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Leonardo Tininini, Paola Bertolazzi, Alessandra Godi, Giuseppe Lancia, "CollHaps: A Heuristic Approach to Haplotype Inference by Parsimony," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 7, no. 3, pp. 511523, JulySeptember, 2010.  
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@article{ 10.1109/TCBB.2008.130, author = {Leonardo Tininini and Paola Bertolazzi and Alessandra Godi and Giuseppe Lancia}, title = {CollHaps: A Heuristic Approach to Haplotype Inference by Parsimony}, journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {7}, number = {3}, issn = {15455963}, year = {2010}, pages = {511523}, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2008.130}, 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  CollHaps: A Heuristic Approach to Haplotype Inference by Parsimony IS  3 SN  15455963 SP511 EP523 EPD  511523 A1  Leonardo Tininini, A1  Paola Bertolazzi, A1  Alessandra Godi, A1  Giuseppe Lancia, PY  2010 KW  Biology and genetics KW  heuristic methods KW  discrete mathematics. VL  7 JA  IEEE/ACM Transactions on Computational Biology and Bioinformatics ER   
[1] J.C. Venter et al., "The Sequence of the Human Genome," Science, vol. 291, pp. 13041351, 2001.
[2] L. Jin, P.A. Underhill, V. Doctor, R.W. Davis, P. Shen, L.L. CavalliSforza, and P.J. Oefner, "Distribution of Haplotypes from a Chromosome 21 Region Distinguishes Multiple Prehistoric Human Migiration," Proc. Nat'l Academy of Sciences USA, vol. 96, pp. 37963800, 1999.
[3] M.R. Hoehe, K. Köpke, B. Wendel, K. Rohde, C. Flachmeier, K.K. Kidd, W.H. Berrettini, and C.G. M, "Sequence Variability and Candidate Gene Analysis in Complex Disease: Association of $\mu$ Opioid Receptor Gene Variation with Substance Dependence," Human Molecular Genetics, vol. 9, pp. 28952908, 2000.
[4] D. Gusfield and S.H. Orzack, "Haplotype Inference," Handbook of Computational Molecular Biology, S. Aluru, ed., pp. 1811828, CRC Press, 2005.
[5] B.V. Halldorsson, V. Bafna, N. Edwards, R. Lippert, S. Yooseph, and S. Istrail, "A Survey of Computational Methods for Determining Haplotypes," Proc. DIMACS/RECOMB Satellite Workshop Computational Methods for SNPs and Haplotype Inference, pp. 2647, 2002.
[6] G. Lancia, M.C. Pinotti, and R. Rizzi, "Haplotyping Populations by Pure Parsimony: Complexity of Exact and Approximation Algorithms," INFORMS J. Computing, vol. 16, pp. 348359, 2004.
[7] S. Clark, "Inference of Haplotypes from PcrAmplified Samples of Diploid Populations," Molecular Biology and Evolution, vol. 7, pp. 111122, 1990.
[8] E. Hubbell, "Finding a Maximum Parsimony Solution to Haplotype Phase Is NPHard," personal comm., 2000.
[9] R. Sharan, B.V. 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.
[10] L. Wang and Y. Xu, "Haplotype Inference by Maximum Parsimony," Bioinformatics, vol. 19, pp. 17731780, 2003.
[11] D. Gusfield, "Haplotype Inference by Pure Parsimony," Proc. 14th Ann. Symp. Combinatorial Pattern Matching (CPM '03), pp. 144155, 2003.
[12] D.G. Brown and I.M. Harrower, "Integer Programming Approaches to Haplotype Inference by Pure Parsimony," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 3, no. 2, pp. 141154, Apr.June 2006.
[13] I. Lynce and J. MarquesSilva, "Sat in Bioinformatics: Making the Case with Haplotype Inference," Proc. Int'l Conf. Theory and Applications of Satisfiability Testing (SAT), pp. 283296, 2006.
