Elizabeth S. Allman

Elizabeth S. Allman

Associate Professor	US Mail:
Senior Research Associate, IAB	Department of Mathematics and Statistics
Office: Chapman 303B	University of Alaska Fairbanks
Phone: (907) 474-2479	PO Box 756660
E-mail: e.allman@uaf.edu	Fairbanks, AK 99709

Education

University of California at Los Angeles M.A., 1992
University of California at Los Angeles Ph.D., 1995

Research Interests

Biomathematics, including techniques of phylogenetic tree construction, models of evolution
Statistics, Computational Algebraic Statistics, Singular and Macaulay2
Division algebras; Brauer groups; Galois Theory, particularly computational Galois theory

Conference announcements:

June 2008:	Mathematics and Informatics of Evolution and Phylogeny, Montpellier, France
Oct. 2008:	Applications of Algebraic Geometry, Vancouver, BC

Challenge Problem: Determine the ideal defining the fourth secant variety of P^3 x P^3 x P^3.
Some details, including a prize for its solution. Update coming soon.

Recent Papers and Publications

"The identifiability of Covarion models in phylogenetics"
Elizabeth S. Allman and John A. Rhodes, TCBB, to appear.
(Jan 2008)

"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"
(August 2007)

"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.
Preprint or on the arXiv, February 24, 2007, 1-19.
Appendix materials: Maple and Singular code.

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

"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.
Preprint, November 9, 2005, 1-30. covarion.pdf or on the arXiv

"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).

"Lecture Notes: The Mathematics of Phylogenetics"
Elizabeth S. Allman and John A. Rhodes
Park City Mathematics Institute's summer program in Mathematical Biology, undergraduate program
Preprint, June 26, 2005, 1-127.

"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 online Jan 10, 2007.
Preprint, October 20, 2004
http://arxiv.org/abs/math.AG/0410604 or GM2plus.pdf

"Phylogenetic invariants for stationary base composition"
Elizabeth S. Allman and John A. Rhodes
Journal Symbolic Computation, 41 (2006) 138-150.
http://arxiv.org/abs/q-bio.PE/0407035 or basecomp.pdf

"Quartets and Parameter Recovery for the General Markov Model of Sequence Mutation"
Elizabeth S. Allman and John A. Rhodes
AMRX App. Math. Res. Express Vol. 2004, no. 4, 2004, 107--131.
Preprint: quartets.pdf

"Phylogenetic Invariants for the General Markov Model of Sequence Mutation"
Elizabeth S. Allman and John A. Rhodes Math. Biosci. 186(2), 2003, 113-144,
A longer version, with several proofs and an example omitted from the published version, phyloplus.pdf

Mathematical Models in Biology

An Introduction

Elizabeth S. Allman and John A. Rhodes,
Cambridge University Press, January 2004.
Table of Contents, Preface, etc. bookinfo.pdf

Resources: MATLAB mfiles and solution manual: http://publishing.cambridge.org/resources/0521525861/

Solution Manual for Mathematical Models in Biology: An Introduction, (electronic)
Elizabeth S. Allman and John A. Rhodes

List of known errata. (Please e-mail additional errors to e.allman@uaf.edu.)

Instructors may e-mail Cambridge directly to receive online access to the solutions manual: solutions@cambridge.org

Note: The introduction to the book incorrectly gives the web address for MATLAB files and the solution manual. The correct web address (with extension) is: http://www.cup.org/titles/0521525861.htm

Recent/Upcoming talks and short courses

SMBE (poster)

University of Barcelona

Joint Mathematics Meetings, special session on Secant Varieties and Related Topics, San Diego, CA. (Jan 2008) slides

University of Sheffield, Pure Maths Colloquium, Sheffield, England. (Oct 2007)

INI workshop, "Current Challenges and Problems in Phylogenetics", Cambridge, England. (Sept 2007)

IMA Annual Program Year workshop, "Applications in Biology, Dynamics, and Statistics", Minneapolis, MN. (March 2007) slides

Joint Statistics Meetings, special session organized by B. Larget, Seattle, WA, (August 2006)

AMS short course Modeling and Simulation of Biological Networks (Jan 2006 - immediately preceding the Joint Meetings)

AMS and MAA Joint Mathematics Meetings, co-organizer with S. Sullivant of special session on Algebraic Statistics: Theory and Practice (Jan 2006)

Workshop on Algebraic Statistics and Computational Biology at the Clay Mathematics Institute. (Nov. 2005)

Workshop presentation at The Mathematical Biosciences Institute at the Ohio State University as part of MBI's workshop "Phylogeography and Phylogenetics" organized by Craig Moritz, Michael Hickerson, and Dennis Pearl (September 2005)

Satellite conference at University of Buenos Aires (August 2005)

XVI Coloquio Latinoamericano de Álgebra, Uruguay (August 2005)

Institute for Advanced Study - Park City Mathematics Institute "The Mathematics of Phylogenetic Trees", undergraduate course. (June - July 2005)

Mathematics of Evolution and Phylogeny - Institut Henri Poincaré (June 2005)

Evolution 2005 (June 2005)

MEGA 2005 - The Eighth International Symposium on Effective Methods in Algebraic Geometry: "Computing in and with algebraic geometry: Theory, Algorithms, Implementations, Applications." (May 2005) -- slides

Virginia Polytechnic Institute and State University, April 2005.

Northeastern University, (talk by J. Rhodes), April 2005.

Dartmouth College, Feb. 2005.

Maine Medical Center Research Institute, the Jackson Laboratories, University of Maine Orono, Video Lecture "Probabilistic Models of Base Substitution: (the Jukes-Cantor distance)", Computational Methods in Genomics, Nov. 2004.

Colby College Mathematics Colloquium "Phylogenetics: Techniques of Tree Construction", Waterville, ME, Sept. 2004.

Evolution 2004, "Phylogenetic Invariants and Parameter Recovery for the General Markov + Immutable Sites (GM+I) Model, Ft. Collins, CO, July 2004.

Valley Geometry Seminar, "The Algebra of Molecular Evolution and Phylogenetic Tree Construction", Amherst, MA, April 2004.

The New Zealand Annual Phylogeny Meeting, "Constructing phylogenetic invariants for the general Markov model of sequence mutation", Mordor, New Zealand, Feb. 2004.

American Institute of Mathematics Workshop on Computational Algebraic Statistics, "Progress towards Understanding the Phylogenetic Ideal", Palo Alto, CA, Dec. 2003.

Video Conference: "Models of Molecular Evolution: An Introduction", University of Maine Orono/Jackson Laboratory Bar Harbor, ME with exercises. For MAT 500: Computational Methods in Genomics, Nov. 2003.

"Algebraic Techniques of Phylogeny Reconstruction", Statistics, Combinatorics, and Related Areas, University of Southern Maine, Oct. 2003

Mathematics of Phylogenetic Trees, University of California Berkeley , Sept. 2003