The reversal median problem

INFORMS Journal on Computing

Volumn 15, Issue 1, 2003, Pages 93-113

  Caprara, Alberto ^a  

^a UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

Analysis of Algorithms; Networks Graphs, Matchings; Programming, Integer, Algorithms; Programming, Integer, Applications

Indexed keywords

ALGORITHMS; COMPUTATIONAL COMPLEXITY; COMPUTATIONAL METHODS; INTEGER PROGRAMMING; MATHEMATICAL MODELS; OPTIMIZATION; TRAVELING SALESMAN PROBLEM;

ANALYSIS OF ALGORITHMS; MATCHINGS; NETWORK-GRAPHS; REVERSAL MEDIAN PROBLEM (RMP);

PROBLEM SOLVING;

EID: 3843132934     PISSN: 10919856     EISSN: 15265528     Source Type: Journal    
DOI: 10.1287/ijoc.15.1.93.15155     Document Type: Article

References (34)

1. Ausiello, G., P. Crescezi, G. Gambosi, V. Kann, A. Marchetti-Spaccamela, M. Protasi. 1999. Combinatorial Optimization Problems and Their Approximability Properties, Springer-Verlag, Berlin, Germany.
2. Bader, D. A., B. M. E. Moret, M. Yan. 2001. A linear-time algorithm for computing inversion distance between signed permutations with an experimental study. Journal of Computational Biology 8 483-491.
3. Bafna, V., P. A. Pevzner. 1996. Genome rearrangements and sorting by reversals. SIAM Journal on Computing 25 272-289.
4. Berman, P., M. Karpinski. 2000. On some tighter inapproximability results: Further improvements. Proceedings of the 26th International Colloquium on Automata, Languages and Programming, Lecture Notes in Computer Science, No. 1644. Springer Verlag, Berlin, Germany, 200-209.
5. Blanchette, M., G. Bourque, D. Sankoff. 1997. Breakpoint phylogenies. S. Miyano, T. Takagi, eds. Proceedings of Genome Informatics 1997. Universal Academy Press, Tokyo, Japan, 25-34.
6. Blanchette, M. 1999. Personal communication.
7. Bourque, G., P. A. Pevzner. 2002. Genome-scale evolution: Reconstructing gene orders in the ancestral species. Genome Research. Forthcoming.
8. Bryant, D. 2002. A lower bound for the breakpoint bhylogeny problem. Journal of Discrete Algorithms. Forthcoming.
9. Caprara, A. 1999a. Sorting permutations by reversals and Eulerian cycle decompositions. SIAM Journal on Discrete Mathematics 12 91-110.
10. Caprara, A. 1999b. On the tightness of the alternating-cycle lower bound for sorting by reversals. Journal of Combinatorial Optimization 3 149-182.
11. Caprara, A. 1999c. Formulations and hardness of multiple sorting by reversals. Proceedings of the 3rd Annual International Conference on Computational Molecular Biology (RECOMB'99). ACM Press, New York, 84-93.
12. Caprara, A. 2001. The reversal median problem. Research Report OR/01/12, DEIS, University of Bologna, Italy, http:// www.or.deis.unibo.it/alberto/online. htm.
13. Caprara, A., G. Lancia, S. K. Ng. 2001. Sorting permutations by reversals through branch-and-price. INFORMS Journal on Computing 13 224-244.
14. Christie, D. A. 1998. A 3/2 approximation algorithm for sorting by reversals. Proceedings of the 9th Annual ACM-SIAM Symposium on Discrete Algorithms. ACM Press, New York, 244-252.
15. Cosner, M. E., R. K. Jansen, B. M. E. Moret, L. A. Rauberson, L-S. Wang, T. Warnow, S. Wyman. 2000. An empirical comparison of phylogenetic methods on chloroplast gene order data in campanulaceae. D. Sankoff, J. H. Nadeau, eds. Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics. Kluwer Academic Publishers, Dordrecht, The Netherlands, 99-121.
