J. Rhodes

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Identifiability of parameters in latent structure models with many observed variables

C. Matias, E. Allman, J. Rhodes, 2008, 0809.5032.

A concise proof of Kruskal’s theorem on tensor decomposition

J. Rhodes, 2009, 0901.1796.

Phylogenetic invariants for the general Markov model of sequence mutation.

E. Allman, J. Rhodes, 2003, Mathematical biosciences.

Parameter identifiability in a class of random graph mixture models

C. Matias, E. Allman, J. Rhodes, 2010, 1006.0826.

Identifiability of a Markovian model of molecular evolution with gamma-distributed rates

Elizabeth S. Allman, John A. Rhodes, Cecile Ane, 2007, Advances in Applied Probability.

Split Scores: A Tool to Quantify Phylogenetic Signal in Genome‐Scale Data

John A Rhodes, Elizabeth S Allman, Laura S Kubatko, 2016, Systematic biology.

Species Tree Inference from Gene Splits by Unrooted STAR Methods.

John A Rhodes, Elizabeth S Allman, E. Allman, 2018, IEEE/ACM transactions on computational biology and bioinformatics.

Determining species tree topologies from clade probabilities under the coalescent.

John A Rhodes, Elizabeth S Allman, E. Allman, 2011, Journal of theoretical biology.

Maximum likelihood estimation of the Latent Class Model through model boundary decomposition

Piotr Zwiernik, Elizabeth S. Allman, John A. Rhodes, 2017, Journal of Algebraic Statistics.

Split Probabilities and Species Tree Inference Under the Multispecies Coalescent Model

John A Rhodes, Elizabeth S Allman, E. Allman, 2017, Bulletin of mathematical biology.

Quartets and Parameter Recovery for the General Markov Model of Sequence Mutation

E. Allman, J. Rhodes, 2004 .

Algebraic Methods in Phylogenetics

J. Rhodes, M. Casanellas, 2019, Bulletin of mathematical biology.

MOLECULAR PHYLOGENETICS FROM AN ALGEBRAIC VIEWPOINT

E. Allman, J. Rhodes, 2007 .

Algebraic Models in Phylogenetics

J. Rhodes, 2005 .

Bibliography [1] Linda Allen, Stochastic Processes with Applications to Biology, Pearson, New

E. Allman, J. Rhodes, T. Kurtz, 2011 .

Maximum Likelihood Estimates for Binary Random Variables on Trees via Phylogenetic Ideals

E. Allman, J. Rhodes, 2009 .

Slow internalization of human chorionic gonadotropin by cultured granulosa cells

J. Rhodes, D. Albertini, M. Robinson, 1983, Journal of cellular physiology.

Gene tree discord, simplex plots, and statistical tests under the coalescent

Jonathan D. Mitchell, E. Allman, J. Rhodes, 2020, bioRxiv.

The Influence of Passive Stretch and NF‐κB Inhibitors on the Morphology of Dystrophic Muscle Fibers

J. Rhodes, A. Siegel, S. Henley, 2011, Anatomical record.

Relativistic velocity space, Wigner rotation, and Thomas precession

Mark D. Semon, J. Rhodes, 2004, American Journal of Physics.

The tree of blobs of a species network: identifiability under the coalescent

Jonathan D. Mitchell, E. Allman, J. Rhodes, 2022, Journal of Mathematical Biology.

Lecture Notes: The Mathematics of Phylogenetics

E. Allman, J. Rhodes, 2005 .

Identifiability of the Gtr+γ Model of Molecular Evolution

E. Allman, J. Rhodes, C. Ané, 2008 .

Tensors of Nonnegative Rank Two

E. Allman, J. Rhodes, B. Sturmfels, 2013, 1305.0539.

Relativistic velocity space, Wigner rotation, and Thomas precession

Mark D. Semon, J. Rhodes, 2004, American Journal of Physics.

