Haplotype inference

Handbook of Computational Molecular Biology

Volumn , Issue , 2005, Pages 18.1-18.25

  Gusfield, Dan ^a   Orzack, Steven Hecht ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b Fresh Pond Research Institute   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84923219643     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (79)

1. www.hapmap.org.
2. R. M. Adkins. Comparison of the accuracy of methods of computational haplotype inference using a large empirical dataset. BMC Genetics, 5(22), 2004.
3. D. Altshuler and A. Clark. Harvesting medical information from the Human family tree. Science, 307:1052-1053, 2005.
4. V. Bafna, D. Gusfield, S. Hannenhalli, and S. Yooseph. A note on efficient computation of haplotypes via perfect phylogeny. Journal of Computational Biology, 11(5):858-866, 2004.
5. V. Bafna, D. Gusfield, G. Lancia, and S. Yooseph. Haplotyping as perfect phylogeny: A direct approach. Journal of Computational Biology, 10:323-340, 2003.
6. T. Barzuza, J.S. Beckman, R. Shamir, and I. Pe'er. Computational Problems in perfect phylogeny haplotyping: XOR genotypes and TAG SNPs In Thirteenth Annual Symposium on Combinatorial Pattern Matching (CPM'0A), p. 14-31, 2004.
7. T. Barzuza and I. Pe'er. personal communication.
8. R. E. Bixby and D. K. Wagner. An almost linear-time algorithm for graph realization. Mathematics of Operations Research, 13:99-123, 1988.
9. P. Bonizzoni, G. Della Vedova, R. Dondi, and J. Li. The haplotyping problem: Models and solutions. Journal of Computer Science and Technology, 18:675-688, 2003.
10. D. Brown and I. Harrower. A new integer programming formulation for the pure parsimony problem in haplotype analysis. Proceedings of the 2004 Workshop on Algorithms in Bioinformatics, Springer Lecture Notes in Bioinformatics, LNCS, Vol. 3240 p. 254-265.
11. D. Brown and I. Harrower. A new formulation for haplotype inference by pure parsimony. Technical report, University of Waterloo, School of Computer Science. Report CS-2005-03.
12. R.H. Chung and D. Gusfield. Empirical exploration of perfect phylogeny haplotyping and haplotypers. Proceedings of the 9th International Conference on Computing and Combinatorics COCOON03. Springer Lecture Notes in Computer Science, Vol. 2697, pages 5-19, 2003.
13. R.H. Chung and D. Gusfield. Perfect phylogeny haplotyper: Haplotype inferral using atree model. Bioinformatics, 19(6):780-781, 2003.
14. A. Clark. Inference of haplotypes from PCR-amplified samples of diploid populations. Molecular Biology and Evolution, 7:111-122, 1990.
15. A. Clark, K. Weiss, D. Nickerson, and S. Taylor et al. Haplotype structure and population genetic inferences from nucleotide sequence variation in human lipoprotein lipase. American Journal of Human Genetics, 63:595-612, 1998.
16. A. G. Clark. Finding genes underlying risk of complex disease by linkage disequilibrium mapping. Current Opinion in Genetics & Development, 13:296-302, 2003.
17. International HapMap Consortium. HapMap project. Nature, 426:789-796, 2003.
18. M. Daly, J. Rioux, S. Schaffner and T. Hudson et al. High-resolution haplotype structure in the human genome. Nature Genetics, 29:229-232, 2001.
19. P. Damaschke. Fast perfect phylogeny haplotype inference. 14th Symposium on Fundamentals of Computation Theory FCT, 2751:183-194, 2003.
20. P. Damaschke. Incremental haplotype inference, phylogeny and almost bipartite graphs. 2nd RECOMB Satellite Workshop on Computational Methods for SNPs and Haplotypes, pages 1-11, 2004.
21. I. De Vivo, G. S. Huggins, S. E. Hankinson, and P. J. Lescault et al. A functional polymorphism in the promoter of the progesterone receptor gene associated with endometrial cancer risk. Proceedings of the National Academy of Science (USA), 99:12263-12268, 2002.
22. Z. Ding, V. Filkov, and D. Gusfield. A linear-time algorithm for the perfect phylogeny haplotyping problem. Proceedings of the Ninth Annual International Conference on Computational Biology (RECOMB 2005). S. Miyano, J. Mesirov, S. Kasif, and S. Istrail et al. (eds). Springer Lecture Notes in Bioinformatics, LNCS Vol. 3500 p. 585-600.
23. P. Donnelly. Comments made in a lecture given at the DIMACS conference on Computational Methods for SNPs and Haplotype Inference, November 2002.
24. N. El-Mabrouk and D. Labuda. Haplotype histories as pathways of recombinations. Bioinformatics, 20:1836-1841, 2004.
25. E. Eskin, E. Halperin, and R. M. Karp. Large scale reconstruction of haplotypes from genotype data. Proceedings of the 7th Annual International Conference on Computational Biology (RECOMB 2003). p. 104-113
26. E. Eskin, E. Halperin, and R. M. Karp. Efficient reconstruction of haplotype structure via perfect phylogeny. Journal of Bioinformatics and Computational Biology, 1:1-20, 2003.
