Ruth Davidson

I am at the University of Illinois Urbana-Champaign Department of Mathematics as an NSF postdoctoral fellow (DMS-1401591). Tandy Warnow is my sponsoring scientist for this grant. I am also a J.L. Doob Research Assistant Professor. My professional mentor in the Department of Mathematics is Bruce Reznick.


Contact: redavid2@illinois.edu

Office: 165 Altgeld Hall

Office Hours Spring 2017: By Appointment-I will not be in Illinois for most of Spring 2017. Appointment requests (Skype too..) are always welcome!

Esto semestre estoy visitando CIMAT durante la primavera 2017 para hacer una investigación con Abraham Martín del Campo Sanchéz. Mi oficina a CIMAT es K304. Por favor enviarme mensajes en utilisando correo electrónico, si quiere usted encontrarse conmigo a CIMAT o UIUC.

This semester I am visiting CIMAT during Spring 2017 to do research with Abraham Martín del Campo Sanchéz. My office at CIMAT is K304. Please communicate with me via email. I will be making several trips to the U.S. during Spring 2017, so email me if you want to schedule a meeting at UIUC, or if you are at CIMAT and wish to meet.

My CV

Research

My main areas of research interest are mathematical phylogenetics, geometric combinatorics, and algebraic statistics.

Publications istribution of Distance Data File

(In Preparation) Chuan Du, Adarsh Manawa, Christopher Szul, Titan Wibowo, Nima Rasekh, Ruth Davidson, and Rosemary Guzman. Image-based data analysis via discrete Morse theory and persistent homology.

(In Preparation) Ruth Davidson and James Degnan. When is it surprising that all gene trees are unique? An application of the generalized birthday problem.

Hector Banos, Nathaniel Bushek, Ruth Davidson, Elizabeth Gross, Pamela E. Harris, Robert Krone, Colby Long, Allen Stewart, and Robert Walker. Phylogenetic Trees: A Macaulay2 Package. Submitted. arXiv: 1611.05805

Ruth Davidson, Augustine O'Keefe, and Daniel Parry. A new shellability proof of an identity of Dixon. Submitted. arXiv:1512.00080

Ruth Davidson, MaLyn Lawhorn, and Joseph Rusinko, and Noah Weber: Efficient Quartet Representations of Trees and Applications to Supertree and Summary Methods. Preprint in IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) December 14, 2016: DOI: 10.1109/TCBB.2016.2638911 , arXiv: 1512.05302

Ruth Davidson, Joseph Rusinko, Zoe Vernon, and Jing Xi: Modeling the distribution of distance data in Euclidean space. In the AMS Contemporary Mathematics Series book Algebraic and Geometric Methods in Applied Discrete Mathematics. Volume 685, 2017 arXiv:1606.06146 . Link to AMS bookstore.

Ruth Davidson, Pranjal Vachaspati, Siavash Mirarab, and Tandy Warnow: Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer. RECOMB-Comparative Genomics 2015, and BMC Genomics, 2015.

Jed Chou, Ashu Gupta, Shashank Yaduvanshi, Ruth Davidson, Mike Nute, Siavash Mirarab, and Tandy Warnow: A comparative study of SVDquartets and other coalescent-based species tree estimation methods. RECOMB-Comparative Genomics 2015, and BMC Genomics, 2015.

Ruth Davidson and Seth Sullivant: Distance-based phylogenetic methods around a polytomy. IEEE/ACM Transactions on Computational Biology and Bioinformatics 11 (2014), no. 1: 325-335. Associated Software.

Ruth Davidson and Patricia Hersh: A lexicographic shellability characterization of geometric lattices. Journal of Combinatorial Theory, Series A 123 (2014), no. 1: 8-13.

Ruth Davidson and Seth Sullivant: Polyhedral Combinatorics of UPGMA Cones. Advances in Applied Math 50 (2013), no. 2, 327-338. Supplementary Materials.

 

Confirmed Upcoming Activities and Travel Schedule

Estoy a CIMAT durante la primavera 2017.

Attending the Bay Area Discrete Math Day (BAD) April 29, 2017 (I will be arriving early to work with my MRC group in Algebraic Statistics in Phylogenetics.)

Speaking in the AMS Special Session on Mathematical Phylogenetics at Hunter College, New York, NY, May 7. (Part of the AMS Eastern Sectional Meeting).

Visiting the Rabadan Lab at Columbia University May 8-10, 2017

Speaking at the "Algebraic and Combinatorial Phylogenetics" Workshop June 26-30, 2017, part of the Mediterranean Month in Phylogenetics, June 12th-July 10th, 2017 in Barcelona and Porquerolles, sponsored by BGS Math.

Speaking at the SIAM Annual Meeting, July 10-14 2017, David Lawrence Convention Center, Pittsburgh, PA.

Speaking and Organizing at the SIAM Conference on Applied Algebraic Geometry, July 31-August 4, 2017 at the Georgia Institute of Technology in Atlanta, Georgia. (see "Organizing" below...)

Visiting Scholarship at the University of Tasmania Fall 2017. This will coincide with the theoretical phylogenetics conference Phylomania.

Teaching

Spring 2017

I will be on research sabbatical at CIMAT during Spring 2017, but remotely supervising an Illinois Geometry Lab project and making trips to UIUC during this semester. Please contact me if you would like to meet.

Fall 2016

This Fall I am supervising three projects in the Illinois Geometry Lab. Please see the website for project information.

Spring 2016

Here is a flyer advertising the graduate class "Polyhedra in the Wild" that I taught in Spring 2016, and the main course page.

I also supervised a project in the Illinois Geometry Lab titled "Discrete Morse Theory, Vector Fields, and Materials Science" that is continuing in Fall 2016.

Academic Family

In 2014, I received my Ph.D. from the Mathematics department at North Carolina State University under the supervision of Patricia Hersh and Seth Sullivant.

In 2009, I received my B.S. in Mathematics at the University of Washington, Seattle. My undergraduate thesis supervisor was Sara Billey.

In 2006, I received my A.A. from Seattle Central College, formerly known as Seattle Central Community College.

Organizing

I am organizing a special session at the SIAM Applied Algebraic Geometry Conference in Atlanta, July 31-August 4, 2017 at Georgia Tech. The minisymposium is entitled "Algebraic and Topological Biology." Please see this wiki for an overview of minisymposia at the conference. Note, early career travel grants had a deadline of 2/3/17 which has been extended to 2/24/17.

Selected Past Activities

Talks and Events : talks, activities and events I've organized, and other conferences and workshops I've attended.

(Some of) the Seminars I (try to) attend at UIUC

UIUC has a tremendous amount of seminar opportunities! If you are a student please consider making time for seminars. Seminar attendance will have a lasting impact-regardless of your career goals.

Mathematical Biology Seminar

Algebraic Geometry Seminar

Systematics Discussion Group (no website): Fall 2016 Time and Place 407 Morrill Hall, 1 pm- contact me (though I am not the leader--) if you want to participate in this reading group

Program in Ecology, Evolution, and Conservation Biology (PEEC) seminar

Graph Theory and Combinatorics Seminar

Algebra-Geometry-Combinatorics Seminar (co-organizer, see above)

Distribution of Distance Data Files