Publications of Ruriko Yoshida    :chronological  alphabetical  combined  bibtex listing:

Papers Published

1. 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]
2. 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]
3. 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
4. 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
5. 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
6. R. Yoshida, MJOIN (November, 2004) (The GNU General Public Licensed software.) [mjoin]  [abs]
7. 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]
8. 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]
9. 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
10. 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
11. 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
12. D. Levy, F. Su, and R. Yoshida, Algorithms for reconstructing phylogenetic trees from dissimilarity maps, RECOMB 2004 meeting abstracts (2004), pp. 19 [available here]
13. 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]
14. P. Huggins, J. B. Kadane, and R. Yoshida, Fairground game computations, Significance, vol. 2 no. 2 , pp. 92 [available here]

Papers Submitted

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