27. E. Eskin, E. Halperin, and R. Sharan. Optimally phasing long genomic regions using local haplotype predictions. In Proceedings of the Second RECOMB Satellite Workshop on Computational Methods for SNPs and Haplotypes, February 2004. Pittsburgh, USA.
28. L. Excoffier and M. Slatkin. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Molecular Biology and Evolution, 12:921-927, 1995.
29. S. M. Fullerton, A. Clark, C. Sing and D.A. Nickerson et al. Apolipoprotein E variation at the sequence haplotype level: implications for the origin and maintenance of a major human polymorphism. American Journal of Human Genetics, 67:881-900, 2000.
30. S. M. Fullerton, A. V. Buchanan, V. A. Sonpar and S. L. Taylor et al. The effects of scale: variation in the apoa1/c3/a4/a5 gene cluster. Human Genetics, 115:36-56, 2004.
31. F. Gavril and R. Tamari. An algorithm for constructing edge-trees from hypergraphs. Networks, 13:377-388, 1983.
32. J. Gramm, T. Nierhoff, R. Sharan, and T. Tantau. On the complexity of haplotyping via perfect phylogeny. In Second RECOMB Satellite Workshop on Computational Methods for SNPs and Haplotypes, Pittsburgh, USA, February 2004. In Springer Lecture Notes in Bioinformatics, LNCS 2004.
33. J. Gramm, T. Nierhoff, and T. Tantau. Perfect path phylogeny haplotyping with missing data is fixed-parameter tractable. In First International Workshop on Parameterized and Exact Computation (IWPEC 2004), Bergen, Norway, September 2004. In Springer LNCS 3162, 174-186.
34. D. Gusfield. Efficient algorithms for inferring evolutionary history. Networks, 21:19-28, 1991.
35. D. Gusfield. Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology. Cambridge University Press, Cambridge, UK, 1997.
36. D. Gusfield. A practical algorithm for deducing haplotypes in diploid populations. In Proceedings of 8th International Conference on Intelligent Systems in Molecular Biology, pages 183-189. AAAI Press, 2000.
37. D. Gusfield. Inference of haplotypes from samples of diploid populations: complexity and algorithms. Journal of Computational Biology, 8(3):305-323, 2001.
38. D. Gusfield. Haplotyping as Perfect Phylogeny: Conceptual Framework and Efficient Solutions. In Proceedings of RECOMB 2002: The Sixth Annual International Conference on Computational Biology, pages 166-175, 2002. Extended Abstract.
39. D. Gusfield. Haplotype inference by pure parsimony. In E. Chavez R. Baeza-Yates and M. Crochemore, editors, 1Ąth Annual Symposium on Combinatorial Pattern Matching (CPM'03), volume 2676, pages 144-155. Springer LNCS, 2003.
40. D. Gusfield. An overview of combinatorial methods for haplotype inference. In S. Istrail, M. Waterman, and A. Clark, editors, Computational Methods for SNPs and Haplotype Inference, volume 2983, pages 9-25. Springer, 2004. Lecture Notes in Computer Science.
41. B. Halldorsson, V. Bafna, N. Edwards and R. Lipert et al. Combinatorial problems arising in SNP and haplotype analysis. In C. Calude, M. Dinneen, and V. Vajnovski, editors, Discrete Mathematics and Theoretical Computer Science. Proceedings of DMTCS 2003, volume 2731, pages 26-47. Springer, 2003. Springer Lecture Notes in Computer Science.
42. B. Halldorsson, V. Bafna, N. Edwards and R. Lipert et al. A survey of computational methods for determining haplotypes. In Proceedings ofthe First RECOMB Satellite on Computational Methods for SNPs and Haplotype Inference. Springer Lecture Notes in Bioinformatics, LNCS, Vol. 2983 p. 26-47, 2003.
43. E. Halperin and E. Eskin. Haplotype reconstruction from genotype data using imperfect phylogeny. Bioinformatics, 20:1842-1849, 2004.
44. E. Halperin and R. Karp. Perfect phylogeny and haplotype assignment. Proceedings of The 8th Ann. International Conference Research in Computational Molecular Biology (RECOMB 2004, pages 10-19. ACM Press, 2004.
45. M. Hawley and K. Kidd. HAPLO: a program using the EM algorithm to estimate the frequencies of multi-site haplotypes. Journal of Heredity, 86:409-411, 1995.
46. J. He and A. Zelikovsky. Linear reduction for haplotype inference. In Proc. of2004 Workshop on Algorithms in Bioinformatics, Springer Lecture Notes in Bioinformatics, LNCS Vol. 3240. pages 242-253.
47. L. Helmuth. Genome research: Map of the human genome 3.0. Science, 293:583-585, 2001.
48. D. Hinds, L. Stuve, G. Nilsen, E. Halperin, E. Eskin, D. Gallinger, K. Frazer, and D. Cox. Whole-genome patterns of common DNA variation in three human populations. Science, 307:1072-1079, 2005.
