John Rhodes
2005 | Professor of Mathematics
Massachusetts Institute of Technology 1986, PhD
CH 208B | 907-474-5445
j.rhodes@alaska.edu
My research is primarily in Mathematical Biology, and more specifically in Phylogenetics. It focuses on theory and methods for inferring relationships between organisms from biological sequences such as DNA or proteins. Most recently it has moved from finding evolutionary trees to more difficult problems where hybridization or other forms of horizontal gene transfer results in network relationships, and the signal of these is confounded with population genetic effects captured by a coalescent model. In addition to drawing on probability, discrete math, and modeling, my work often uses an algebraic geometry perspective and computational algebra tools.
Highlighted works:
E.S. Allman, H.D. Banos*, J.D. Mitchell*, and J.A. Rhodes MSCquartets 1.0: Quartet methods for species trees and networks under the multispecies coalescent model in R, Bioinformatics, 10, 2020.
J.A. Rhodes, Topological metrizations of trees, and new quartet methods of tree inference, IEEE/ACM Transactions in Computational Biology and Bioinformatics, 17(6), 2020, 2107--2118.
E.S. Allman, H. Banos*, J.A. Rhodes, NANUQ: A method for inferring species networks from gene trees under the coalescent model, Algorithms for Molecular Biology, 14(24), 2019, 1-- 25.
E.S. Allman, C. Long*, and J.A. Rhodes, Species tree inference from genomic sequences using the log-det distance, SIAM Journal on Applied Algebra and Geometry, 3(1), 2019, 107--127.
J.A. Rhodes and S. Sullivant, Identifiability of large phylogenetic mixture models, Bulletin of Mathematical Biology, 74, 2012, 212--231.
*denotes UAF graduate students or postdocs