Publications of Ruriko Yoshida    :recent first  alphabetical  combined  bibtex listing:

Papers Published

1. P. Huggins, J. B. Kadane, and R. Yoshida, Fairground game computations, Significance, vol. 2 no. 2 , pp. 92 [available here]
2. S.Aoki, A. Takemura, and R. Yoshida, Indispensable monomials of toric ideals and Markov bases, edited by Sung-il Pae, Hyungju Park, The Asian Symposium on Computer Mathematics (ASCM) , pp. 200 -- 202, Korea Institute for Advanced Study [math.ST/0511290]
3. D. Levy, F. Su, and R. Yoshida, Algorithms for reconstructing phylogenetic trees from dissimilarity maps, RECOMB 2004 meeting abstracts (2004), pp. 19 [available here]
4. J. De Loera, D. Haws, R. Hemmecke, P. Huggins, and R. Yoshida, Three Kinds of Integer Programming Algorithms based on Barvinok's Rational Functions, in Integer Programming and Combinatorial Optimization: 10th International IPCO Conference, edited by D. Bienstock and G. Nemhauser (2004), pp. 244 -- 255, Springer
5. J. De Loera, R. Hemmecke, J. Tauzer, and R. Yoshida, Effective Lattice Point Counting in Rational Convex Polytopes, The Journal of Symbolic Computation, vol. 38 no. 4 (2004), pp. 1273--1302
6. J. De Loera, D. Haws, R. Hemmecke, P. Huggins, B. Sturmfels, and R. Yoshida, Short Rational Functions for Toric Algebra and Applications, The Journal of Symbolic Computation, vol. 38 no. 2 (2004), pp. 959--973
7. De Loera, J., Haws, D., Hemmecke, R., Huggins, P., Tauzer, J., and Yoshida, R., Lattice Point Enumeration (January, 2004) (The GNU General Public Licensed software.) [~latte]  [abs]
8. R. Yoshida, Barvinok's Rational Functions: Algorithms and Applications to Optimization, Statistics, and Algebra, Ph D thesis (June, 2004), Department of Mathematics, University of California, Davis [math.CO/0406284]
9. R. Yoshida, MJOIN (November, 2004) (The GNU General Public Licensed software.) [mjoin]  [abs]
10. J. De Loera, D. Haws, R. Hemmecke, P. Huggins, and R. Yoshida, A Computational Study of Integer Programming Algorithms Based on Barvinok's Rational Functions, 2, The Journal of Discrete Optimization, vol. 2 (June 30, 2005), pp. 135-144
11. R. Sainudiin and R. Yoshida, Applications of Interval Methods to Phylogenetic trees, in Algebraic Statistics for Computational Biology, edited by L. Pachter and B. Stermfels (October, 2005), pp. 359 -- 374, Cambridge University Press
12. K. Woods and R. Yoshida, Short Rational Generating Functions and Their Applications to Integer Programming, SIAG/OPT Views-and-News, the newsletter of SIAM's Activity Group on Optimization, vol. 16 no. 1 -- 2 (October, 2005), pp. 15 -- 19, SIAM
13. A. Hobolth, R. Yoshida, Maximum likelihood estimation of phylogenetic tree and substitution rates via generalized neighbor-joining and the EM algorithm, edited by H. Anai and K. Horimoto, Algebraic Biology Algebraic Biology 2005, vol. 1 (December, 2005), pp. 41 - 50, Universal Academy Press, INC. [q-bio.QM/0511034]
14. 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]

Papers Submitted

1. A. Takemura and R. Yoshida, A generalization of the integer linear infeasibility problem, Discrete Optimization (2006) [math.ST/0603108]  [abs]
2. M. B\'ona, H. Ju, and R. Yoshida, Enumerations of Weighted Graphs, Discrete Applied Math (June, 2006) [math.CO/0606163]
3. R. Hemmecke, A. Takemura, and R. Yoshida, Computing holes in semi-groups, Journal on Discrete and Computational Geometry (July, 2006) [math.CO/0607599]
4. 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 (September, 2006) [math.CO/0605479]