
This Article  
 
Share  
Bibliographic References  
Add to:  
Digg Furl Spurl Blink Simpy Del.icio.us Y!MyWeb  
Search  
 
ASCII Text  x  
Ana ArribasGil, Dirk Metzler, JeanLouis Plouhinec, "Statistical Alignment with a Sequence Evolution Model Allowing Rate Heterogeneity along the Sequence," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, no. 2, pp. 281295, AprilJune, 2009.  
BibTex  x  
@article{ 10.1109/TCBB.2007.70246, author = {Ana ArribasGil and Dirk Metzler and JeanLouis Plouhinec}, title = {Statistical Alignment with a Sequence Evolution Model Allowing Rate Heterogeneity along the Sequence}, journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {6}, number = {2}, issn = {15455963}, year = {2009}, pages = {281295}, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2007.70246}, 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  Statistical Alignment with a Sequence Evolution Model Allowing Rate Heterogeneity along the Sequence IS  2 SN  15455963 SP281 EP295 EPD  281295 A1  Ana ArribasGil, A1  Dirk Metzler, A1  JeanLouis Plouhinec, PY  2009 KW  Markov processes KW  probabilistic algorithms KW  mathematics and statistics KW  sequence evolution KW  biology and genetics. VL  6 JA  IEEE/ACM Transactions on Computational Biology and Bioinformatics ER   
[1] R. Durbin, S. Eddy, A. Krogh, and G. Mitchison, Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge Univ. Press, 1998.
[2] F. Ronquist and J.P. Huelsenbeck, “Mrbayes 3: Bayesian Phylogenetic Inference under Mixed Models,” Bioinformatics, vol. 19, pp.15721574, 2003.
[3] J. Felsenstein, Inferring Phylogenies. Sinauer Assoc., 2004.
[4] T. Jukes and C. Cantor, Evolution of Protein Molecules in Mammalian Protein Metabolism, H.N. Munro, ed., pp. 21132. Academic Press, 1969.
[5] M. Dayhoff, R. Schwartz, and B. Orcutt, “A Model of Evolutionary Change in Proteins,” Atlas of Protein Structure, vol. 5, no. 3, pp. 345352, Nat'l Biomedical Research Foundation, 1978.
[6] J. Thorne, H. Kishino, and J. Felsenstein, “An Evolutionary Model for Maximum Likelihood Alignment of DNA Sequences,” J.Molecular Evolution, vol. 33, pp. 114124, 1991.
[7] J. Thorne, H. Kishino, and J. Felsenstein, “Inching toward Reality: An Improved Likelihood Model of Sequence Evolution,” J.Molecular Evolution, vol. 34, pp. 316, 1992.
[8] D. Metzler, R. Fleissner, A. Wakolbinger, and A. von Haeseler, “Assessing Variability by Joint Sampling of Alignments and Mutation Rates,” J. Molecular Evolution, vol. 53, no. 6, pp. 660669, 2001.
[9] D. Metzler, “Statistical Alignment Based on Fragment Insertion and Deletion Models,” Bioinformatics, vol. 19, no. 4, pp. 490499, 2003.
[10] J. Hein, C. Wiuf, B. Knudsen, M. Moller, and G. Wibling, “Statistical Alignment: Computational Properties, Homology Testing and GoodnessofFit,” J. Molecular Biology, vol. 302, pp.265279, 2000.
[11] I. Miklos, G.A. Lunter, and I. Holmes, “A ‘Long Indel’ Model for Evolutionary Sequence Alignment,” Molecular Biology and Evolution, vol. 21, no. 3, pp. 529540, 2004.
[12] G. Lunter, C. Ponting, and J. Hein, “GenomeWide Identification of Human Functional DNA Using a Neutral Indel Model,” PLoS Computational Biology, vol. 2, no. 1, p. e5, 2006.
[13] F. Chiaromonte, R. Weber, K. Roskin, M. Diekhans, W. Kent, and D. Haussler, “The Share of Human Genomic DNA under Selection Estimated from HumanMouse Genomic Alignments,” Proc. Cold Spring Harbor Symp. Quantitative Biology, vol. 68, pp. 245254, 2003.
[14] G. Bejerano, M. Pheasant, I. Makunin, S. Stephen, W. Kent, J. Mattick, and D. Haussler, “Ultraconserved Elements in the Human Genome,” Science, vol. 304, no. 5675, pp. 13211325, 2004.
