메뉴 건너뛰기




Volumn 4598 LNCS, Issue , 2007, Pages 51-64

Integer programming formulations and computations solving phylogenetic and population genetic problems with missing or genotypic data

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; COMBINATORIAL OPTIMIZATION; INTEGER PROGRAMMING; PROBLEM SOLVING;

EID: 37849054103     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-73545-8_8     Document Type: Conference Paper
Times cited : (29)

References (31)
  • 1
    • 37849037319 scopus 로고    scopus 로고
    • Bafna, V., Bansal, V.: Improved recombination lower bounds for haplotype data. In: McLysaght, A., Huson, D.H. (eds.) RECOMB 2005. LNCS (LNBI), 3678, Springer, Heidelberg (2005)
    • Bafna, V., Bansal, V.: Improved recombination lower bounds for haplotype data. In: McLysaght, A., Huson, D.H. (eds.) RECOMB 2005. LNCS (LNBI), vol. 3678, Springer, Heidelberg (2005)
  • 3
    • 33750715305 scopus 로고    scopus 로고
    • A new formulation for haplotype inference by pure parsimony, report cs-2005-03
    • Technical report, University of Waterloo, School of Computer Science
    • Brown, D., Harrower, I.: A new formulation for haplotype inference by pure parsimony, report cs-2005-03. Technical report, University of Waterloo, School of Computer Science (2005)
    • (2005)
    • Brown, D.1    Harrower, I.2
  • 5
    • 79959524146 scopus 로고    scopus 로고
    • A haplotype map of the human genome
    • International HapMap Consortium
    • International HapMap Consortium. A haplotype map of the human genome. Nature, 437 1299-1320 (2005)
    • (2005) Nature , vol.437 , pp. 1299-1320
  • 6
    • 26444521262 scopus 로고    scopus 로고
    • Ding, Z., Filkov, V., Gusfield, D.: A linear-time algorithm for the perfect phylogeny haplotyping problem. In: Miyano, S., Mesirov, J., Kasif, S., Istrail, S., Pevzner, P., Waterman, M. (eds.) RECOMB 2005. LNCS (LNBI), 3500, pp. 585-600. Springer, Heidelberg (2005)
    • Ding, Z., Filkov, V., Gusfield, D.: A linear-time algorithm for the perfect phylogeny haplotyping problem. In: Miyano, S., Mesirov, J., Kasif, S., Istrail, S., Pevzner, P., Waterman, M. (eds.) RECOMB 2005. LNCS (LNBI), vol. 3500, pp. 585-600. Springer, Heidelberg (2005)
  • 8
    • 84987049379 scopus 로고
    • Efficient algorithms for inferring evolutionary history
    • Gusfield, D.: Efficient algorithms for inferring evolutionary history. Networks 21, 19-28 (1991)
    • (1991) Networks , vol.21 , pp. 19-28
    • Gusfield, D.1
  • 11
    • 33644509032 scopus 로고    scopus 로고
    • Gusfield, D.: Haplotype inference by pure parsimony. In: Baeza-Yates, R.A., Chavez, E., Crochemore, M. (eds.) CPM 2003. LNCS, 2676, pp. 144-155. Springer, Heidelberg (2003)
    • Gusfield, D.: Haplotype inference by pure parsimony. In: Baeza-Yates, R.A., Chavez, E., Crochemore, M. (eds.) CPM 2003. LNCS, vol. 2676, pp. 144-155. Springer, Heidelberg (2003)
  • 12
    • 84923219643 scopus 로고    scopus 로고
    • Haplotype inference
    • Aluru, S, ed, Chapman and Hall/CRC, Boca Raton
    • Gusfield, D., Orzack, S.: Haplotype inference. In: Aluru, S. (ed.) Handbook of Computational Molecular Biology, vol. 18, pp. 1-25. Chapman and Hall/CRC, Boca Raton (2005)
    • (2005) Handbook of Computational Molecular Biology , vol.18 , pp. 1-25
    • Gusfield, D.1    Orzack, S.2
  • 13
    • 4444367508 scopus 로고    scopus 로고
    • Haplotype reconstruction from genotype data using Imperfect Phylogeny
    • Halperin, E., Eskin, E.: Haplotype reconstruction from genotype data using Imperfect Phylogeny. Bioinformatics 20, 1842-1849 (2004)
    • (2004) Bioinformatics , vol.20 , pp. 1842-1849
    • Halperin, E.1    Eskin, E.2
  • 15
    • 0036184745 scopus 로고    scopus 로고
    • Generating samples under the Wright-Fisher neutral model of genetic variation
    • Hudson, R.: Generating samples under the Wright-Fisher neutral model of genetic variation. Bioinformatics 18(2), 337-338 (2002)
    • (2002) Bioinformatics , vol.18 , Issue.2 , pp. 337-338
    • Hudson, R.1
  • 16
    • 0022211482 scopus 로고
    • Statistical properties of the number of recombination events in the history of a sample of DNA sequences
    • Hudson, R., Kaplan, N.: Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111, 147-164 (1985)
