
This Article  
 
Share  
Bibliographic References  
Add to:  
Digg Furl Spurl Blink Simpy Del.icio.us Y!MyWeb  
Search  
 
ASCII Text  x  
Michael R. Fellows, Tzvika Hartman, Danny Hermelin, Gad M. Landau, Frances Rosamond, Liat Rozenberg, "Haplotype Inference Constrained by Plausible Haplotype Data," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no. 6, pp. 16921699, November/December, 2011.  
BibTex  x  
@article{ 10.1109/TCBB.2010.72, author = {Michael R. Fellows and Tzvika Hartman and Danny Hermelin and Gad M. Landau and Frances Rosamond and Liat Rozenberg}, title = {Haplotype Inference Constrained by Plausible Haplotype Data}, journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {8}, number = {6}, issn = {15455963}, year = {2011}, pages = {16921699}, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.72}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }  
RefWorks Procite/RefMan/Endnote  x  
TY  JOUR JO  IEEE/ACM Transactions on Computational Biology and Bioinformatics TI  Haplotype Inference Constrained by Plausible Haplotype Data IS  6 SN  15455963 SP1692 EP1699 EPD  16921699 A1  Michael R. Fellows, A1  Tzvika Hartman, A1  Danny Hermelin, A1  Gad M. Landau, A1  Frances Rosamond, A1  Liat Rozenberg, PY  2011 KW  Haplotyping KW  perfect phylogeny KW  pure parsimony KW  polynomialtime algorithms KW  parameterized complexity. VL  8 JA  IEEE/ACM Transactions on Computational Biology and Bioinformatics ER   
[1] “The International HapMap Project,” Nature, vol. 426, pp. 789796, 2003.
[2] B. Aspvall, M.F. Plass, and R.E. Tarjan, “A LinearTime Algorithm for Testing the Truth of Certain Quantified Boolean Formulas,” Information Processing Letters, vol. 8, no. 3, pp. 121123, 1979.
[3] V. Bafna, D. Gusfield, S. Hannenhalli, and S. Yooseph, “A Note on Efficient Computation of Haplotypes via Perfect Phylogeny,” J. Computational Biology, vol. 11, pp. 858866, 2004.
[4] V. Bafna, D. Gusfield, G. Lancia, and S. Yooseph, “Haplotyping as Perfect Phylogeny: A Direct Approach,” J. Computational Biology, vol. 10, pp. 323340, 2003.
[5] T. Barzuza, J.S. Beckmann, R. Shamir, and I. Peer, “Computational Problems in Perfect Phylogeny Haplotyping: XORGenotypes and Tag SNPs,” Proc. 15th Ann. Symp. Combinatorial Pattern Matching (CPM), pp. 1431, 2004.
[6] D. Brown and I.M. Harrower, “A New Integer Programming Formulation for the Pure Parsimony Problem in Haplotype Analysis,” Proc. Int'l Workshop Algorithms in Bioinformatics (WABI), pp. 254265, 2004.
[7] R. Cilibrasi, L. van Iersel, S. Kelk, and J. Tromp, “On the Complexity of Several Haplotyping Problems,” Proc. Int'l Workshop Algorithms in Bioinformatics (WABI), pp. 128139, 2005.
[8] P. Damaschke, “Fast Perfect Phylogeny Haplotype Inference,” Proc. 14th Symp. Fundamentals of Computation Theory (FCT), pp. 183194, 2003.
[9] Z. Ding, V. Filkov, and D. Gusfield, “A LinearTime Algorithm for the Perfect Phylogeny Haplotyping (PPH) Problem,” J. Computational Biology, vol. 13, pp. 522553, 2006.
[10] R. Downey and M. Fellows, Parameterized Complexity. SpringerVerlag, 1999.
[11] M. Elberfeld and T. Tantau, “Phylogeny and ParsimonyBased Haplotype Inference with Constraints,” Proc. 21st Ann. Symp. Combinatorial Pattern Matching (CPM), 2010.
[12] E. Eskin, E. Halperin, and R. Karp, “Efficient Reconstruction of Haplotype Structure via Perfect Phylogeny,” J. Bioinformatics and Computational Biology, vol. 1, pp. 120, 2003.
[13] R. Fleischer, J. Guo, R. Niedermeier, J. Uhlmann, Y. Wang, M. Weller, and X. Wu, “Extended Islands of Tractability for Parsimony Haplotyping,” Proc. 21st Ann. Symp. Combinatorial Pattern Matching (CPM), 2010.
