Efficient haplotype inference with Boolean Satisfiability

Proceedings of the National Conference on Artificial Intelligence

Volumn 1, Issue , 2006, Pages 104-109

  Lynce, Inês ^a   Marques Silva, João ^b  

^a INESC ID   (Portugal)

^b UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; DATA ACQUISITION; GENES; MATHEMATICAL MODELS; MEDICAL COMPUTING; MUTAGENESIS;

BOOLEAN SATISFIABILITY; GENETIC DISEASES; HAPLOTYPE DATA; MUTATIONS; PROGRAMMING MODELS;

BOOLEAN ALGEBRA;

EID: 33750742445     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (13)

1. Brown, D., and Harrower, I. 2004. A new integer programming formulation for the pure parsimony problem in haplotype analysis. In Proceedings of the 4th Workshop on Algorithms in Bioinformatics (WABI'04).
2. Brown, D., and Harrower, I. 2005a. A new formulation for haplotype inference by pure parsimony. Technical Report CS-2005-03, University of Waterloo, School of Computer Science.
3. Brown, D., and Harrower, I. 2005b. Personal communication.
4. Eén, N., and Sörensson, N. 2003. An extensible satsolver. In Proceedings of the 6th International Conference on Theory and Applications of Satisfiability Testing (SAT'03), 502-518.
5. Frisch, A.; Hnich, B.; Kiziltan, Z.; Miguel, I.; and Walsh, T. 2002. Global constraints for lexicographic orderings. In Proceedings of the 8th International Conference on Principles and Practice of Constraint Programming (CP'02).
6. Gusfield, D., and Orzach, S. 2005. Handbook on Computational Molecular Biology, volume 9 of Chapman and Hall/CRC Computer and Information Science Series. CRC Press, chapter Haplotype Inference.
7. Gusfield, D. 2003. Haplotype inference by pure parsimony. In Proceedings of the 14th Annual Symposium on Combinatorial Pattern Matching (CPM'03), 144-155.
8. Halperin, E., and Karp, R. M. 2004. Perfect phylogeny and haplotype assignment. In Proceedings of the 8th Annual International Conference on Computational Molecular Biology (RECOMB'04), 10-19.
9. Hudson, R. R. 2002. Generating samples under a wrightfisher neutral model of genetic variation. Bio informatics 18(2):337-338.
10. Lancia, G.; Pinotti, C. M.; and Rizzi, R. 2004. Haplotyping populations by pure parsimony: complexity of exact and approximation algorithms. INFORMS Journal on Computing 16(4):348-359.
11. Stephens, M.; Smith, N.; and Donelly, P. 2001. A new statistical method for haplotype reconstruction. American Journal of Human Genetics 68:978-989.
12. The International HapMap Consortium. 2003. The international hapmap project. Nature 426:789-796.
13. Wang, L., and Xu, Y. 2003. Haplotype inference by maximum parsimony. Bioinformatics 19(14):1773-1780.