    • (1985) Genetics , vol.111 , pp. 147-164
    • Hudson, R.1    Kaplan, N.2
  • 17
    • 11844254788 scopus 로고    scopus 로고
    • GERBIL: Genotype resolution and block identification using likelihood
    • Kimmel, G., Shamir, R.: GERBIL: Genotype resolution and block identification using likelihood. PNAS 102, 158-162 (2005)
    • (2005) PNAS , vol.102 , pp. 158-162
    • Kimmel, G.1    Shamir, R.2
  • 18
    • 85149607858 scopus 로고    scopus 로고
    • Lancia, G., Pinotti, C., Rizzi, R.: Haplotyping populations by pure parsimony: Complexity, exact and approximation algorithms. INFORMS J. on Computing, special issue on Computational Biology 16, 348-359 (2004)
    • Lancia, G., Pinotti, C., Rizzi, R.: Haplotyping populations by pure parsimony: Complexity, exact and approximation algorithms. INFORMS J. on Computing, special issue on Computational Biology 16, 348-359 (2004)
  • 20
    • 33344458848 scopus 로고    scopus 로고
    • A comparison of phasing algorithms for trios and unrelated individuals
    • Marchini, J., Donnelly, P., et al.: A comparison of phasing algorithms for trios and unrelated individuals. Am. J. of Human Genetics 78, 437-450 (2006)
    • (2006) Am. J. of Human Genetics , vol.78 , pp. 437-450
    • Marchini, J.1    Donnelly, P.2
  • 22
    • 33745301284 scopus 로고    scopus 로고
    • An optimal algorithm for perfect phylogeny haplotyping
    • IEEE Computer Society Press, Los Alamitos
    • Satya, R.V., Mukherjee, A.: An optimal algorithm for perfect phylogeny haplotyping. In: Proceedings of 4th CSB Bioinformatics Conference, IEEE Computer Society Press, Los Alamitos (2005)
    • (2005) Proceedings of 4th CSB Bioinformatics Conference
    • Satya, R.V.1    Mukherjee, A.2
  • 23
    • 85142151067 scopus 로고    scopus 로고
    • Constructing near-perfect phylogenies with multiple homoplasy events. Bioinformatics 22, 514-522 (2006) Bioinformatics Suppl
    • Satya, R.V., Mukherjee, A., Alexe, G., Parida, L., Bhanot, G.: Constructing near-perfect phylogenies with multiple homoplasy events. Bioinformatics 22, 514-522 (2006) Bioinformatics Suppl., Proceedings of ISMB 2006
    • (2006) Proceedings of ISMB
    • Satya, R.V.1    Mukherjee, A.2    Alexe, G.3    Parida, L.4    Bhanot, G.5
  • 24
    • 33644974019 scopus 로고    scopus 로고
    • A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotypic phase
    • Scheet, P., Stephens, M.: A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am. J. Human Genetics 78, 629-644 (2006)
    • (2006) Am. J. Human Genetics , vol.78 , pp. 629-644
    • Scheet, P.1    Stephens, M.2
  • 26
    • 37849030737 scopus 로고    scopus 로고
    • Song, Y.S., Wu, Y., Gusfield, D.: Haplotyping with one homoplasy or recombination event. In: Casadio, R., Myers, G. (eds.) WABI 2005. LNCS (LNBI), 3692, Springer, Heidelberg (2005)
    • Song, Y.S., Wu, Y., Gusfield, D.: Haplotyping with one homoplasy or recombination event. In: Casadio, R., Myers, G. (eds.) WABI 2005. LNCS (LNBI), vol. 3692, Springer, Heidelberg (2005)
  • 27
    • 52449147252 scopus 로고
    • The complexity of reconstructing trees from qualitative characters and subtrees
    • Steel, M.: The complexity of reconstructing trees from qualitative characters and subtrees. J. of Classification 9, 91-116 (1992)
    • (1992) J. of Classification , vol.9 , pp. 91-116
    • Steel, M.1
  • 28
    • 0035071957 scopus 로고    scopus 로고
    • A new statistical method for haplotype reconstruction from population data
    • Stephens, M., Smith, N., Donnelly, P.: A new statistical method for haplotype reconstruction from population data. Am. J. Human Genetics 68, 978-989 (2001)
    • (2001) Am. J. Human Genetics , vol.68 , pp. 978-989
    • Stephens, M.1    Smith, N.2    Donnelly, P.3
  • 29
    • 1642360208 scopus 로고    scopus 로고
    • Inference of recombination and block structure using unphased data
    • Wiuf, C.: Inference of recombination and block structure using unphased data. Genetics 166, 537-545 (2004)
    • (2004) Genetics , vol.166 , pp. 537-545
    • Wiuf, C.1
  • 30
    • 37849043928 scopus 로고    scopus 로고
    • Personal Communication
    • Wu, Y.: Personal Communication
    • Wu, Y.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.