Ruriko Yoshida

rcama2's picture
Ph.D. UC Davis 2004

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. 


Computational Biology, Discrete Optimization, Algebraic Statistics


PubMed Publications*: 
  • 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 ;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
  • Bachoura, A ;Yoshida, R.;Lattermann, C.;Kamineni, S "Late removal of titanium hardware from the elbow is problematic." ISRN orthopedics 2012, (0): 256239. Details.
  • 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
  • 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
  • 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
* Publications are automatically pulled from based on a user-specific query. Results may include incorrect citations. See: Tutorial on improving PubMed results.
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