[14] J. Gramm, T. Nierhoff, R. Sharan, and T. Tantau, “On the Complexity of Haplotyping via Perfect Phylogeny,” Proc. RECOMB Satellite Workshop Computational Methods for SNPs and Haplotypes, 2004.
[15] J. Gramm, T. Nierhoff, R. Sharan, and T. Tantau, “Haplotyping with Missing Data via Perfect Path Phylogenies,” Discrete Applied Math., vol. 155, pp. 788805, 2007.
[16] G. Greenspan and D. Geiger, “ModelBased Inference of Haplotype Block Variation,” Proc. Seventh Ann. Int'l Conf. Research in Computational Molecular Biology (RECOMB '03), pp. 131137, 2003.
[17] D. Gusfield, “Haplotyping As Perfect Phylogeny: Conceptual Framework and Efficient Solutions (Extended Abstract),” Proc. Sixth Ann. Int'l Conf. Research in Computational Molecular Biology (RECOMB), pp. 166175, 2002.
[18] D. Gusfield, “Haplotype Inference by Pure Parsimony,” Proc. 14th Ann. Symp. Combinatorial Pattern Matching (CPM), pp. 144155, 2003.
[19] D. Gusfield and S.H. Orzack, “Haplotype Inference,” Handbook of Computational Molecular Biology, S. Aluru, ed., Chapman Hall/CRC Press, 2006.
[20] D. Gusfield, Y. Song, and Y. Wu, “Algorithms for Imperfect Phylogeny Haplotyping with a Single Homoplasy or Recombination Event,” Proc. Int'l Workshop Algorithms in Bioinformatics (WABI), pp. 152164, 2005.
[21] B. Halldórsson, V. Bafna, N. Edwards, R. Lippert, S. Yooseph, and S. Istrail, “A Survey of Computational Methods for Determining Haplotypes,” Proc. RECOMB Satellite Workshop Computational Methods for SNPs and Haplotype Inference, pp. 2647, 2003.
[22] E. Halperin and E. Eskin, “Haplotype Reconstruction from Genotype Data Using Imperfect Phylogeny,” Bioinformatics, vol. 20, pp. 18421849, 2004.
[23] E. Halperin and R.M. Karp, “Perfect Phylogeny and Haplotype Assignment,” Proc. Eighth Ann. Int'l Conf. Research in Computational Molecular Biology (RECOMB), pp. 1019, 2004.
[24] R. Hudson, “Gene Genealogies and the Coalescent Process,” Oxford Survey of Evolutionary Biology, vol. 7, pp. 144, 1990.
[25] L. Van Iersel, J. Keijsper, S. Kelk, and L. Stougie, “Beaches of Islands of Tractability: Algorithms for Parsimony and Minimum Perfect Phylogeny Haplotyping Problems,” Proc. Int'l Workshop Algorithms in Bioinformatics (WABI), pp. 8091, 2006.
[26] G. Kimmel and R. Shamir, “The Incomplete Perfect Phylogeny Haplotype Problem,” J. Bioinformatics and Computational Biology, vol. 3, pp. 359384, 2005.
[27] G. Lancia, C. Pinotti, and R. Rizzi, “Haplotyping Population by Pure Parsimony: Complexity, Exact and Approximation Algorithms,” INFORMS J. Computing, Special Issue on Computational Biology, vol. 16, pp. 348359, 2004.
[28] G. Lancia and R. Rizzi, “A Polynomial Case of the Parsimony Haplotyping Problem,” Operations Research Letters, vol. 34, pp. 289295, 2006.
[29] P. Rastas, M. Koivisto, H. Mannila, and E. Ukkonnen, “A Hidden Markov Technique for Haplotype Reconstruction,” Proc. Int'l Workshop Algorithms in Bioinformatics (WABI), pp. 140151, 2005.
[30] R.V. Satya and A. Mukherjee, “An Optimal Algorithm for Perfect Phylogeny Haplotyping,” J. Computational Biology, vol. 13, no. 4, pp. 897928, 2006.
[31] R. Sharan, B. Halldorsson, and S. Istrail, “Islands of Tractability for Parsimony Haplotyping,” IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 3, no. 3, pp. 303311, JulySept. 2006.
[32] S. Tavare, “Calibrating the Clock: Using Stochastic Process to Measure the Rate of Evolution,” Calculating the Secrets of Life, E. Lander and M. Waterman, eds., Nat'l Academy Press, 1995.
[33] L. Wang and L. Xu, “Haplotype Inference by Maximum Parsimony,” Bioinformatics, vol. 19, pp. 17731780, 2003.