| Year |
Citation |
Score |
| 2024 |
Aliatimis G, Yoshida R, Boyacı B, Grant JA. Tropical Logistic Regression Model on Space of Phylogenetic Trees. Bulletin of Mathematical Biology. 86: 99. PMID 38954147 DOI: 10.1007/s11538-024-01327-8 |
0.361 |
|
| 2024 |
Yoshida R, Barnhill D, Miura K, Howe D. Tropical Density Estimation of Phylogenetic Trees. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 38941208 DOI: 10.1109/TCBB.2024.3420815 |
0.333 |
|
| 2020 |
Page R, Yoshida R, Zhang L. Tropical principal component analysis on the space of phylogenetic trees. Bioinformatics (Oxford, England). PMID 32516398 DOI: 10.1093/Bioinformatics/Btaa564 |
0.368 |
|
| 2018 |
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. PMID 30507538 DOI: 10.1109/Tcbb.2018.2884459 |
0.402 |
|
| 2018 |
Kang Q, Schardl CW, Moore N, Yoshida R. CURatio: Genome-wide phylogenomic analysis method using ratios of total branch lengths. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 30387738 DOI: 10.1109/Tcbb.2018.2878564 |
0.404 |
|
| 2018 |
Yoshida R, Zhang L, Zhang X. Tropical Principal Component Analysis and Its Application to Phylogenetics. Bulletin of Mathematical Biology. PMID 30206809 DOI: 10.1007/S11538-018-0493-4 |
0.382 |
|
| 2017 |
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: 901-922. PMID 29422694 DOI: 10.1093/Biomet/Asx047 |
0.415 |
|
| 2017 |
Lin B, Sturmfels B, Tang X, Yoshida R. Convexity in Tree Spaces Siam Journal On Discrete Mathematics. 31: 2015-2038. DOI: 10.1137/16M1079841 |
0.364 |
|
| 2017 |
Yoshida R, Fukumizu K, Vogiatzis C. Multilocus phylogenetic analysis with gene tree clustering Annals of Operations Research. 276: 293-313. DOI: 10.1007/S10479-017-2456-9 |
0.362 |
|
| 2017 |
Kahle D, Yoshida R, Garcia-Puente L. Hybrid schemes for exact conditional inference in discrete exponential families Annals of the Institute of Statistical Mathematics. 70: 983-1011. DOI: 10.1007/S10463-017-0615-Z |
0.308 |
|
| 2016 |
Weyenberg G, Yoshida R, Howe D. Normalizing kernels in the Billera-Holmes-Vogtmann treespace. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 28113725 DOI: 10.1109/Tcbb.2016.2565475 |
0.4 |
|
| 2016 |
Yoshida R, Nei M. Efficiencies of the NJp, maximum likelihood, and Bayesian methods of phylogenetic construction for compositional and non-compositional genes. Molecular Biology and Evolution. PMID 26929244 DOI: 10.1093/Molbev/Msw042 |
0.348 |
|
| 2016 |
Xi J, Xie J, Yoshida R. Distributions of topological tree metrics between a species tree and a gene tree Annals of the Institute of Statistical Mathematics. 1-25. DOI: 10.1007/S10463-016-0557-X |
0.416 |
|
| 2015 |
Xi J, Yoshida R. The characteristic imset polytope of Bayesian networks with ordered nodes Siam Journal On Discrete Mathematics. 29: 697-715. DOI: 10.1137/130933848 |
0.334 |
|
| 2014 |
Weyenberg G, Huggins PM, Schardl CL, Howe DK, Yoshida R. kdetrees: Non-parametric estimation of phylogenetic tree distributions. Bioinformatics (Oxford, England). 30: 2280-7. PMID 24764459 DOI: 10.1093/Bioinformatics/Btu258 |
0.328 |
|
| 2014 |
Haws D, Del Campo AM, Takemura A, Yoshida R. Markov degree of the three-state toric homogeneous Markov chain model Beitrage Zur Algebra Und Geometrie. 55: 161-188. DOI: 10.1007/s13366-013-0178-y |
0.665 |
|
| 2013 |
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, ... ... Yoshida R, et al. Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci. Plos Genetics. 9: e1003323. PMID 23468653 DOI: 10.1371/Journal.Pgen.1003323 |
0.697 |
|
| 2013 |
Zhao J, Yoshida R, Cheung SS, Haws D. Approximate Techniques in Solving Optimal Camera Placement Problems International Journal of Distributed Sensor Networks. 9: 241913. DOI: 10.1155/2013/241913 |
0.723 |
|
| 2012 |
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: 210. PMID 22909268 DOI: 10.1186/1471-2105-13-210 |
0.74 |
|
| 2012 |
Xi J, Yoshida R, Haws D. Estimating the number of zero-one multi-way tables via sequential importance sampling Annals of the Institute of Statistical Mathematics. 65: 763-783. DOI: 10.1007/S10463-012-0392-7 |
0.719 |
|
| 2011 |
Huggins PM, Li W, Haws D, Friedrich T, Liu J, Yoshida R. Bayes estimators for phylogenetic reconstruction. Systematic Biology. 60: 528-40. PMID 21471560 DOI: 10.1093/Sysbio/Syr021 |
0.732 |
|
