Office Location: | 218 Physics Bldg |

Office Phone: | (919) 660 - 2848 |

Email Address: | |

Web Page: | http://www.math.duke.edu/~ruriko/ |

**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 neighbor-joining 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

**Recent 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 semi-groups*, 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. 491-498 [q-bio.QM/0508001], [491] - A. Takemura and R. Yoshida,
*A generalization of the integer linear infeasibility problem*, Discrete Optimization (Submitted, 2006) [math.ST/0603108] [abs]

- A. Takemura and R. Yoshida,

**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