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Department of Statistics - Ruriko Yoshida

Ruriko!

ruriko.yoshida@uky.edu
Department of Statistics
University of Kentucky
805A Patterson Office Tower
Lexington, KY 40506-0027
Tel: (859) 257-5698

Publications

  • "Barvinok's Rational Functions: Algorithms and Applications to Optimization, Statistics, and Algebra." Ph.D. Thesis PDF and book.

Books

  1. Integer Points in Polyhedra (Matthias Beck, Christian Haase, Bruce Reznick, Michele Vergne, Volkmar Welker, Ruriko Yoshida). American Mathematical Society (26 Jun 2008). ISBN:978-0821841730. Order the book.

2010

  1. "Statistical analysis on detecting recombination sites in DNA-beta satellites associated with the old world geminiviruses" (with K. Xu), submitted. Available at http://arxiv.org/abs/1006.4397
  2. "Open Problems on Connectivity of Fibers with Positive Margins in Multi-dimensional Contingency Tables" to appear in J of Algebraic Statistics.
  3. "Statistical Phylogenetic Tree Analysis Using Differences of Means" (with Elissaveta Arnaoudova, David Haws, Peter Huggins, Jerzy W. Jaromczyk, Neil Moore, Chris Schardl), to appear in Frontiers in Systems Biology. Available at http://arxiv.org/abs/1004.2101.
  4. "Markov bases and subbases for bounded contingency tables" (with Fabio Rapallo), Annals of the Institution of Statistical Mathematics, 62(4), 2010, 785--805. (Available at arxiv:0905.4841 and DOI).
  5. "Book review on Markov Processes and Applications" the journal of the American Statistical Association, 10, June 2010, 3 - 4.
  6. "On connectivity of fibers with positive marginals in multiple logistic regression" (with H. Hara and A. Takemura), J of Multivariate Analysis. 101(4), 2010, 909-925. Available at http://dx.doi.org/10.1016/j.jmva.2009.12.014 and http://arxiv.org/abs/0810.1793.
  7. "Optimality of the Neighbor Joining Algorithm and Faces of the Balanced Minimum Evolution Polytope" (with D. Haws and T. Hodge), submitted. Available at http://arxiv.org/abs/1004.2073.
  8. "Bayes estimators for phylogenetic reconstruction" (with P Huggins, W. Li, D. Haws, T. Friedrich, J. Liu). To be accepted conditionally in Systematic Biology. Available at http://arxiv.org/abs/0911.0645.
  9. "Counting Tables using the Double Saddlepoint Approximation" (with J. Booth and V. Zipunnikov), the Journal of Computational and Graphical Statistics, 18(4) December 1, 2009, 915-929. PDF.

2009

  1. "Computing holes in semi-groups and its applications to transportation problems" (with R. Hemmecke and A. Takemura), Contributions to Discrete Mathematics, Volume 4, Number 1, 2009, 81 - 91. Available at Contributions to Discrete Mathematics
  2. "A Generating Function for all Magic Squares and the Volume of the Birkhoff Polytope" (with J. Deloera and F. Liu), Journal of Algebraic Combinatorics, 30(1), 2009, 113 -- 139. Available at J of Algebraic Combinatorics.
  3. "Markov Bases for Two-way Subtable Sum Problems" (with H. Hara and A. Takemura), in the special issue ``THEORETICAL EFFECTIVITY AND PRACTICAL EFFECTIVITY OF GROEBNER BASES'' of the Journal of Pure and Applied Algebra, 213(8), 2009, 1507 - 1521. (Available at arxiv:0708.2312).
  4. "Markov Bases of Population Genetic Statistics" (with R. Sainudiin, K. Thornton, J. Booth, and M. Stillman), submitted.
  5. "First steps toward the geometry of cophylogeny" (with P. Huggins and M. Owen), submitted. Available at arxiv.org/abs/0809.1908.
  6. "A Markov Basis for Conditional Test of Common Diagonal Effect in Quasi-Independence Model for Two-Way Contingency Tables" (with H. Hara and A. Takemura). J of Computational Statistics and Data Analysis. 53 (2009) 1006 - 1014. Available at arXiv:0802.2603.
  7. "Holes in semigroups and their applications to the two-way common diagonal effect model" (with A. Takemura and P. Thomas). In: Proceedings of the 2008 International Conference on Information Theory and Statistical Learning, ITSL 2008, CSREA Press, ISBN: 1-60132-079-5, p67-72. PDF. (Even though this is published in 2008 I am posting this paper here for my convenience reason).

