Phylogeny
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Pitfalls of Heterogeneous Processes for Phylogenetic Reconstruction
D. Stefankovic and E. Vigoda
Systematic Biology 56(1): 113-124, 2007.
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Closely related paper:
Phylogeny of Mixture Models: Robustness of Maximum Likelihood and Non-identifiable Distributions
D. Stefankovic and E. Vigoda
Journal of Computational Biology 14(2): 156-189, 2007.
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Phylogenetic MCMC Algorithms are Misleading on Mixtures of Trees
E. Mossel and E. Vigoda
Science, September 30, 2005, 309:2207-2209.
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Mathematical version of the paper:
Limitations of Markov Chain Monte Carlo Algorithms for Bayesian Inference of Phylogeny.
E. Mossel and E. Vigoda
Annals of Applied Probability 16(4): 2215-2234, 2006.
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Molecular Evolution
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Heterogeneous Genomic Molecular Clocks in Primates
S-H. Kim, N. Elango, C. Warden, E. Vigoda, and S. Yi
PLOS Genetics, October 2006, 2(10), paper e163.
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Mutations of Different Molecular Origins Exhibit Contrasting Patterns of Regional Substitution Rate Variation
N. Elango, S-H. Kim, NISC Comparative Sequencing Program, E. Vigoda, and S. Yi
PLOS Computational Biology, 4(2):e1000015, 2008.
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Mathematical Biology
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Analysis of Top-Swap Shuffling for Genome Rearrangements
N. Bhatnagar, P. Caputo, P. Tetali, and E. Vigoda
Annals of Applied Probability, 17(4):1424-1445, 2007.
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