: a fast and accurate search tool for similar RNA 3D structures, in: 8th International Conference on Bioinformatics (InCoB 2009), Singapore, 2009.
  5. Y.-F. Chang, Y.-L. Huang and C.L. Lu*, SARSA: a web tool for structural alignment of RNA using a structural alphabet, in: 7th International Conference on Bioinformatics (InCoB 2008), Taipei, Taiwan, 2008.
  6. Y.-L. Huang, C.-J. Wu, H.-T. Chiu, C.Y. Tang and C.L. Lu*, A bioinformatics approach to improving the prediction of programmed -1 ribosomal frameshifting, in: 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2007) & 6th European Conference on Computational Biology (ECCB 2007), Vienna, Austria, 2007.