Ruriko Yoshida is an Associate Professor in the Department of Statistics.
Research Statement
My main research interest is to apply algebraic geometry and combinatorics to computational problems in phylogenetics, the combination of two major fields in life sciences: Genomics, i.e. the study of the function and structure of genes and genomes; and Molecular Phylogenetics, i.e., the study of the hierarchical evolutionary relationships among organisms or genes.
Recent Publications
"Solving optimal camera placement problems" (with Jian Zhao, David Haws, and Sen-ching Samson Cheung) submitted.
"Optimality of the Neighbor Joining Algorithm and Faces of the Balanced Minimum Evolution Polytope" (with D. Haws and T. Hodge), to appear in the Bulletin of Mathematical Biology. Available at http://arxiv.org/abs/1004.2073.
"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.
"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
"Bayes estimators for phylogenetic reconstruction" (with P Huggins, W. Li, D. Haws, T. Friedrich, J. Liu). To appear in Systematic Biology. Available at http://arxiv.org/abs/0911.0645.
"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.
"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).
"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).
"Book review on Markov Processes and Applications" the journal of the American Statistical Association, 10, June 2010, 3 - 4.
"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.
"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.