| 2011 |
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: 2627-48. PMID 21373975 DOI: 10.1007/S11538-011-9640-X |
0.747 |
|
| 2011 |
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: 829-72. PMID 21181503 DOI: 10.1007/S11538-010-9605-5 |
0.36 |
|
| 2010 |
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. PMID 20802801 DOI: 10.7490/F1000Research.253.1 |
0.746 |
|
| 2010 |
Yoshida R. Open Problems on Connectivity of Fibers with Positive Margins in Multi-dimensional Contingency Tables Journal of Algebraic Statistics. 1. DOI: 10.18409/jas.v1i1.5 |
0.334 |
|
| 2010 |
Arnaoudova E, Jaromczyk JW, Moore N, Schardl CL, Yoshida R. Phylotree – a toolkit for computing experiments with distance-based methods for genome coevolution Bmc Bioinformatics. 11. DOI: 10.1186/1471-2105-11-S4-P6 |
0.343 |
|
| 2010 |
Rapallo F, Yoshida R. Markov bases and subbases for bounded contingency tables Annals of the Institute of Statistical Mathematics. 62: 785-805. DOI: 10.1007/S10463-010-0289-2 |
0.386 |
|
| 2009 |
Zipunnikov V, Booth JG, Yoshida R. Counting Tables Using the Double-Saddlepoint Approximation Journal of Computational and Graphical Statistics. 18: 915-929. DOI: 10.1198/Jcgs.2009.07154 |
0.39 |
|
| 2009 |
Hemmecke R, Takemura A, Yoshida R. Computing holes in semi-groups and its applications to transportation problems Contributions to Discrete Mathematics. 4. DOI: 10.11575/Cdm.V4I1.62036.G46699 |
0.384 |
|
| 2009 |
Hara H, Takemura A, Yoshida R. Markov bases for two-way subtable sum problems Journal of Pure and Applied Algebra. 213: 1507-1521. DOI: 10.1016/J.Jpaa.2008.11.019 |
0.36 |
|
| 2009 |
Hara H, Takemura A, Yoshida R. A Markov basis for conditional test of common diagonal effect in quasi-independence model for square contingency tables Computational Statistics & Data Analysis. 53: 1006-1014. DOI: 10.1016/J.Csda.2008.11.030 |
0.342 |
|
| 2008 |
Schardl CL, Craven KD, Speakman S, Stromberg A, Lindstrom A, Yoshida R. A novel test for host-symbiont codivergence indicates ancient origin of fungal endophytes in grasses. Systematic Biology. 57: 483-98. PMID 18570040 DOI: 10.1080/10635150802172184 |
0.355 |
|
| 2008 |
Eickmeyer K, Huggins P, Pachter L, Yoshida R. On the optimality of the neighbor-joining algorithm. Algorithms For Molecular Biology : Amb. 3: 5. PMID 18447942 DOI: 10.1186/1748-7188-3-5 |
0.436 |
|
| 2008 |
Aoki S, Takemura A, Yoshida R. Indispensable monomials of toric ideals and Markov bases Journal of Symbolic Computation. 43: 490-507. DOI: 10.1016/J.Jsc.2007.07.012 |
0.377 |
|
| 2008 |
Takemura A, Yoshida R. A generalization of the integer linear infeasibility problem Discrete Optimization. 5: 36-52. DOI: 10.1016/J.Disopt.2007.10.004 |
0.373 |
|
| 2008 |
Eickmeyer K, Yoshida R. The geometry of the neighbor-joining algorithm for small trees Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5147: 81-95. DOI: 10.1007/978-3-540-85101-1_7 |
0.308 |
|
| 2006 |
Levy D, Yoshida R, Pachter L. Beyond pairwise distances: neighbor-joining with phylogenetic diversity estimates. Molecular Biology and Evolution. 23: 491-8. PMID 16280538 DOI: 10.1093/Molbev/Msj059 |
0.459 |
|
| 2005 |
Sainudiin R, Yoshida R. Applications of interval methods to phylogenetics Algebraic Statistics For Computational Biology. 359-374. DOI: 10.1017/CBO9780511610684.024 |
0.33 |
|
| 2005 |
De Loera JA, Haws D, Hemmecke R, Huggins P, Yoshida R. A computational study of integer programming algorithms based on Barvinok's rational functions Discrete Optimization. 2: 135-144. DOI: 10.1016/J.Disopt.2005.04.001 |
0.723 |
|
| 2004 |
De Loera JA, Haws D, Hemmecke R, Huggins P, Sturmfels B, Yoshida R. Short rational functions for toric algebra and applications Journal of Symbolic Computation. 38: 959-973. DOI: 10.1016/J.Jsc.2004.02.001 |
0.728 |
|
| 2004 |
De Loera JA, Hemmecke R, Tauzer J, Yoshida R. Effective lattice point counting in rational convex polytopes Journal of Symbolic Computation. 38: 1273-1302. DOI: 10.1016/J.Jsc.2003.04.003 |
0.413 |
|
| 2004 |
De Loera JA, Haws D, Hemmecke R, Huggins P, Yoshida R. Three kinds of integer programming algorithms based on Barvinok's rational functions Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3064: 244-255. |
0.715 |
|
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