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Department of Statistics - Ruriko Yoshida

Ruriko!

ruriko.yoshida@uky.edu
Department of Statistics
University of Kentucky
325D Multidisplinary Science Building
Lexington, KY 40506-0082
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.

2011

  1. "Evacuation planning for livestock in a case of a nuclear power plant accident" (with C. Vogiatzis, I. Aviles-Spadoni and S. Imamoto), submitted.
  2. "Estimating the number of zero-one multi-way tables via sequential importance sampling" (with J. Xi and D. Haws). Submitted. Available at http://arxiv.org/abs/1108.5939.
  3. "Late Removal of Titanium Hardware from the Elbow is Problematic" (with Abdo Bachoura, Christian Lattermann, and Srinath Kamineni). To appear in ISRN Orthopedics. Available at ISRN Orthopedics
  4. "A support vector machine based test for incongruence between sets of trees in tree space" (with David Haws, Peter Huggins, Eric M. O'Neill, David W. Weisrock). Submitted.
  5. "Chemical engineering by plant symbionts to enhance niche adaptation: A 12-genome comparison reveals dynamic alkaloid loci", (with Christopher Schardl, Jerzy Jaromczyk, Neil Moore, David Haws, Thomas Bullock, et al.), submitted.
  6. "Degree bounds for a minimal Markov basis for the three-state toric homogeneous Markov chain model" (with David Haws and Abraham Martin del Campo) to appear in the Proceedings of the Second CREST--SBM International Conference ``Harmony of Gröbner Bases and the Modern Industrial Society.'' Available at http://arxiv.org/abs/1108.0481.
  7. "First steps toward the geometry of cophylogeny" (with P. Huggins and M. Owen) to appear in the Proceedings of the Second CREST--SBM International Conference ``Harmony of Gröbner Bases and the Modern Industrial Society.'' Available at http://arxiv.org/abs/0809.1908.
  8. "Chondrocyte response to Tensile and Compressive cyclic loading modalities " (with Srinath Kamineni, Zubair Wani, Kai-Nan An, Zong-Ping Luo), submitted.
  9. "Solving optimal camera placement problems" (with Jian Zhao, David Haws, and Sen-ching Samson Cheung) to appear in the Eleventh IEEE International Workshop on Visual Surveillance.
  10. "Algebraic methods for molecular phylogenetics." To appear in Annals of Institute of Statistical Mathematics.
  11. "Bayes estimators for phylogenetic reconstruction" (with P Huggins, W. Li, D. Haws, T. Friedrich, J. Liu). 2011. LINK. Volume 60, Issue 4, Systematic Biology. Page 528-540. Available at http://arxiv.org/abs/0911.0645.
  12. "Optimality of the Neighbor Joining Algorithm and Faces of the Balanced Minimum Evolution Polytope" (with D. Haws and T. Hodge), 2011. the Bulletin of Mathematical Biology. Volume 73, Number 11, 2627-2648. Available at http://arxiv.org/abs/1004.2073.
  13. "Experiments with the site frequency spectrum" (Raazesh Sainudiin, Kevin Thornton, Jennifer Harlow, James Booth, Michael Stillman, Ruriko Yoshida, Robert Griffiths, Gil McVean, and Peter Donnelly), 2011, 829-872. Volume 73, issue 4. Bulletin of Mathematical Biology. LINK.

2010

  1. "Statistical analysis on detecting recombination sites in DNA-beta satellites associated with the old world geminiviruses" (with K. Xu), Front. Psychiatry. 2010. doi: 10.3389/fpsyt.2010.00138 Available at http://arxiv.org/abs/1006.4397
  2. "Statistical Phylogenetic Tree Analysis Using Differences of Means" (with Elissaveta Arnaoudova, David Haws, Peter Huggins, Jerzy W. Jaromczyk, Neil Moore, Chris Schardl), Front. Psychiatry volume 1 number 47. doi:10.3389/fnins.2010.0004. Available at http://arxiv.org/abs/1004.2101.
  3. "Phylotree - a toolkit for computing experiments with distance-based methods for genome coevolution" (Elissaveta Arnaoudova, Jerzy W Jaromczyk, Neil Moore, Christopher L Schardl, Ruriko Yoshida). BMC Bioinformatics 2010, 11(Suppl 4):P6 (23 July 2010).
  4. "Open Problems on Connectivity of Fibers with Positive Margins in Multi-dimensional Contingency Tables" Vol. 1, No. 1, 2010, 13-26 ISSN 1309-3452, J of Algebraic Statistics.
  5. "Markov bases and subbases for bounded contingency tables" (with Fabio Rapallo), Annals of the Institute of Statistical Mathematics, 62(4), 2010, 785--805. (Available at arxiv:0905.4841 and DOI).
  6. "Book review on Markov Processes and Applications" the journal of the American Statistical Association, 10, June 2010, 3 - 4.
  7. "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.
  8. "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. "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.
  5. "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.