Ruriko Yoshida

Education:
Ph.D. UC Davis 2004
Biography:

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.

Research Interests:
Computational Biology, Discrete Optimization, Algebraic Statistics
Research

Computational Biology, Discrete Optimization, Algebraic Statistics

 

Selected Publications:

See http://polytopes.net/research/publications.php

PubMed Publications*: 
  • R Page; R Yoshida; L Zhang"Tropical principal component analysis on the space of phylogenetic trees."Bioinformatics (Oxford, England)36.17(2020):4590-4598.Details. Full text
  • R Yoshida; L Zhang; X Zhang"Tropical Principal Component Analysis and Its Application to Phylogenetics."Bulletin of mathematical biology81.2(2019):568-597.Details. Full text
  • Q Kang; CL Schardl; N Moore; R Yoshida"CURatio: Genome-wide phylogenomic analysis method using ratios of total branch lengths."IEEE/ACM transactions on computational biology and bioinformatics(2018):Details. Full text
  • TMW Nye; X Tang; G Weyenberg; R Yoshida"Principal component analysis and the locus of the Fréchet mean in the space of phylogenetic trees."Biometrika104.4(2017):901-922.Details. Full text
  • R Yoshida; M Nei"Efficiencies of the NJp, Maximum Likelihood, and Bayesian Methods of Phylogenetic Construction for Compositional and Noncompositional Genes."Molecular biology and evolution33.6(2016):1618-24.Details. Full text
  • G Weyenberg; PM Huggins; CL Schardl; DK Howe; R Yoshida"kdetrees: Non-parametric estimation of phylogenetic tree distributions."Bioinformatics (Oxford, England)30.16(2014):2280-7.Details. Full text
  • DC Haws; TL Hodge; R Yoshida"Optimality of the neighbor joining algorithm and faces of the balanced minimum evolution polytope."Bulletin of mathematical biology73.11(2011):2627-48.Details. Full text
  • R Sainudiin; K Thornton; J Harlow; J Booth; M Stillman; R Yoshida; R Griffiths; G McVean; P Donnelly"Experiments with the site frequency spectrum."Bulletin of mathematical biology73.4(2011):829-72.Details. Full text
  • K Eickmeyer; P Huggins; L Pachter; R Yoshida"On the optimality of the neighbor-joining algorithm."Algorithms for molecular biology : AMB3.(2008):5.Details. Full text
  • D Levy; R Yoshida; L Pachter"Beyond pairwise distances: neighbor-joining with phylogenetic diversity estimates."Molecular biology and evolution23.3(2006):491-8.Details. Full text
  • G Weyenberg; R Yoshida; D Howe"Normalizing Kernels in the Billera-Holmes-Vogtmann Treespace."IEEE/ACM transactions on computational biology and bioinformatics14.6(1969):1359-1365.Details. Full text
  • N Yasui; C Vogiatzis; R Yoshida; K Fukumizu"imPhy: Imputing Phylogenetic Trees with Missing Information Using Mathematical Programming."IEEE/ACM transactions on computational biology and bioinformatics17.4(1969):1222-1230.Details. Full text
  • E Arnaoudova; DC Haws; P Huggins; JW Jaromczyk; N Moore; CL Schardl; R Yoshida"Statistical phylogenetic tree analysis using differences of means."Frontiers in neuroscience4.(0):Details. Full text
  • K Xu; R Yoshida"Statistical Analysis on Detecting Recombination Sites in DNA-β Satellites Associated with Old World Geminiviruses."Frontiers in psychiatry1.(0):138.Details. Full text
  • CL Schardl; CA Young; U Hesse; SG Amyotte; K Andreeva; PJ Calie; DJ Fleetwood; DC Haws; N Moore; B Oeser; DG Panaccione; KK Schweri; CR Voisey; ML Farman; JW Jaromczyk; BA Roe; DM O'Sullivan; B Scott; P Tudzynski; Z An; EG Arnaoudova; CT Bullock; ND Charlton; L Chen; M Cox; RD Dinkins; S Florea; AE Glenn; A Gordon; U Güldener; DR Harris; W Hollin; J Jaromczyk; RD Johnson; AK Khan; E Leistner; A Leuchtmann; C Li; J Liu; J Liu; M Liu; W Mace; C Machado; P Nagabhyru; J Pan; J Schmid; K Sugawara; U Steiner; JE Takach; E Tanaka; JS Webb; EV Wilson; JL Wiseman; R Yoshida; Z Zeng"Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci."PLoS genetics9.2(0):e1003323.Details. Full text
  • A Bachoura; R Yoshida; C Lattermann; S Kamineni"Late removal of titanium hardware from the elbow is problematic."ISRN orthopedics2012.(0):256239.Details.
* Publications are automatically pulled from pubmed.gov based on a user-specific query. Results may include incorrect citations. See: Tutorial on improving PubMed results.