2008

  1. "Markov Chains, Quotient Ideals, and Connectivity with Positive Margins" (with Y. Chen and I. Dinwoodie). in ``Algebraic and Geometric Methods in Statistics'' dedicated to Professor Giovanni Pistone (P. Gibilisco, E. Riccomagno, M.-P. Rogantin, H. P. Wynn, eds.). 2008. PDF. p99 - 110.
  2. "Parametric k-best alignment" (with P. Huggins), preprint. Available at arxiv.org/abs/0809.1473.
  3. "Geometry of Neighbor-Joining Algorithm for Small Trees" (with K. Eickmeyer), the proceedings of Algebraic Biology, Springer LNC Series (2008), p82-96. Available at arXiv:0908.0098.
  4. "A novel test for significant codivergence between cool-season grasses and their symbiotic fungal endophytes" (with C. L. Schardl, K. D. Craven, A. Lindstrom, S. Speakman, and A. Stromberg). Systematic Biology. Volume 57, Issue 3, (2008), p483 - 498. Available at arXiv:q-bio.PE/0611084.
  5. "On the optimality of the neighbor-joining algorithm" (With K. Eickmeyer, P. Huggins, and L. Pachter). Algorithms for Molecular Biology. Volume 3, Issue 5, (2008). (Available at arxiv:0710.5142).
  6. "Indispensable Monomials of Toric Ideals and Markov Bases" (with S. Aoki and A. Takemura). J of Symbolic Computations Volume 43 (2008) p490-509. (Also available at arXiv:math.ST/0511290.)
  7. Integer Points in Polyhedra (Matthias Beck, Christian Haase, Bruce Reznick, Michele Vergne, Volkmar Welker, Ruriko Yoshida). American Mathematical Society (26 Jun 2008). ISBN:978-0821841730. Order the book.
  8. "Saturation points on faces of a rational polyhedral cone" (with A. Takemura), in Joint Summer Research Conference proceedings. Contemporary Mathematics. Volume 452. American Mathematical Society (2008), p147--162. Available at arXiv:math.CO/0605479.
  9. "A generalization of the integer linear infeasibility problem" (with A. Takemura), Discrete Optimization, Volume 5, Issue 1 (2008) p36-52. (Available at Discrete Optimization).

2007

  1. "On the enumeration of certain weighted graphs" (with B\'ona and Ju), Volume 155, Issue 11, 1 June 2007, p1481-1496, Discrete Applied Math. Available at arXiv:math.CO/0606163.
  2. "Partitioning the Sample Space on Five Taxa for the Neighbor Joining Algorithm" (with K. Eickmeyer). Preprint. Available at math.CO/0703081.
  3. "Formulas for the Volumes of the Polytope of Doubly-Stochastic Matrices and its faces" (with J. DeLoera and F. Liu). Preprint. Available at math.CO/0701866.

2006

  1. "Computing holes in semi-groups" (with R. Hemmecke and A. Takemura). Preprint. Available at arXiv:math.CO/0607599.
  2. "Beyond Pairwise Distances: Neighbor Joining with Phylogenetic Diversity Estimates" (with D. Levy and L. Pachter), the Molecular Biology and Evolution, 2006 23(3):491-498. MBE site.

2005

  1. "Applications of Interval Methods to Phylogenetic trees" (with R. Sainudiin), a chapter contributing to a book Algebraic Statistics for Computational Biology edited by Lior Pachter and Bernd Sturmfels, (2005) Cambridge University Press, p359 - 374. ASCB site.
  2. "Fairground game computations" (with P. Huggins and J. B. Kadane), Significance, Letters, Volume 2, Issue 2, (June 2005) p92. PDF.
  3. "A Computational Study of Integer Programming Algorithms Based on Barvinok's Rational Functions" (with J. De Loera, D. Haws, R. Hemmecke, P. Huggins), the Journal of Discrete Optimization, Volume 2, Issue 2, (June 30 2005), P 135-144 PDF.
  4. "Short Rational Generating Functions and Their Applications to Integer Programming" (with K. Woods), SIAG/OPT Views and News, vol. 16 (2005) p15 - 19.PDF.
  5. "Indispensable Monomials of Toric Ideals and Markov Bases" (with S. Aoki and A. Takemura), the Asian Symposium on Computer Mathematics (ASCM) 2005 edited by S. Pae, H. Park, (2005), p200 -- 202, Korea Institute for Advanced Study. PDF. (Also available at arXiv:math.ST/0511290.)
  6. "Maximum likelihood estimation of phylogenetic tree and substitution rates via generalized neighbor-joining and the EM algorithm" (with A. Hobolth), Algebraic Biology 2005, Computer Algebra in Biology, edited by H. Anai and K. Horimoto, vol. 1 (2005) p41 - 50, Universal Academy Press, INC.. PDF. (Also available at arXiv:q-bio.QM/0511034.)

2004

  1. "Effective Lattice Point Counting in Rational Convex Polytopes" (with J. De Loera, R. Hemmecke, J. Tauzer), the Journal of Symbolic Computation, 38 (2004), no. 4, p1273 -- 1302. PDF.
  2. Lattice Point Enumeration: LattE, (with De Loera, J., Haws, D., Hemmecke, R., Huggins, P., Tauzer, J), software to count the number of lattice points inside a rational convex polytope via Barvinok's cone decomposition, available at www.math.ucdavis.edu/~latte, the GNU General Public License, 2004.
  3. "Short Rational Functions for Toric Algebra and Applications" (with J. De Loera, D. Haws, R. Hemmecke, P. Huggins, B. Sturmfels), the Journal of Symbolic Computation, 38 (2004), no. 2, p959--973. PDF.
  4. "Reconstructing trees from dissimilarity maps" (with Levy, D. and Su, F.), RECOMB 2004 meeting abstracts (2004) p. 19. PDF.
  5. "Three Kinds of Integer Programming Algorithms based on Barvinok's Rational Functions" (with J. De Loera, D. Haws, R. Hemmecke, P. Huggins), Integer Programming and Combinatorial Optimization: 10th International IPCO Conference, Springer, (D. Bienstock and G. Nemhauser eds.) p244 -- 255, 2004. PDF.
  6. MJOIN, software to reconstruct phylogenetic trees from DNA sequences via the Neighbor Joining method with subtree weights, available at http://bio.math.berkeley.edu/mjoin/, the GNU General Public License, 2004.