
This Article  
 
Share  
Bibliographic References  
Add to:  
Digg Furl Spurl Blink Simpy Del.icio.us Y!MyWeb  
Search  
 
ASCII Text  x  
ZhiZhong Chen, Lusheng Wang, "Fast Exact Algorithms for the Closest String and Substring Problems with Application to the Planted (L,d)Motif Model," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no. 5, pp. 14001410, September/October, 2011.  
BibTex  x  
@article{ 10.1109/TCBB.2011.21, author = {ZhiZhong Chen and Lusheng Wang}, title = {Fast Exact Algorithms for the Closest String and Substring Problems with Application to the Planted (L,d)Motif Model}, journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {8}, number = {5}, issn = {15455963}, year = {2011}, pages = {14001410}, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.21}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }  
RefWorks Procite/RefMan/Endnote  x  
TY  JOUR JO  IEEE/ACM Transactions on Computational Biology and Bioinformatics TI  Fast Exact Algorithms for the Closest String and Substring Problems with Application to the Planted (L,d)Motif Model IS  5 SN  15455963 SP1400 EP1410 EPD  14001410 A1  ZhiZhong Chen, A1  Lusheng Wang, PY  2011 KW  Parameterized algorithm KW  closest string KW  closest substring KW  DNA motif discovery. VL  8 JA  IEEE/ACM Transactions on Computational Biology and Bioinformatics ER   
[1] A. Andoni, P. Indyk, and M. Patrascu, “On the Optimality of the Dimensionality Reduction Method,” Proc. 47th IEEE Symp. Foundations of Computer Science, pp. 449458, 2006.
[2] A. BenDor, G. Lancia, J. Perone, and R. Ravi, “Banishing Bias from Consensus Sequences,” Proc. Eighth Symp. Combinatorial Pattern Matching, pp. 247261, 1997.
[3] J. Buhler and M. Tompa, “Finding Motifs Using Random Projections,” J. Computational Biology, vol. 9, pp. 225242, 2002.
[4] J. Davila, S. Balla, and S. Rajasekaran, “Fast and Practical Algorithms for Planted (l, d) Motif Search,” IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 4, no. 4, pp. 544552, Oct.Dec. 2007.
[5] X. Deng, G. Li, Z. Li, B. Ma, and L. Wang, “Genetic Design of Drugs without SideEffects,” SIAM J. Computing, vol. 32, pp. 10731090, 2003.
[6] J. Dopazo, A. Rodríguez, J.C. Sáiz, and F. Sobrino, “Design of Primers for PCR Amplification of Highly Variable Genomes,” Computer Applications in the Biosciences, vol. 9, pp. 123125, 1993.
[7] R.G. Downey and M.R. Fellows, Parameterized Complexity. Springer, 1999.
[8] M.R. Fellows, J. Gramm, and R. Niedermeier, “On the Parameterized Intractability of Motif Search Problems,” Combinatorica, vol. 26, pp. 141167, 2006.
[9] M. Frances and A. Litman, “On Covering Problems of Codes,” Theoretical Computer Science, vol. 30, pp. 113119, 1997.
[10] J. Gramm, F. Huffner, and R. Niedermeier, “Closest Strings, Primer Design, and Motif Search,” Currents in Computational Molecular Biology, poster abstracts of RECOMB 2002, pp. 7475, 2002.
[11] J. Gramm, R. Niedermeier, and P. Rossmanith, “FixedParameter Algorithms for Closest String and Related Problems,” Algorithmica, vol. 37, pp. 2542, 2003.
[12] K. Lanctot, M. Li, B. Ma, S. Wang, and L. Zhang, “Distinguishing String Selection Problems,” Information and Computation, vol. 185, pp. 4155, 2003.
[13] M. Li, B. Ma, and L. Wang, “Finding Similar Regions in Many Sequences,” J. Computer and System Sciences, vol. 65, pp. 7396, 2002.
[14] M. Li, B. Ma, and L. Wang, “On the Closest String and Substring Problems,” J. ACM, vol. 49, pp. 157171, 2002.
[15] X. Liu, H. He, and O. Sýkora, “Parallel Genetic Algorithm and Parallel Simulated Annealing Algorithm for the Closest String Problem,” Proc. First Int'l Conf. Advanced Data Mining and Applications (ADMA '05), pp. 591597, 2005.
[16] K. Lucas, M. Busch, S. össinger, and J.A. Thompson, “An Improved Microcomputer Program for Finding Gene or Gene FamilySpecific Oligonucleotides Suitable as Primers for Polymerase Chain Reactions or as Probes,” Computer Applications in the Biosciences, vol. 7, pp. 525529, 1991.
[17] B. Ma and X. Sun, “More Efficient Algorithms for Closest String and Substring Problems,” Proc. 12th Ann. Int'l Conf. Research in Computational Molecular Biology, pp. 396409, 2008.
[18] D. Marx, “The Closest Substring Problem with Small Distances,” Proc. 46th IEEE Symp. Foundations of Computer Science, pp. 6372, 2005.
[19] H. Mauch, M.J. Melzer, and J.S. Hu, “Genetic Algorithm Approach for the Closest String Problem,” Proc. Second IEEE Computer Soc. Bioinformatics Conf., pp. 560561, 2003.
[20] C.N. Meneses, Z. Lu, C.A.S. Oliveira, and P.M. Pardalos, “Optimal Solutions for the Closest String Problem via Integer Programming,” INFORMS J. Computing, vol. 16, pp. 419429, 2004.
[21] P. Pevzner and S.H. Sze, “Combinatorial Approaches to Finding Subtle Signals in DNA Sequences,” Proc. Eighth Int'l Conf. Intelligent Systems for Molecular Biology, pp. 269278, 2000.
[22] V. Proutski and E.C. Holme, “Primer Master: A New Program for the Design and Analysis of PCR Primers,” Computer Applications in the Biosciences, vol. 12, pp. 253255, 1996.
[23] N. Stojanovic, P. Berman, D. Gumucio, R. Hardison, and W. Miller, “A LinearTime Algorithm for the 1Mismatch Problem,” Proc. Fifth Int'l Workshop Algorithms and Data Structures, pp. 126135, 1997.
[24] Y. Wang, W. Chen, X. Li, and B. Cheng, “Degenerated Primer Design to Amplify the Heavy Chain Variable Region from Immunoglobulin cDNA,” BMC Bioinformatics, vol. 7, suppl. 4, p. S9, 2006.
[25] L. Wang and L. Dong, “Randomized Algorithms for Motif Detection,” J. Bioinformatics and Computational Biology, vol. 3, pp. 10381052, 2005.
[26] L. Wang and B. Zhu, “Efficient Algorithms for the Closest String and Distinguishing String Selection Problems,” Proc. Third Int'l Workshop Frontiers in Algorithms, pp. 261270, 2009.