16. Grötschel, M., L. Lovász, A. Schrijver. 1981. The ellipsoid method and its consequences in combinatorial optimization. Combinatorica 1, 169-197.
17. Gusfield, D. 1997. Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology, Cambridge University Press, Cambridge, UK.
18. Hannenhalli, S., C. Chappey, E. V. Koonin, P. A. Pevzner. 1995. Genome sequence comparison and scenarios for gene rearrangements: A test case. Genomics 30 299-311.
19. Hannenhalli, S, P. A. Pevzner. 1999. Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals). Journal of the ACM 48 1-27.
20. Jünger, M., G. Reinelt, G. Rinaldi. 1995. The traveling salesman problem. M. Ball, T. Magnanti, C. Monma, G. Nemhauser, eds. Network Models, Handbooks in Operations Research and Management Science, vol. 7. Elsevier, Amsterdam, The Netherlands, 225-330.
21. Kaplan, H., R. Shamir, R. E. Tarjan. 2000. Faster and simpler algorithm for sorting signed permutations by reversals. SIAM Journal on Computing 29 880-892.
22. Kececioglu, J., D. Sankoff. 1994. Efficient bounds for oriented chromosome inversion distance. Proceedings of 5th Annual Symposium on Combinatorial Pattern Matching, Lecture Notes in Computer Science, No. 807. Springer Verlag, Berlin, Germany, 307-325.
23. Kececioglu, J., D. Sankoff. 1995. Exact and approximation algorithms for sorting by reversals, with application to genome rearrangement. Algorithmica 13 180-210.
24. Moret, B. M. E., J. Tang, L-S. Wang, T. Warnow. 2002. Steps toward accurate reconstructions of phylogenies from gene-order data. Journal of Computer and System Sciences 65(3) 508-525.
25. Moret, B. M. E., L-S. Wang, T. Warnow, S. K. Wyman. 2001a. New approaches to phylogeny reconstruction from gene order data. Bioinformatics 17 165S-173S.
26. Moret, B. M. E., S. K. Wyman, D. A. Bader, T. Warnow, M. Yan. 2001b. A new implementation and detailed study of break-point analysis. Proceedings of the 6th Pacific Symposium on Biocomputing (PSB 2001). World Scientific Publishing, Singapore, 583-594.
27. Pe'er, I., R. Shamir. 1998. The median problems for breakpoints are script N signscript P sign-complete. ECCC Report No. 71, University of Trier, Germany, http://www.eccc.uni-trier.de.
28. Pe'er, I., R. Shamir. 2000. Approximation algorithms for the median problem in the breakpoint model. D. Sankoff, J. H. Nadeau, eds. Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics. Kluwer Academic Publishers, Dordrecht, The Netherlands, 225-241.
29. Sankoff, D., M. Blanchette. 2000. Multiple genome rearrangement and breakpoint phylogenies. Journal of Computational Biology 5 555-570.
30. Sankoff, D., D. Bryant, M. Denault, B. F. Lang, G. Burger. 2000. Early eukaryote evolution based on mitochondrial gene order breakpoints. Journal of Computational Biology 7 521-536.
31. Sankoff, D., N. El-Mabrouk. 2000. Duplication, rearrangement and reconciliation. D. Sankoff, J. H. Nadeau, eds. Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics. Kluwer Academic Publishers, Dordrecht, The Netherlands, 537-550.
32. Sankoff, D., J. H. Nadeau, eds. 2000. Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics. Kluwer Academic Publishers, Dordrecht, The Netherlands.
33. Sankoff, D., G. Sundaram, J. Kececioglu. 1996. Steiner points in the space of genome rearrangements. International Journal of Foundations of Computer Science 7 1-9.
34. Setubal, J., J. Meidanis. 1997. Introduction to Computational Molecular Biology. PWS Publishing, Boston, MA.