A new integer programming formulation for the pure parsimony problem in haplotype analysis

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 3240, Issue , 2004, Pages 254-265

  Brown, Daniel G ^a   Harrower, Ian M ^a  

^a UNIVERSITY OF WATERLOO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; PROBLEM SOLVING;

EFFICIENT TIME; HAPLOTYPE INFERENCE; HAPLOTYPES; INTEGER PROGRAM; INTEGER PROGRAMMING FORMULATIONS;

INTEGER PROGRAMMING;

EID: 33751173122     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-30219-3_22     Document Type: Article

References (10)

1. A. G. Clark. Inference of haplotypes from PCR-amplified samples of diploid populations. Molecular Biology and Evolution, 7(2):111-112, 1990.
2. D. Gusfield. Haplotype inference by pure parsimony. In Proceedings of the 14th Annual Symposium on Combinatorial Pattern Matching (CPM 2003), volume 2676 of LNCS, pages 144-155. Springer-Verlag, 2003.
3. D. Gusfield. Personal communication, June 2004.
4. B. V. Halldórsson, V. Bafna, N. Edwards, R. Lippert, S. Yooseph, and Sorin Istrail. A survey of computational methods for determining haplotypes. In Computational Methods for SNPs and Haplotype Inference: DIMACS/RECOMB Satellite Workshop, volume 2983 of LNCS, pages 26-47. Springer-Verlag, 2002.
5. R. R. Hudson. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics, 18(2):337-338, 2002.
6. G. Lancia, C. M. Pinotti, and R. Rizzi. Haplotyping populations: Complexity and approximations. Techical report DIT-02-0080, University of Ternto, October 2002.
7. G. Lancia, C. M. Pinotti, and R. Rizzi. Haplotyping populations by pure parsimony: Complexity, exact, and approximation algorithms. INFORMS Journal of Computing, 2004. To appear.
8. T. Niu, Z. S. Qin, X. Xu, and J. S. Liu. Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. American Journal of Human Genetics, 70(1):157-159, 2002.
9. M. Stephens, N. J. Smith, and P. Donnelly. A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics, 68(4):978-979, 2001.
10. L. Wang and Y. Xu. Haplotype inference by maximum parsimony. Bioinformatics, 19(14):1773-1780, 2003.