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 | 437 | 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 | 308 | 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 | 143 | 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 | 84 | 2013 |
Tropical principal component analysis and its application to phylogenetics R Yoshida, L Zhang, X Zhang Bulletin of mathematical biology 81, 568-597, 2019 | 68 | 2019 |
Convexity in tree spaces B Lin, B Sturmfels, X Tang, R Yoshida SIAM Journal on Discrete Mathematics 31 (3), 2015-2038, 2017 | 58 | 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 | 55 | 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 | 54 | 2004 |
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 | 52 | 2009 |
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 | 51 | 2017 |
kdetrees: non-parametric estimation of phylogenetic tree distributions G Weyenberg, PM Huggins, CL Schardl, DK Howe, R Yoshida Bioinformatics 30 (16), 2280-2287, 2014 | 50 | 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 | 47 | 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 | 45 | 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 | 45 | 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 | 43 | 2011 |
Tropical Fermat--Weber points B Lin, R Yoshida SIAM Journal on Discrete Mathematics 32 (2), 1229-1245, 2018 | 37 | 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 | 33* | 2003 |
Computing holes in semi-groups and its applications to transportation problems R Hemmecke, A Takemura, R Yoshida arXiv preprint math/0607599, 2006 | 32 | 2006 |
Tropical geometry of phylogenetic tree space: a statistical perspective A Monod, B Lin, R Yoshida, Q Kang arXiv preprint arXiv:1805.12400, 2018 | 29 | 2018 |
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 | 29 | 2010 |