Ruriko Yoshida

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  • Associate Professor of Statistics
  • Statistics
325D Multidisciplinary Sciences Building
Research Interests:

Ph.D. UC Davis 2004


My primary research involves phylogenomics, which is the combination of two major fields in life sciences: Genomics, i.e. the function and structure of genes and genomes; and Molecular Phylogenetics, i.e., the hierarchical evolutionary relationships among organisms or genes. My work involves a synergy of large-scale computational and statistical problems, due to the sheer size and nature of genomic data.


Computational Biology, Discrete Optimization, Algebraic Statistics


PubMed Publications*: 
  • Page, R ;Yoshida, R.;Zhang, L. "Tropical principal component analysis on the space of phylogenetic trees." Bioinformatics (Oxford, England) 36, 17 (2020): 4590-4598. Details. Full text
  • Yoshida, R.;Zhang, L.;Zhang, X. "Tropical Principal Component Analysis and Its Application to Phylogenetics." Bulletin of mathematical biology 81, 2 (2019): 568-597. Details. Full text
  • Kang, Q ;Schardl, CL ;Moore, N.;Yoshida, R. "CURatio: Genome-wide phylogenomic analysis method using ratios of total branch lengths." IEEE/ACM transactions on computational biology and bioinformatics (2018): Details. Full text
  • Nye, TMW ;Tang, X ;Weyenberg, G ;Yoshida, R. "Principal component analysis and the locus of the Fréchet mean in the space of phylogenetic trees." Biometrika 104, 4 (2017): 901-922. Details. Full text
  • Yoshida, R.;Nei, M "Efficiencies of the NJp, Maximum Likelihood, and Bayesian Methods of Phylogenetic Construction for Compositional and Noncompositional Genes." Molecular biology and evolution 33, 6 (2016): 1618-24. Details. Full text
  • Weyenberg, G ;Huggins, PM ;Schardl, CL ;Howe, DK ;Yoshida, R. "kdetrees: Non-parametric estimation of phylogenetic tree distributions." Bioinformatics (Oxford, England) 30, 16 (2014): 2280-7. Details. Full text
  • Haws, DC ;Huggins, P.;O'Neill, EM ;Weisrock, DW ;Yoshida, R. "A support vector machine based test for incongruence between sets of trees in tree space." BMC bioinformatics 13, (2012): 210. Details. Full text
  • Haws, DC ;Hodge, TL ;Yoshida, R. "Optimality of the neighbor joining algorithm and faces of the balanced minimum evolution polytope." Bulletin of mathematical biology 73, 11 (2011): 2627-48. Details. Full text
  • Sainudiin, R.;Thornton, K.;Harlow, J.;Booth, J.;Stillman, M.;Yoshida, R.;Griffiths, R.;McVean, G.;Donnelly, P. "Experiments with the site frequency spectrum." Bulletin of mathematical biology 73, 4 (2011): 829-72. Details. Full text
  • Eickmeyer, K.;Huggins, P.;Pachter, L.;Yoshida, R. "On the optimality of the neighbor-joining algorithm." Algorithms for molecular biology : AMB 3, (2008): 5. Details. Full text
  • Levy, D.;Yoshida, R.;Pachter, L. "Beyond pairwise distances: neighbor-joining with phylogenetic diversity estimates." Molecular biology and evolution 23, 3 (2006): 491-8. Details. Full text
  • Yasui, N ;Vogiatzis, C ;Yoshida, R.;Fukumizu, K "imPhy: Imputing Phylogenetic Trees with Missing Information Using Mathematical Programming." IEEE/ACM transactions on computational biology and bioinformatics 17, 4 (1969): 1222-1230. Details. Full text
  • Weyenberg, G ;Yoshida, R.;Howe, D "Normalizing Kernels in the Billera-Holmes-Vogtmann Treespace." IEEE/ACM transactions on computational biology and bioinformatics 14, 6 (1969): 1359-1365. Details. Full text
  • Arnaoudova, E.;Haws, DC ;Huggins, P.;Jaromczyk, JW ;Moore, N.;Schardl, CL ;Yoshida, R. "Statistical phylogenetic tree analysis using differences of means." Frontiers in neuroscience 4, (0): Details. Full text
  • Xu, K.;Yoshida, R. "Statistical Analysis on Detecting Recombination Sites in DNA-β Satellites Associated with Old World Geminiviruses." Frontiers in psychiatry 1, (0): 138. Details. Full text
  • Schardl, CL ;Young, CA ;Hesse, U.;Amyotte, SG ;Andreeva, K.;Calie, PJ ;Fleetwood, DJ ;Haws, DC ;Moore, N.;Oeser, B.;Panaccione, DG ;Schweri, KK ;Voisey, CR ;Farman, ML ;Jaromczyk, JW ;Roe, BA ;O'Sullivan, DM ;Scott, B.;Tudzynski, P.;An, Z.;Arnaoudova, EG ;Bullock, CT ;Charlton, ND ;Chen, L.;Cox, M.;Dinkins, RD ;Florea, S.;Glenn, AE ;Gordon, A.;Güldener, U.;Harris, DR ;Hollin, W.;Jaromczyk, J.;Johnson, RD ;Khan, AK ;Leistner, E.;Leuchtmann, A.;Li, C.;Liu, J.;Liu, J.;Liu, M.;Mace, W.;Machado, C.;Nagabhyru, P.;Pan, J.;Schmid, J.;Sugawara, K.;Steiner, U.;Takach, JE ;Tanaka, E.;Webb, JS ;Wilson, EV ;Wiseman, JL ;Yoshida, R.;Zeng, Z. "Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci." PLoS genetics 9, 2 (0): e1003323. Details. Full text
  • Bachoura, A ;Yoshida, R.;Lattermann, C.;Kamineni, S "Late removal of titanium hardware from the elbow is problematic." ISRN orthopedics 2012, (0): 256239. Details.
* Publications are automatically pulled from based on a user-specific query. Results may include incorrect citations. See: Tutorial on improving PubMed results.