[15] A. Siepel, G. Bejerano, J. Pedersen, A. Hinrichs, M. Hou, K. Rosenbloom, H. Clawson, J. Spieth, L. Hillier, S. Richards, G. Weinstock, R. Wilson, R. Gibbs, W. Kent, W. Miller, and D. Haussler, “Evolutionarily Conserved Elements in Vertebrate, Insect, Worm, and Yeast Genomes,” Genome Research, vol. 15, no. 8, pp. 10341050, 2005.
[16] A. Stathopoulos and M. Levine, “Genomic Regulatory Networks and Animal Development,” Developmental Cell, vol. 9, no. 4, pp.449462, 2005.
[17] J. Felsenstein and G. Churchill, “A Hidden Markov Model Approach to Variation among Sites in Rate of Evolution,” Molecular Biology and Evolution, vol. 13, pp. 93104, 1996.
[18] A. Dempster, N. Laird, and D. Rubin, “Maximum Likelihood from Incomplete Data via the EM Algorithm,” J. Royal Statistical Soc. B, vol. 39, pp. 138, 1977.
[19] I. Holmes, “Using Evolutionary Expectation Maximization to Estimate Indel Rates,” Bioinformatics, vol. 21, no. 10, pp. 22942300, 2005.
[20] B. Delyon, M. Lavielle, and E. Moulines, “Convergence of a Stochastic Approximation Version of the EM Algorithm,” The Annals of Statistics, vol. 27, pp. 94128, 1999.
[21] J. Liu and C.E. Lawrence, “Bayesian Inference on Biopolymer Models,” Bioinformatics, vol. 15, no. 1, pp. 3852, 1999.
[22] C. Robert and G. Casella, Monte Carlo Statistical Methods. Springer, 2004.
[23] N. Metropolis, A. Rosenbluth, M. Rosenbluth, A. Teller, and E. Teller, “Equations of State Calculations by Fast Computing Machines,” J. Chemical Physics, vol. 21, no. 6, pp. 10871092, 1953.
[24] W. Hastings, “Monte Carlo Sampling Methods Using Markov Chains and Their Applications,” Biometrika, vol. 57, no. 1, pp. 97109, 1970.
[25] E. Kuhn and M. Lavielle, “Coupling a Stochastic Approximation Version of EM with a MCMC Procedure,” ESAIM Probability and Statistics, vol. 8, pp. 115131, 2004.
[26] M. Powell, “A Fast Algorithm for Nonlinearly Constrained Optimization Calculations,” Lecture Notes in Math., vol. 630, pp.144157, 1978.
[27] X. Li and Z. Zhao, “Relative Error Measures for Evaluation of Estimation Algorithms,” Proc. Eighth Int'l Conf. Information Fusion, 2005.
[28] A. ArribasGil, E. Gassiat, and C. Matias, “Parameter Estimation in Pair Hidden Markov Models,” Scandinavian J. Statistics, vol. 33, no. 4, pp. 651671, 2006.
[29] D. Kurokawa, H. Kiyonari, R. Nakayama, C. KimuraYoshida, I. Matsuo, and S. Aizawa, “Regulation of Otx2 Expression and Its Functions in Mouse Forebrain and Midbrain,” Development, vol. 131, no. 14, pp. 33193331, 2004.
[30] D. Kurokawa, N. Takasaki, H. Kiyonari, R. Nakayama, C. KimuraYoshida, I. Matsuo, and S. Aizawa, “Regulation of Otx2 Expression and Its Functions in Mouse Epiblast and Anterior Neuroectoderm,” Development, vol. 131, no. 14, pp. 33073317, 2004.
[31] I. Holmes and W. Bruno, “Evolutionary HMMs: A Bayesian Approach to Multiple Alignment,” Bioinformatics, vol. 17, pp. 803820, 2001.
[32] R. Fleissner, D. Metzler, and A. von Haeseler, “Simultaneous Statistical Multiple Alignment and Phylogeny Reconstruction,” Systematic Biology, vol. 54, no. 4, pp. 548561, 2005.
[33] G. Lunter, I. Miklos, A. Drummond, J. Jensen, and J. Hein, “Bayesian Coestimation of Phylogeny and Sequence Alignment,” BMC Bioinformatics, pp. 683, 2005.