49. Y.T. Huang, K.M. Chao, and T. Chen. An approximation algorithm for haplotype inference by maximum parsimony. ACM Symposium for Applied Computing SAC'05, 2005.
50. E. Hubbell. Personal communication.
51. R. Hudson. Gene genealogies and the coalescent process. Oxford Survey of Evolutionary Biology, 7:1-44, 1990.
52. S. Iwata. University of Tokyo. Personal Communication.
53. G. Kimmel and R. Shamir. The Incomplete Perfect Phylogeny Haplotype Problem. Journal of Bioinformatics and Computational Biology, 3:1-25, 2005
54. P.Y. Kwok. Genomics: Genetic association by whole-genome analysis? Science, 294:1669-1670, 2001.
55. G. Lancia, C. Pinotti, and R. Rizzi. Haplotyping populations: Complexity and approximations. Technical Report dit-02-082, University of Trento, 2002.
56. G. Lancia, C. Pinotti, and R. Rizzi. Haplotyping populations by pure parsimony: Complexity, exact and approximation algorithms. INFORMS Journal on Computing, Special issue on Computational Biology, 16:348-359, 2004.
57. J. Lee. U.T. Austin. Personal Communication.
58. Z. Li, W. Zhou, X. Zhang, and L. Chen. A Parsimonious tree-grow method for haplotype inference. Bioinformatics. 21:3475-3481, 2005.
59. S. Lin, D. Cutler, M. Zwick, and A. Chakravarti. Haplotype inference in random population samples. American Journal of Human Genetics, 71:1129-1137, 2003.
60. L. Loüfgren. Irredundant and redundant boolean branch networks. IRE Transactions on Circuit Theory, CT-6:158-175, 1959.
61. J.C. Long, R.C. William, and M. Urbanek. An E-M algorithm and testing strategy for multiple-locus haplotypes. American Journal of Human Genetics, 56:799-810, 1995.
62. T. Niu, Z. Qin, X. Xu, and J.S. Liu. Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. American Journal of Human Genetics, 70:157-169, 2002.
63. T. Ohto. An experimental analysis of the Bixby-Wagner algorithm for graph realization problems. IPSJ SIGNotes ALgorithms Abstract, http://www.ipsj.or.jp/members/SIGNotes/Eng/16/2002/084/articleúúl.html, 084-001, 2002.
64. S.H. Orzack, D. Gusfield, J. Olson and S. Nesbitt et al. Analysis and exploration of the use of rule-based algorithms and consensus methods for the inferral of haplotypes. Genetics, 165:915-928, 2003.
65. S.H. Orzack, L. Subrahmanyan, D. Gusfield and S. Lissargue et al. A comparison of an exact method and algorithmic method for haplotype frequency inferral. Preprint, 2005.
66. D. Posada and K. Crandall. Intraspecific gene genealogies: trees grafting into networks. Trends in Ecology and Evolution, 16:37-45, 2001.
67. Z. Qin, T. Niu, and J.S. Liu. Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms. American Journal of Human Genetics, 71:1242-1247, 2002.
68. R. V. Satya and A. Mukherjee. An Optimal Algorithm for Perfect Phylogeny Haplotyping. Proceedings of Ąth CSB Bioinformatics Conference. IEEE Press, Los Alamitos, CA, 2005.
69. M. Stephens and P. Donnelly. A comparison of Bayesian methods for haplotype reconstruction from population genotype data. American Journal of Human Genetics, 73:1162-1169, 2003.
70. M. Stephens, N. Smith, and P. Donnelly. A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics, 68:978-989, 2001.
71. Y. Song, Y. Wu and D. Gusfield. Haplotyping with one homoplasy or recombination event. Proceedings of Workshop on Algorithms in Bioinformatics (WABI) 2005. Springer, Lecture Notes in Bioinformatics, LNCS Vol. 3692.
72. S. Tavare. Calibrating the clock: Using stochastic processes to measure the rate of evolution. In E. Lander and M. Waterman, editors, Calculating the Secrets of Life. National Academy Press, 1995.
73. J. D. Wall and J. K. Pritchard. Haplotype blocks and linkage disequilibrium in the human genome. Nature Reviews, 4:587-597, 2003.
74. L. Wang and L. Xu. Haplotype inference by maximum parsimony. Bioinformatics, 19:1773-1780, 2003.
75. B. S. Weir. Genetic Data Analysis II Sinauer Associates 1996.
76. W. T. Whitney. 2-isomorphic graphs. American Mathematics Journal, 55:245-254, 1933.
77. C. Wiuf. Inference of recombination and block structure using unphased data. Genetics, 166:537-545, 2004.
78. R. Y. L. Zee, H. H. Hegener, N. R. Cook, and P. M. Ridker. C-reactive protein gene polymorphisms and the risk of venous thromboembolism: a haplotype-based analysis. Journal of Thrombosis and Haemostasis, 2:1240-1243, 2004.
79. J. Zhang, W. Rowe, A. Clark, and K. Buetow. Genomewide distribution of high-frequency, completely mismatching SNP haplotype pairs observed to be common across Human populations. American Journal of Human Genetics, 73:1073-1081, 2003.