The contractile basis of ameboid movement. II. Structure and contractility of motile extracts and plasmalemma-ectoplasm ghosts

J. Rhodes, D. Taylor, S. Hammond, 1976, The Journal of cell biology.

Parameter Identifiability of a Multitype Pure-Birth Model of Speciation

E. Allman, J. Rhodes, Dakota Dragomir, 2022, J. Comput. Biol..

A generalized AIC for models with singularities and boundaries

Jonathan D. Mitchell, E. Allman, J. Rhodes, 2022, 2211.04136.

Identifiability of Large Phylogenetic Mixture Models

J. Rhodes, S. Sullivant, 2011, Bulletin of Mathematical Biology.

Testing Multispecies Coalescent Simulators using Summary Statistics.

E. Allman, J. Rhodes, H. Baños, 2019, IEEE/ACM transactions on computational biology and bioinformatics.

MSCquartets 1.0: Quartet methods for species trees and networks under the multispecies coalescent model in R

Jonathan D. Mitchell, E. Allman, J. Rhodes, 2020, bioRxiv.

NANUQ: a method for inferring species networks from gene trees under the coalescent model

John Rhodes, Elizabeth Allman, Hector Banos, 2019, Algorithms for Molecular Biology.

Estimating trees from filtered data: identifiability of models for morphological phylogenetics.

John A Rhodes, Elizabeth S Allman, E. Allman, 2009, Journal of theoretical biology.

Mathematical Models in Biology - Introduction

Elizabeth S. Allman, John A. Rhodes, E. Allman, 2004 .

Trees, Fast and Accurate

John A Rhodes, Elizabeth S Allman, E. Allman, 2010, Science.

NJst and ASTRID are not statistically consistent under a random model of missing data

Michael G. Nute, J. Rhodes, T. Warnow, 2020, 2001.07844.

Species Tree Inference from Gene Splits by Unrooted STAR Methods

James H. Degnan, Elizabeth S. Allman, John A. Rhodes, 2016, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Species Tree Inference by the STAR Method and Its Generalizations

James H. Degnan, Elizabeth S. Allman, John A. Rhodes, 2013, J. Comput. Biol..

There are no caterpillars in a wicked forest.

J. Rhodes, J. Degnan, 2015, Theoretical population biology.

The Identifiability of Covarion Models in Phylogenetics

Elizabeth S. Allman, John A. Rhodes, E. Allman, 2008, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

The Identifiability of Tree Topology for Phylogenetic Models, Including Covarion and Mixture Models

Elizabeth S. Allman, John A. Rhodes, E. Allman, 2005, J. Comput. Biol..

Identifiability of species network topologies from genomic sequences using the logDet distance

Elizabeth S. Allman, John A. Rhodes, Hector Banos, 2021, Journal of Mathematical Biology.

Hypothesis testing near singularities and boundaries.

Jonathan D. Mitchell, E. Allman, J. Rhodes, 2018, Electronic journal of statistics.

Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent

John A Rhodes, Elizabeth S Allman, E. Allman, 2009, Journal of mathematical biology.

Species Tree Inference from Genomic Sequences Using the Log-Det Distance

Colby Long, Elizabeth S. Allman, John A. Rhodes, 2018, SIAM J. Appl. Algebra Geom..

Tensor Rank, Invariants, Inequalities, and Applications

Peter D. Jarvis, Jeremy G. Sumner, Elizabeth S. Allman, 2012, SIAM J. Matrix Anal. Appl..

Parameter Identifiability for a Profile Mixture Model of Protein Evolution

Elizabeth S. Allman, John A. Rhodes, Samaneh Yourdkhani, 2020, J. Comput. Biol..

Parameter Identifiability of Discrete Bayesian Networks with Hidden Variables

Marco Valtorta, Elena Stanghellini, Elizabeth S. Allman, 2014, 1406.0541.

A Semialgebraic Description of the General Markov Model on Phylogenetic Trees

Amelia Taylor, Elizabeth S. Allman, John A. Rhodes, 2012, SIAM J. Discret. Math..