[14] I. Lynce and J. MarquesSilva, "Haplotype Inference with Boolean Satisfiability," Int'l J. Artificial Intelligence Tools, vol. 17, pp. 355387, 2008.
[15] L. Excoffier and M. Slatkin, "MaximumLikelihood Estimation of Molecular Haplotype Frequencies in a Diploid Population," Molecular Biology and Evolution, vol. 12, pp. 921927, 1995.
[16] M.E. Hawley and K.K. Kidd, "Haplo: A Program Using the EM Algorithm to Estimate the Frequencies of MultiSite Haplotypes," J. Heredity, vol. 86, pp. 409411, 1995.
[17] J.C. Long, R.C. Williams, and M. Urbanek, "An EM Algorithm and Testing Strategy for MultipleLocus Haplotypes," Am. J. Human Genetics, vol. 56, pp. 799810, 1995.
[18] G. Kimmel and R. Shamir, "Gerbil: Genotype Resolution and Block Identification Using Likelihood," Proc. Nat'l Academy of Sciences USA, vol. 102, pp. 158162, 2005.
[19] M. Stephens and P. Donnelly, "A Comparison of Bayesian Methods for Haplotype Reconstruction from Population Genotype Data," Am. J. Human Genetics, vol. 73, pp. 11621169, 2003.
[20] R.R. Hudson, "Gene Genealogies and the Coalescent Process," Oxford Surveys in Evolutionary Biology, D.J. Futuyma and J. Antonovics, eds., vol. 7, pp. 144, Oxford Univ. Press, 2006.
[21] P. Scheet and M. Stephens, "A Fast and Flexible Statistical Model for LargeScale Population Genotype Data: Applications to Inferring Missing Genotypes and Haplotypic Phase," Am. J. Human Genetics, vol. 78, pp. 629644, 2006.
[22] T. Niu, Z.S. Qin, X. Xu, and J.S. Liu, "Bayesian Haplotype Inference for Multiple Linked SingleNucleotide Polymorphisms," Am. J. Human Genetics, vol. 70, pp. 157169, 2002.
[23] G. Lancia and P. Serafini, "A Covering Approach with ColumnGeneration for Parsimony Haplotyping," Technical Report 407, Dip. di Matematica e Informatica, Univ. of Udine, 2007.
[24] R.R. Hudson, "Generating Samples under a WrightFisher Neutral Model of Genetic Variation," Bioinformatics, vol. 18, pp. 337338, 2002.
[25] M. Stephens, N. Smith, and P. Donnelly, "A New Statistical Method for Haplotype Reconstruction from Population Data," Am. J. Human Genetics, vol. 68, pp. 978989, 2001.
[26] S. Lin, D.J. Cutler, E. Zwick, and A. Chakravarti, "Haplotype Inference in Random Population Samples," Am. J. Human Genetics, vol. 71, pp. 11291137, 2002.
[27] M.J. Rieder, S.L. Taylor, A.G. Clark, and D.A. Nickerson, "Sequence Variation in the Human Angiotensin Converting Enzyme," Nature Genetics, vol. 22, pp. 5962, 1999.
[28] B. Kerem, J.M. Rommens, J.A. Buchanan, D. Marliewicz, T.K. Cox, A. Chakravarti, M. Buchwald, and L. Tsui, "Identification of the Cystic Fibrosis Gene: Genetic Analysis," Science, vol. 245, pp. 10731080, 1989.
[29] D. Fallin and N.J. Schork, "Accuracy of Haplotype Frequency Estimation for Biallelic Loci, via the ExpectationMaximization Algorithm for Unphased Diploid Genotype Data," Am. J. Human Genetics, vol. 67, pp. 947959, 2000.
[30] M.J. Daly, J.D. Rioux, S.F. Schaffner, T.J. Hudson, and E.S. Lander, "HighResolution Haplotype Structure in the Human Genome," Nature Genetics, vol. 29, pp. 229232, 2001.