%% Papers Published
@article{fds43337,
Author = {D. Levy and R. Yoshida and L. Pachter},
Title = {Beyond Pairwise Distances: Neighbor Joining with
Phylogenetic Diversity Estimates},
Journal = {the Molecular Biology and Evolution},
Volume = {23},
Number = {3},
Pages = {491-498},
Year = {2006},
Month = {March},
url = {http://mbe.oxfordjournals.org/cgi/content/abstract/23/3/491},
Key = {fds43337}
}
@article{fds43247,
Author = {A. Hobolth and R. Yoshida},
Title = {Maximum likelihood estimation of phylogenetic tree and
substitution rates via generalized neighbor-joining and the
EM algorithm},
Journal = {Algebraic Biology Algebraic Biology 2005},
Volume = {1},
Pages = {41 - 50},
Publisher = {Universal Academy Press, INC.},
Editor = {H. Anai and K. Horimoto},
Year = {2005},
Month = {December},
url = {http://arxiv.org/abs/q-bio/0511034},
Key = {fds43247}
}
@article{fds42629,
Author = {K. Woods and R. Yoshida},
Title = {Short Rational Generating Functions and Their Applications
to Integer Programming},
Journal = {the newsletter of SIAM's Activity Group on
Optimization},
Volume = {16},
Series = {SIAG/OPT Views-and-News},
Number = {1 -- 2},
Pages = {15 -- 19},
Publisher = {SIAM},
Year = {2005},
Month = {October},
Key = {fds42629}
}
@article{fds42389,
Author = {R. Sainudiin and R. Yoshida},
Title = {Applications of Interval Methods to Phylogenetic
trees},
Pages = {359 -- 374},
Booktitle = {Algebraic Statistics for Computational Biology},
Publisher = {Cambridge University Press},
Editor = {L. Pachter and B. Stermfels},
Year = {2005},
Month = {October},
Key = {fds42389}
}
@article{fds44042,
Author = {J. De Loera and D. Haws and R. Hemmecke and P. Huggins and R.
Yoshida},
Title = {A Computational Study of Integer Programming Algorithms
Based on Barvinok's Rational Functions},
Journal = {The Journal of Discrete Optimization},
Volume = {2},
Series = {2},
Pages = {135-144},
Year = {2005},
Month = {June},
Key = {fds44042}
}
@article{fds28300,
Author = {R. Yoshida},
Title = {MJOIN},
Year = {2004},
Month = {November},
url = {http://bio.math.berkeley.edu/mjoin},
Abstract = {The software to reconstruct phylogenetic trees from DNA
sequences via the Neighbor Joining method with subtree
weights.},
Key = {fds28300}
}
@article{fds28419,
Author = {R. Yoshida},
Title = {Barvinok's Rational Functions: Algorithms and Applications
to Optimization, Statistics, and Algebra},
Journal = {Ph D thesis},
Publisher = {Department of Mathematics, University of California,
Davis},
Year = {2004},
Month = {June},
url = {http://arxiv.org/abs/math/0406284},
Key = {fds28419}
}
@article{fds28296,
Author = {De Loera and J., Haws and D., Hemmecke and R., Huggins and P., Tauzer and J. and Yoshida, R.},
Title = {Lattice Point Enumeration},
Year = {2004},
Month = {January},
url = {http://www.math.ucdavis.edu/~latte},
Abstract = {The software to count the number of lattice points inside a
rational convex polytope via Barvinok's cone
decomposition.},
Key = {fds28296}
}
@article{fds28032,
Author = {J. De Loera and R. Hemmecke and J. Tauzer and R.
Yoshida},
Title = {Effective Lattice Point Counting in Rational Convex
Polytopes},
Journal = {The Journal of Symbolic Computation},
Volume = {38},
Number = {4},
Pages = {1273--1302},
Year = {2004},
Key = {fds28032}
}
@article{fds28033,
Author = {J. De Loera and D. Haws and R. Hemmecke and P. Huggins and B. Sturmfels and R. Yoshida},
Title = {Short Rational Functions for Toric Algebra and
Applications},
Journal = {The Journal of Symbolic Computation},
Volume = {38},
Number = {2},
Pages = {959--973},
Year = {2004},
Key = {fds28033}
}
@article{fds25196,
Author = {J. De Loera and D. Haws and R. Hemmecke and P. Huggins and R.
