Publications of Ruriko Yoshida
Papers Published
- 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
- 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.
- 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
- 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
- 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
- R. Yoshida, MJOIN
(November, 2004) (The GNU General Public Licensed software.)
- 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
- 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.)
- 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
- 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
- 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
- D. Levy, F. Su, and R. Yoshida, Algorithms for reconstructing phylogenetic trees from dissimilarity maps,
RECOMB 2004 meeting abstracts
(2004),
pp. 19
- 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
- P. Huggins, J. B. Kadane, and R. Yoshida, Fairground game computations,
Significance, vol. 2 no. 2
,
pp. 92
Papers Submitted
- 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)
- R. Hemmecke, A. Takemura, and R. Yoshida, Computing holes in semi-groups,
Journal on Discrete and Computational Geometry
(July, 2006)
- M. B\'ona, H. Ju, and R. Yoshida, Enumerations of Weighted Graphs,
Discrete Applied Math
(June, 2006)
- A. Takemura and R. Yoshida, A generalization of the integer linear infeasibility problem,
Discrete Optimization
(2006)