Identifiability of Large Phylogenetic Mixture Models

Seth Sullivant, John A Rhodes, J. Rhodes, 2010, Bulletin of mathematical biology.

Identifiability of latent class models with many observed variables

Elizabeth S. Allman, John A. Rhodes, Catherine Matias, 2008 .

Phylogenetic trees and Euclidean embeddings

J. Rhodes, M. Layer, 2016, Journal of mathematical biology.

Gene tree discord, simplex plots, and statistical tests under the coalescent.

Jonathan D. Mitchell, E. Allman, J. Rhodes, 2021, Systematic biology.

Inferring Metric Trees from Weighted Quartets via an Intertaxon Distance

J. Rhodes, Samaneh Yourdkhani, 2020, Bulletin of Mathematical Biology.

Topological Metrizations of Trees, and New Quartet Methods of Tree Inference

John A Rhodes, J. Rhodes, 2017, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Split Probabilities and Species Tree Inference Under the Multispecies Coalescent Model

E. Allman, J. Rhodes, J. Degnan, 2017, Bulletin of Mathematical Biology.

Phylogenetic trees and Euclidean embeddings

J. Rhodes, Mark Layer, 2016, Journal of Mathematical Biology.

Species tree inference by the STAR method, and generalizations

E. Allman, J. Rhodes, J. Degnan, 2012, 1204.4413.

Mathematical models in biology : an introduction

Elizabeth S. Allman, John A. Rhodes, E. Allman, 2003 .

Statistically Consistent k-mer Methods for Phylogenetic Tree Reconstruction

Seth Sullivant, Elizabeth S. Allman, John A. Rhodes, 2015, J. Comput. Biol..

Identifiability of Two-Tree Mixtures for Group-Based Models

Seth Sullivant, Elizabeth S. Allman, John A. Rhodes, 2009, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Phylogenetic ideals and varieties for the general Markov model

Elizabeth S. Allman, John A. Rhodes, E. Allman, 2004, Adv. Appl. Math..

Phylogenomic Models from Tree Symmetries

J. Rhodes, Colby Long, Elizabeth A. Allman, 2023, arXiv.org.

ANOMALOUS NETWORKS UNDER THE MULTISPECIES COALESCENT: THEORY AND PREVALENCE

E. Allman, J. Rhodes, H. Baños, 2023, bioRxiv.

Phylogenetic invariants for stationary base composition

Elizabeth S. Allman, John A. Rhodes, E. Allman, 2004, J. Symb. Comput..

Topological Metrizations of Trees, and New Quartet Methods of Tree Inference

J. Rhodes, 2017, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Hypothesis testing near singularities and boundaries.

Jonathan D. Mitchell, E. Allman, J. Rhodes, 2018, Electronic journal of statistics.

The theta multiplier for number fields via p-adic planes

J. Rhodes, 1997 .

When do phylogenetic mixture models mimic other phylogenetic models?

Seth Sullivant, John A Rhodes, Elizabeth S Allman, 2012, Systematic biology.

Identifiability of Two-Tree Mixtures for Group-Based Models

E. Allman, J. Rhodes, S. Sullivant, 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Identifiability of Large Phylogenetic Mixture Models

J. Rhodes, S. Sullivant, 2010, Bulletin of Mathematical Biology.

The contractile basis of amoeboid movement III. Structure and dynamics of motile extracts and membrane fragments from Dictyostelium discoideum and Amoeba proteus.

J. Rhodes, J. Condeelis, D. Taylor, 1977, Progress in clinical and biological research.

Sequences of metrics on compact Riemann surfaces

J. Rhodes, 1993 .

Identifiability of latent class models with many observed variables

C. Matias, E. Allman, J. Rhodes, 2008 .

Identifying evolutionary trees and substitution parameters for the general Markov model with invariable sites.

John A Rhodes, Elizabeth S Allman, E. Allman, 2007, Mathematical biosciences.