Recent Papers and Publications

"Tensors of nonnegative rank two"
Elizabeth S. Allman, John A. Rhodes, B. Sturmfels, and P. Zwiernik
Linear Algebra and its Applications, to appear.

"A semialgebraic description of the general Markov model on phylogenetic trees"
Elizabeth S. Allman, John A. Rhodes, and Amelia Taylor
Preprint on the arXiv, December 2012

"Tensor Rank, Invariants, Inequalities, and Applications"
Elizabeth S. Allman, Peter D. Jarvis, John A. Rhodes, and Jeremy G. Sumner
SIAM Journal on Matrix Analysis and Applications, 34 no. 3 (2013) 1014-1045.

"Species tree inference by the STAR method, and generalizations"
Elizabeth S. Allman, James H. Degnan, and John A. Rhodes
J. Computational Biology, 20 no. 1 (2013) 50-61.

"When Do Phylogenetic Mixture Models Mimic Other Phylogenetic Models?"
Elizabeth S. Allman, John A. Rhodes, and Seth Sullivant
Systematic Biology, 61 no. 6 (2012) 1049-1059.

"Determining species tree topologies from clade probabilities under the coalescent"
Elizabeth S. Allman, James H. Degnan, and John A. Rhodes
Journal of Theoretical Biology, 289 (2011) 96-106.

"Parameter Identifiability in a class of random graph mixture models"
Elizabeth S. Allman, Catherine Matias, and John A. Rhodes
Journal of Statistical Planning and Inference, 141 no. 5 (2011) 1719-1736.

"Identifying the Rooted Species Tree from the Distribution of Unrooted Gene Trees under the Coalescent"
Elizabeth S. Allman, James H. Degnan, and John A. Rhodes
Journal of Mathematical Biology, 62 no.6 (2011) 833-862.

"Identifiability of 2-tree mixtures for group-based models"
Elizabeth S. Allman, Sonja Petrovic, John A. Rhodes, and Seth Sullivant
IEEE/ACM Transactions in Computational Biology and Bioinformatics, 8 no. 3 (2011) 710-722.
Supplementary materials

"Trees, Fast and Accurate"
Elizabeth S. Allman and John A. Rhodes
Science, 327 (2010) 1334-1335.

"Estimating trees from filtered data: Identifiability of models for morphological phylogenetics"
Elizabeth S. Allman, Mark T. Holder, and John A. Rhodes
Journal of Theoretical Biology, 263 (2010) 108-119.

"Identifiability of parameters in latent structure models with many observed variables"
Elizabeth S. Allman, Catherine Matias, and John A. Rhodes
Annals of Statistics, 37 no.6A (2009) 3099-3132.

"The identifiability of Covarion models in phylogenetics"
Elizabeth S. Allman and John A. Rhodes
IEEE/ACM Transactions in Computational Biology and Bioinformatics, 6 no. 1 (2009) 76-88.

"Identifiability of a Markovian model of molecular evolution with gamma-distributed rates"
Elizabeth S. Allman, Cecile Ane, and John A. Rhodes
Advances in Applied Probability, 40 no. 1 (2008) 228-249.
Former title was "Identifiability of the GTR+Gamma model of molecular evolution"

"The Gaps in the proof of identifiability of the GTR+Gamma+I model"
Elizabeth S. Allman, Cecile Ane, and John A. Rhodes
This is now included as an appendix to the paper listed above. (June 2007)

"Identifying evolutionary trees and substitution parameters for the general Markov model with invariable sites "
Elizabeth S. Allman and John A. Rhodes
Mathematical Biosciences, 211 no. 1 (2008) 18-33.
Appendix materials: Maple and Singular code.

"Phylogenetic Ideals and Varieties for the General Markov Model"
Elizabeth S. Allman and John A. Rhodes 
Advances in Applied Mathematics, 40 no. 2 (2008) 127-148.   Available (finally) online Jan 10, 2007.

"Molecular Phylogenetics from an Algebraic Viewpoint "
Elizabeth S. Allman and John A. Rhodes
Statistica Sinica, 17 no. 4 (2007) 1299-1316.

"Phylogenetic Invariants"
Elizabeth S. Allman and John A. Rhodes
Chapter 4 in Reconstructing Evolution New Mathematical and Computational Advances,
edited by O. Gascuel and M. Steel (2007).

"Phylogenetics"
Elizabeth S. Allman and John A. Rhodes
Lecture notes for AMS Short Course "Modeling and Simulation of Biological Networks"
Chapter 2 in Proceedings of Symposia in Applied Mathematics,
edited by R. Laubenbacher (2007).

"The identifiability of tree topology for phylogenetic models, including covarion and mixture models"
Elizabeth S. Allman and John A. Rhodes
Journal of Computational Biology, 13 no. 5 (2006) 1101-1113.

Other papers are available here.