Core set approach to reduce uncertainty of gene trees (2006)
Okabayashi, Takahisa, Kitazoe, Yasuhiro, Kishino, Hirohisa, Watabe, Teruaki, Nakajima, Noriaki, Okuhara, Yoshiyasu, ...
Abstract Background A genealogy based on gene sequences within a species plays an essential role in the estimation of the character, structure, and evolutionary history of that species. Because...
Genome Informatics 14: 514--515 (2003) Predict Functionally Important Residues Responsible (2004)
Feng Wang, Hirohisa Kishino, Yasuhiko Wada
Introduction The estrogen receptor (ER) is a ligand-activated transcription factor that mediates the physiological e#ects of the female sex steroid hormone 17 beta estradiol (E2), and regulates the...
Peter J. Waddell, Hirohisa Kishino
At present, there is a lack of a sound methodology to infer causal gene expression relationships on a genome wide basis. We address this first by examining the behaviour of some of the latest and...
Yasuhiko Wada, Hirohisa Kishino, Nobuhisa Kashiwagi
Introduction It is important to develop the genome database for searching the genetic regions or genes responsible for economic traits. We have developed an animal genome database and its search...
Mobile Agent System for Animal Genome Database (1998)
Yasuhiko Wada, Hirohisa Kishino, Nobuhisa Kashiwagi
Introduction It is important to develop the genome database for searching the genetic regions or genes responsible for economic traits. We have developed an animal genome database and its search...
Seo, Tae-Kun, Kishino, Hirohisa, Thorne, Jeffrey L.
Because of the increase of genomic data, multiple genes are often available for the inference of phylogenetic relationships. The simple approach for combining multiple genes from the same taxon is to...
Positive Selection Acting on a Surface Membrane Protein of the Plant-Pathogenic Phytoplasmas†
Kakizawa, Shigeyuki, Oshima, Kenro, Jung, Hee-Young, Suzuki, Shiho, Nishigawa, Hisashi, Arashida, Ryo, ...
Phytoplasmas are plant-pathogenic bacteria that cause numerous diseases. This study shows a strong positive selection on the phytoplasma antigenic membrane protein (Amp). The ratio of nonsynonymous...
Core set approach to reduce uncertainty of gene trees
Okabayashi, Takahisa, Kitazoe, Yasuhiro, Kishino, Hirohisa, Watabe, Teruaki, Nakajima, Noriaki, Okuhara, Yoshiyasu, ...
Watabe, Teruaki, Kishino, Hirohisa, Okuhara, Yoshiyasu, Kitazoe, Yasuhiro
The third hypervariable (V3) region of the HIV-1 gp120 protein is responsible for many aspects of viral infectivity. The tertiary structure of the V3 loop seems to influence the coreceptor usage of...
Estimation of effective population size of HIV-1 within a host: a pseudomaximum-likelihood approach.
Seo, Tae-Kun, Thorne, Jeffrey L, Hasegawa, Masami, Kishino, Hirohisa
Using pseudomaximum-likelihood approaches to phylogenetic inference and coalescent theory, we develop a computationally tractable method of estimating effective population size from serially sampled...
Genomic background predicts the fate of duplicated genes: evidence from the yeast genome.
Gene duplication with subsequent divergence plays a central role in the acquisition of genes with novel function and complexity during the course of evolution. With reduced functional constraints or...
Kitada, Shuichi, Kishino, Hirohisa
We propose a new method for simultaneously detecting linkage disequilibrium and genetic structure in subdivided populations. Taking subpopulation structure into account with a hierarchical model, we...
Kitakado, Toshihide, Kitada, Shuichi, Obata, Yasuhiro, Kishino, Hirohisa
In stock enhancement programs, it is important to assess mixing rates of released individuals in stocks. For this purpose, genetic stock identification has been applied. The allele frequencies in a...
An Integrated-Likelihood Method for Estimating Genetic Differentiation Between Populations
Kitakado, Toshihide, Kitada, Shuichi, Kishino, Hirohisa, Skaug, Hans Julius
The aim of this article is to develop an integrated-likelihood (IL) approach to estimate the genetic differentiation between populations. The conventional maximum-likelihood (ML) and pseudolikelihood...
