Math @ Duke

search www.math.duke.edu.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. 491498 [qbio.QM/0508001], [491]
 A. Hobolth, R. Yoshida, Maximum likelihood estimation of phylogenetic tree and substitution rates via generalized neighborjoining 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. [qbio.QM/0511034]
 K. Woods and R. Yoshida, Short Rational Generating Functions and Their Applications to Integer Programming, SIAG/OPT ViewsandNews,
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. 135144
 R. Yoshida, MJOIN
(November, 2004) (The GNU General Public Licensed software.) [mjoin] [abs]
 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]
 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]
 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. 12731302
 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. 959973
 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 [available here]
 S.Aoki, A. Takemura, and R. Yoshida, Indispensable monomials of toric ideals and Markov bases, edited by Sungil Pae, Hyungju Park,
The Asian Symposium on Computer Mathematics (ASCM)
,
pp. 200  202, Korea Institute for Advanced Study [math.ST/0511290]
 P. Huggins, J. B. Kadane, and R. Yoshida, Fairground game computations,
Significance, vol. 2 no. 2
,
pp. 92 [available here]
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) [math.CO/0605479]
 R. Hemmecke, A. Takemura, and R. Yoshida, Computing holes in semigroups,
Journal on Discrete and Computational Geometry
(July, 2006) [math.CO/0607599]
 M. B\'ona, H. Ju, and R. Yoshida, Enumerations of Weighted Graphs,
Discrete Applied Math
(June, 2006) [math.CO/0606163]
 A. Takemura and R. Yoshida, A generalization of the integer linear infeasibility problem,
Discrete Optimization
(2006) [math.ST/0603108] [abs]


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ph: 919.660.2800
fax: 919.660.2821
 
Mathematics Department
Duke University, Box 90320
Durham, NC 277080320

