Ruriko Yoshida
Ruriko Yoshida
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Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the Clavicipitaceae reveals dynamics of alkaloid loci
CL Schardl, CA Young, U Hesse, SG Amyotte, K Andreeva, PJ Calie, ...
PLoS genetics 9 (2), e1003323, 2013
Effective lattice point counting in rational convex polytopes
JA De Loera, R Hemmecke, J Tauzer, R Yoshida
Journal of symbolic computation 38 (4), 1273-1302, 2004
A novel test for host-symbiont codivergence indicates ancient origin of fungal endophytes in grasses
CL Schardl, KD Craven, S Speakman, A Stromberg, A Lindstrom, ...
Systematic Biology 57 (3), 483-498, 2008
Approximate techniques in solving optimal camera placement problems
J Zhao, R Yoshida, SS Cheung, D Haws
International Journal of Distributed Sensor Networks 9 (11), 241913, 2013
Tropical principal component analysis and its application to phylogenetics
R Yoshida, L Zhang, X Zhang
Bulletin of mathematical biology 81, 568-597, 2019
Convexity in tree spaces
B Lin, B Sturmfels, X Tang, R Yoshida
SIAM Journal on Discrete Mathematics 31 (3), 2015-2038, 2017
On the optimality of the neighbor-joining algorithm
K Eickmeyer, P Huggins, L Pachter, R Yoshida
Algorithms for Molecular Biology 3, 1-11, 2008
Short rational functions for toric algebra and applications
JA De Loera, D Haws, R Hemmecke, P Huggins, B Sturmfels, R Yoshida
Journal of Symbolic Computation 38 (2), 959-973, 2004
Principal component analysis and the locus of the Fréchet mean in the space of phylogenetic trees
TMW Nye, X Tang, G Weyenberg, R Yoshida
Biometrika 104 (4), 901-922, 2017
A generating function for all semi-magic squares and the volume of the Birkhoff polytope
JA De Loera, F Liu, R Yoshida
Journal of Algebraic Combinatorics 30, 113-139, 2009
kdetrees: non-parametric estimation of phylogenetic tree distributions
G Weyenberg, PM Huggins, CL Schardl, DK Howe, R Yoshida
Bioinformatics 30 (16), 2280-2287, 2014
Efficiencies of the NJp, maximum likelihood, and Bayesian methods of phylogenetic construction for compositional and noncompositional genes
R Yoshida, M Nei
Molecular biology and evolution 33 (6), 1618-1624, 2016
Indispensable monomials of toric ideals and Markov bases
S Aoki, A Takemura, R Yoshida
Journal of Symbolic Computation 43 (6-7), 490-507, 2008
Beyond pairwise distances: neighbor-joining with phylogenetic diversity estimates
D Levy, R Yoshida, L Pachter
Molecular Biology and Evolution 23 (3), 491-498, 2006
Optimality of the neighbor joining algorithm and faces of the balanced minimum evolution polytope
DC Haws, TL Hodge, R Yoshida
Bulletin of mathematical biology 73, 2627-2648, 2011
Tropical Fermat--Weber points
B Lin, R Yoshida
SIAM Journal on Discrete Mathematics 32 (2), 1229-1245, 2018
A user’s guide for latte v1. 1
JA De Loera, D Haws, R Hemmecke, P Huggins, J Tauzer, R Yoshida
University of California, Davis, 2003
Computing holes in semi-groups and its applications to transportation problems
R Hemmecke, A Takemura, R Yoshida
arXiv preprint math/0607599, 2006
On connectivity of fibers with positive marginals in multiple logistic regression
H Hara, A Takemura, R Yoshida
Journal of Multivariate Analysis 101 (4), 909-925, 2010
Tropical principal component analysis on the space of phylogenetic trees
R Page, R Yoshida, L Zhang
Bioinformatics 36 (17), 4590-4598, 2020
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