Yoshida},
Title = {Three Kinds of Integer Programming Algorithms based on
Barvinok's Rational Functions},
Pages = {244 -- 255},
Booktitle = {Integer Programming and Combinatorial Optimization: 10th
International IPCO Conference},
Publisher = {Springer},
Editor = {D. Bienstock and G. Nemhauser},
Year = {2004},
Key = {fds25196}
}
@article{fds43622,
Author = {D. Levy and F. Su and R. Yoshida},
Title = {Algorithms for reconstructing phylogenetic trees from
dissimilarity maps},
Journal = {RECOMB 2004 meeting abstracts},
Pages = {19},
Year = {2004},
url = {http://bio.math.berkeley.edu/classes/290/fa2003/},
Key = {fds43622}
}
@article{fds45096,
Author = {S.Aoki, A. Takemura and R. Yoshida},
Title = {Indispensable monomials of toric ideals and Markov
bases},
Journal = {The Asian Symposium on Computer Mathematics
(ASCM)},
Pages = {200 -- 202},
Publisher = {Korea Institute for Advanced Study},
Editor = {Sung-il Pae and Hyungju Park},
url = {http://arxiv.org/abs/math/0511290},
Key = {fds45096}
}
@article{fds47940,
Author = {P. Huggins and J. B. Kadane and R. Yoshida},
Title = {Fairground game computations},
Journal = {Significance},
Volume = {2},
Number = {2},
Pages = {92},
url = {http://www.math.duke.edu/~ruriko/research/Game/},
Key = {fds47940}
}
%% Papers Submitted
@article{fds48893,
Author = {A. Takemura and R. Yoshida},
Title = {Saturation Points on Faces of a Rational Polyhedral
Cone},
Journal = {Proceedings of Integer Points In Polyhedra Geometry, Number
Theory, Representation Theory Algebra, Optimization,
Statistics, Joint Summer Research Conferences},
Year = {2006},
Month = {September},
url = {http://arxiv.org/abs/math/0605479},
Key = {fds48893}
}
@article{fds48631,
Author = {R. Hemmecke and A. Takemura and R. Yoshida},
Title = {Computing holes in semi-groups},
Journal = {Journal on Discrete and Computational Geometry},
Year = {2006},
Month = {July},
url = {http://arxiv.org/abs/math/0607599},
Key = {fds48631}
}
@article{fds47664,
Author = {M. B\'ona and H. Ju and R. Yoshida},
Title = {Enumerations of Weighted Graphs},
Journal = {Discrete Applied Math},
Year = {2006},
Month = {June},
url = {http://arxiv.org/abs/math/0606163},
Key = {fds47664}
}
@article{fds47936,
Author = {A. Takemura and R. Yoshida},
Title = {A generalization of the integer linear infeasibility
problem},
Journal = {Discrete Optimization},
Year = {2006},
url = {http://arxiv.org/abs/math/0603108},
Abstract = {Does a given system of linear equations with nonnegative
constraints have an integer solution? This problem appears
in many areas, such as number theory, operations research,
and statistics. To study a family of systems with no integer
solution, we focus on a commutative semigroup generated by
the columns of its defining matrix. In this paper we will
study a commutative semigroup generated by a finite subset
of $\Z^d$ and its saturation. We show the necessary and
sufficient conditions for the given semigroup to have a
finite number of elements in the difference between the
semigroup and its saturation. Also we define fundamental
holes and saturation points of a commutative semigroup.
Then, we show the simultaneous finiteness of the difference
between the semigroup and its saturation, the set of
non-saturation points of the semigroup, and the set of
generators for saturation points, which is a set of
generator of a monoid. We apply our results to some three
and four dimensional contingency tables.},
Key = {fds47936}
}
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Mathematics Department