Math @ Duke

Ruriko Yoshida, Assistant Research Professor
Please note: Ruriko has left the Mathematics department at Duke University; some info here might not be up to date.  Contact Info:
 Office Hours:
 MF 2:30 PM  3:20PM
 Education:
PhD  University of California, Davis  2004 
BA  University of California, Berkeley  2000 
 Specialties:

Geometry
Applied Math
 Research Interests: Computational Algebraic Statistics, Computational Biology
Current projects:
Working on the followings:, (1)Studying coevolution between plants and endophytes., (2)Studying on Semigroups generated by the columns of an integral matrix and its saturation (and its applycations to markov bases for contingency tables)., (3)Applications of short rational functions to statistics., (4)Working on maximum likelihood estimation (MLE) of phylogenetic tree and substitution rates via generalized neighborjoining and the EM algorithm (joint work with Asger Hobolth).
Interested in reconstructing phylogenetic trees via distance based methods and/or Maximum Likelihood Estimations, applying algebraic techniques to contingency table problems, and lattice points in rational convex polyhedra.
 Areas of Interest:
Computational Biology Computational Algebraic Statistics Discrete Optimization
 Keywords:
Phylogenetic trees • Neighbor Joining method • Markov bases • Gr\"obner bases • Contingency tables • lattice points • Barvinok's rational functions • Linear integer programming
 Curriculum Vitae
 Recent Publications
(More Publications)
(search)
 A. Takemura and R. Yoshida, Saturation Points on Faces of a Rational Polyhedral Cone,
Proceedings of Integer Points In Polyhedra Geometry, Number Theory, Representation Theory Algebra, Optimization, Statistics, Joint Summer Research Conferences
(Submitted, September, 2006) [math.CO/0605479]
 R. Hemmecke, A. Takemura, and R. Yoshida, Computing holes in semigroups,
Journal on Discrete and Computational Geometry
(Submitted, July, 2006) [math.CO/0607599]
 M. B\'ona, H. Ju, and R. Yoshida, Enumerations of Weighted Graphs,
Discrete Applied Math
(June, Submitted, 2006) [math.CO/0606163]
 D. Levy, R. Yoshida and L. Pachter, Beyond Pairwise Distances: Neighbor Joining with Phylogenetic Diversity Estimates,
the Molecular Biology and Evolution, vol. 23 no. 3
(March, 2006),
pp. 491498 [qbio.QM/0508001], [491]
 A. Takemura and R. Yoshida, A generalization of the integer linear infeasibility problem,
Discrete Optimization
(Submitted, 2006) [math.ST/0603108] [abs]
 Conferences Organized
 The 2nd International Conference on Algebraic Biology, Program Committee, July 2, 2007
 Algebraic Biology (AB2005), Computer Algebra in Biology, Organizing and program committee, November 2005
 Integer Points In Polyhedra Geometry, Number Theory, Representation Theory Algebra, Optimization, Statistics, Organizer, June 11, 2005


dept@math.duke.edu
ph: 919.660.2800
fax: 919.660.2821
 
Mathematics Department
Duke University, Box 90320
Durham, NC 277080320

