A note on efficient computation of haplotypes via perfect phylogeny

Journal of Computational Biology

Volumn 11, Issue 5, 2004, Pages 858-866

  Bafna, Vineet ^a   Gusfield, Dan ^b   Hannenhalli, Sridhar ^c   Yooseph, Shibu ^d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b University of California   (United States)

^c UNIVERSITY OF PENNSYLVANIA   (United States)

^d J CRAIG VENTER INSTITUTE   (United States)

Author keywords

Genotype; Haplotype; Matrix multiplication; Perfect phylogeny

Indexed keywords

ARTICLE; BIOINFORMATICS; GENOTYPE; HAPLOTYPE; PARSIMONY ANALYSIS; PHYLOGENY; PRIORITY JOURNAL;

COMPUTATIONAL BIOLOGY; DATA INTERPRETATION, STATISTICAL; GENOTYPE; HAPLOTYPES; PHYLOGENY;

EID: 8444232868     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2004.11.858     Document Type: Article

References (24)

1. Bafna, V., Gusfield, D., Lancia, G., and Yooseph, S. 2003. Haplotyping as perfect phylogeny: A direct approach. J. Comp. Biol. 10(3-4), 323-340.
2. Chung, R.H., and Gusfield, D. 2003a. Empirical exploration of perfect phylogeny haplotyping and haplotypers. Proc. 9th Int. Conf. on Computing and Combinatorics, 2697 of LNCS, 5-19.
3. Chung, R.H., and Gusfield, D. 2003b. Perfect phylogeny haplotyper: Haplotype inferral using a tree model. Bioinformatics 19(6), 780-781.
4. Clark, A. 1990. Inference of haplotypes from PCR-amplified samples of diploid populations. Mol. Biol. Evol. 7, 111-122.
5. Coppersmith, D. 1997. Rectangular matrix multiplication revisited. J. Complexity 13(1), 42-49.
6. Daly, M., Rioux, J., Schaffner, S., Hudson, T., and Lander, E. 2001. High-resolution haplotype structure in the human genome. Nature 29, 229-232.
7. Eskin, E., Halperin, E., and Karp, R.M. 2003. Large scale reconstruction of haplotypes from genotype data. Proc. 7th Int. Conf. on Research in Computational Molecular Biology (RECOMB), 104-113.
8. Excoffier, L., and Slatkin, M. 1995. Maximum-liklihood estimation of molecular haplotype frequencies in a diploid population. Mol. Biol. Evol. 12, 921-927.
9. Fallin, D., Cohen, A., Essioux, L., Chumakov, I., Blumenfeld, M., Cohen, D., and Schork, N.J. 2001. Genetic analysis of case/control data using estimated haplotype frequencies: Application to APOE locus variation and Alzheimer's disease. Genome Res. 11(1), 143-151.
10. Friss, L., Hudson, R., Bartoszewicz, A., Wall, J., Donfalk, T., and Di Rienzo, A. 2001. Gene conversion and differential population histories may explain the contrast between polymorphism and linkage disequilibrium levels. Am. J. Human Genet. 69, 831-843.
11. Garey, M., and Johnson, D. 1979. Computers and Intractability, Freeman, San Francisco.
12. Gusfield, D. 1991. Efficient algorithms for inferring evolutionary history. Networks 21, 19-28.
13. Gusfield, D. 1997. Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology, Cambridge University Press.
14. Gusfield, D. 2002. Haplotyping as perfect phylogeny: Conceptual framework and efficient solutions (extended abstract). Proc. 6th Int. Conf. Computational Biology, 166-175.
15. Gusfield, D. 2003. Haplotype inference by pure parsimony. In R. Baeza-Yates, E. Chavez, and M. Chrochemore, eds., 14th Ann. Symp. on Combinatorial Pattern Matching 2676, 144-155.
16. Helmuth, L. 2001. Genome research: Map of the human genome 3.0. Science 293(5530), 583-585.
17. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409, 860-921.
18. Lancia, G., Pinotti, C., and Rizzi, R. 2002. Haplotyping populations: Complexity and approximations. Technical report dit-02-082, University of Trento.
19. Niu, T., Qin, Z., Xu, X., and Liu, J.S. 2002. Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. Am. J. Hum. Genet. 70, 157-169.
20. Orzack, S., Gusfield, D., Olson, J., Nesbitt, S., and Stanton, V. 2003. Analysis and exploration of the use of rule-based algorithms and consensus methods for the inferral of haplotypes. Genetics 165(2), 915-928.
21. Stephens, J.C., Schneider, J.A., Tanguay, D.A., Choi, J., Acharya, T., Stanley, S.E., Jiang, R., Messer, C.J., Chew, A., Han, J.H., Duan, J., Carr, J.L., Lee, M.S., Koshy, B., Kumar, A.M., Zhang, G., Newell, W.R., Windemuth, A., Xu, C., Kalbfleisch, T.S., Shaner, S.L., Arnold, K., Schulz, V., Drysdale, C.M., Nandabalan, K., Judson, R.S., Ruano, G., and Vovis, G.F. 2001. Haplotype variation and linkage disequilibrium in 313 human genes. Science 293, 489-493.
22. Stephens, M., Smith, N., and Donnelly, P. 2001. A new statistical method for haplotype reconstruction from population data. Am. J. Human Genet. 68, 978-989.
23. Venter, J.C., Adams, M.D., Sutton, G.G., Kerlavage, A.R., Smith, H.O., and Hunkapillar, M. 1998. Shotgun sequencing of the human genome. Science 280, 1540-1542.
24. Wang, L., and Xu, Y. 2003. Haplotype inference by maximum parsimony. Bioinformatics 19(14), 1773-1780.