Seo, Tae-Kun, Kishino, Hirohisa, Thorne, Jeffrey L.
Because of the increase of genomic data, multiple genes are often available for the inference of phylogenetic relationships. The simple approach for combining multiple genes from the same taxon is to...
Positive Selection Acting on a Surface Membrane Protein of the Plant-Pathogenic Phytoplasmas†
Kakizawa, Shigeyuki, Oshima, Kenro, Jung, Hee-Young, Suzuki, Shiho, Nishigawa, Hisashi, Arashida, Ryo, ...
Phytoplasmas are plant-pathogenic bacteria that cause numerous diseases. This study shows a strong positive selection on the phytoplasma antigenic membrane protein (Amp). The ratio of nonsynonymous...
Watabe, Teruaki, Kishino, Hirohisa, Okuhara, Yoshiyasu, Kitazoe, Yasuhiro
The third hypervariable (V3) region of the HIV-1 gp120 protein is responsible for many aspects of viral infectivity. The tertiary structure of the V3 loop seems to influence the coreceptor usage of...
Estimation of effective population size of HIV-1 within a host: a pseudomaximum-likelihood approach.
Seo, Tae-Kun, Thorne, Jeffrey L, Hasegawa, Masami, Kishino, Hirohisa
Using pseudomaximum-likelihood approaches to phylogenetic inference and coalescent theory, we develop a computationally tractable method of estimating effective population size from serially sampled...
Genomic background predicts the fate of duplicated genes: evidence from the yeast genome.
Gene duplication with subsequent divergence plays a central role in the acquisition of genes with novel function and complexity during the course of evolution. With reduced functional constraints or...
Kitada, Shuichi, Kishino, Hirohisa
We propose a new method for simultaneously detecting linkage disequilibrium and genetic structure in subdivided populations. Taking subpopulation structure into account with a hierarchical model, we...
Core set approach to reduce uncertainty of gene trees
Okabayashi, Takahisa, Kitazoe, Yasuhiro, Kishino, Hirohisa, Watabe, Teruaki, Nakajima, Noriaki, Okuhara, Yoshiyasu, ...
Kitakado, Toshihide, Kitada, Shuichi, Obata, Yasuhiro, Kishino, Hirohisa
In stock enhancement programs, it is important to assess mixing rates of released individuals in stocks. For this purpose, genetic stock identification has been applied. The allele frequencies in a...
An Integrated-Likelihood Method for Estimating Genetic Differentiation Between Populations
Kitakado, Toshihide, Kitada, Shuichi, Kishino, Hirohisa, Skaug, Hans Julius
The aim of this article is to develop an integrated-likelihood (IL) approach to estimate the genetic differentiation between populations. The conventional maximum-likelihood (ML) and pseudolikelihood...
Robust Time Estimation Reconciles Views of the Antiquity of Placental Mammals
Kitazoe, Yasuhiro, Kishino, Hirohisa, Waddell, Peter J., Nakajima, Noriaki, Okabayashi, Takahisa, Watabe, Teruaki, ...
Empirical Bayes Inference of Pairwise FST and Its Distribution in the Genome
Kitada, Shuichi, Kitakado, Toshihide, Kishino, Hirohisa
Populations often have very complex hierarchical structure. Therefore, it is crucial in genetic monitoring and conservation biology to have a reliable estimate of the pattern of population...
Phylogenetic Detection of Recombination with a Bayesian Prior on the Distance between Trees
De Oliveira Martins, Leonardo, Leal, Élcio, Kishino, Hirohisa
Genomic regions participating in recombination events may support distinct topologies, and phylogenetic analyses should incorporate this heterogeneity. Existing phylogenetic methods for recombination...
Hirohisa Kishino, Hidehiro Kato, Fujio Kasamatsu, Yoshihiro Fujise
Line transect, population abundance, heterogeneity of biological parameters, post stratification, bootstrap resampling, model selection, AIC,