Publication

Kitada, S., Nakamichi, R., and Kishino, H. (2017). The empirical Bayes estimators of fine-scale population structure in high gene flow species.  Molecular Ecology Resources. accepted.

Kitada, S., Yoshida, R., Fujita, T., Hamasaki, K., Nakamichi, R., and Kishino, H. (2017). Population structure and persistence of Pacific herring following the Great Tohoku earthquake.  Conservation Genetics. 18: 423-437.

Liao, H.-I., Chen, H. and Kishino, H., and Liao, C-T. (2016). A reference-population-based conformance proportion. Journal of Agricultural, Biological, and Environmental Statistics. accepted.

Yonezawa, T., Segawa, T., Mori, H., Campos, P. F., Hongoh, Y., Endo, H., Akiyoshi, A., Kohno, N., Nishida, S., Wu, J., Jin, H., Adachi, J., Kishino, H., Kurokawa, K., Nogi, Y., Tanabe, H., Mukoyama, H., Yoshida, K., Rasoamiaramanana, A., Yamagishi, S., Hayashi, Y., Yoshida, A., Koike, H., Akishinonomiya, F., Willerslev, E. and Hasegawa, M. (2016). Phylogenomics and morphology of extinct paleognaths reveal the origin and evolution of the ratites.Current Biology. 27: 68-77.

Jin, H., Yonezawa, T., Zhong, Y., Kishino, H., and Hasegawa, M. (2016). Cretaceous origin of the giant rhinoceros beetles (Dynastini; Coleoptera) and the correlation of their evolution with Pangean breakup. Genes & Genetic Systems. accepted.

Chen, H., Nagai, S., and Kishino, H. (2016). Assessment of the network of protected areas for birds in Taiwan with regard to functional and phylogenetic diversity. Pacific Conservation Biology. 22: 61-71.

Lee, H-J., Kishino, H., Rodrigue, N., and Thorne, J. L. (2016). Grouping substitution types into different relaxed molecular clocks. Philosophical Transactions of Royal Society B. 371: 20150141.

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Chen, H. and Kishino, H. (2015). Hypothesis testing of inclusion of the tolerance interval for the assessment of food safety. PLoS ONE. 10(10): e0141117.

Chen, H. and Kishino, H. (2015). Global pattern of phylogenetic species composition of shark and its conservation priority.  Ecology and Evolution. 5(19): 4455-4465.

Chen, H., Shao, K-T., and Kishino, H. (2015). A Bayesian hierarchical ANOVA model of stochastic seasonality for Diodon Holocanthus in northern Taiwan. the Journal of Marine Science and Technology. accepted.

Miyashita, S., Ishibashi, K., Kishino, H., and Ishikawa, M. (2015). Viruses roll the dice: The stochastic behavior of viral genome molecules accelerates viral adaptation at the cell and tissue levels. PLoS Biology. 13(3): e1002094.

Chen, H., Shao, K-T., and Kishino, H. (2015). Phylogenetic skew: an index of community diversity. Molecular Ecology. 24: 759-770.

Chen, H., Yamagishi, J., and Kishino, H. (2014). Bayesian inference of baseline fertility and treatment effects via a crop yield-fertility model. PLoS ONE. 9 (11): e112785.

Hong, B., Fisher, T., Sult, T., Maxwell, C., Mickelson, J., Kishino, H., and Locke, M. (2014). Model-based tolerance intervals derived from cumulative historical composition data: Application for substantial equivalence assessment of a genetically modified crop. Journal of Agricultural and Food Chemistry. 62: 9916-9926.

Koyano,H., Tsubouchi, T., Kishino, H., and Akutsu, T. (2014). Archaeal β diversity patterns under the seafloor along geochemical gradients. Journal of Geophysical Research G. 119: 1770-1788.

Machida, J., Nishiyama, T., Kishino, H., Yamaguchi, S., Kimura, M., Shibata, A., Tatematsu, T., Kamamoto, M., Yamamoto, K., Makino, S., Miyachi, H., Shimozato, K., and Tokita, Y. (2014). Genetic epidemiology of tooth agenesis in Japan: a population-and family-based study. Clinical Genetics. 88: 167-171.

Mimura, K., Kishino, H., Karino, G., Nitta, E., Senoo, A., Ikegami, K., Kunikata, T.,Yamanouchi, H., Nakamura, S., and Koshiba, M. (2014). Potential of a smartphone as a stress-free sensor of daily human behaviour. Behavioural Brain Research. 276: 181-189.

Koshiba, M., Kakei, H., Honda, M., Karino, G., Niitsu, M., Miyaji, T., Kishino, H., Nakamura, S., Kunikata, T., and Yamanouchi, H. (2014). Early-infant diagnostic predictors of the neuro-behavioural development after neonatal care. Behavioural Brain Research. 276: 143-150.

Nakajima, K., Kitada, S., Habara, Y., Sano, S., Yokoyama, E., Sugaya, T., Iwamoto, W., Kishino, H., and Hamasaki, K. (2014). Genetic effects of marine stock enhancement: a case study based on the highly piscivorous Japanese Spanish mackerel. Canadian Journal of Fisheries and Aquatic Sciences. 71: 1-14.

Nishiyama, T., Suzuki, M., Adachi, K., Sumi, S., Okada, K., Kishino, H., Sakai, S., Kamio, Y., Kojima, M., Suzuki, S., and Kanne, S. M. (2014). Comprehensive comparison of self-administered questionnaires for measuring quantitative autistic traits in adults. Journal of autism and developmental disorders. 44: 993-1007.

Watabe, T. and Kishino, H. (2013). Spatial distribution of selection pressure on a protein based on the hierarchical Bayesian model. Molecular Biology and Evolution. 30: 2714-2722.

Koshiba, M., Senoo, A., Mimura, K., Shirakawa, Y., Karino, G., Obara, S., Ozawa, S., Sekihara, H., Fukushima, Y., Ueda, T., Kishino, H., Tanaka, T., Ishibashi, H., Yamanouchi, H., Yui, K., and Nakamura, S. (2013). A cross-species socio-emotional behaviour development revealed by a multivariate analysis.  Scientific Reports. 3: article number 2630.

Tanabe,K., Jombart, T., Horibe, S., Nirianne M. Q. Palacpac, N. M. Q., Honma, H., Tachibana, S., Nakamura, M., Horii, T., Kishino, H., and Mita, T. (2013). Plasmodium falciparum mitochondrial genetic diversity exhibits isolation-by-distance patterns supporting a sub-Saharan African origin. Mitochondrion. 13: 630-636.

Koyano, H., Serbezov, D., Kishino, H., and Schweder, T. (2013). Fractional parentage analysis and a scale-free reproductive network of brown trout. Journal of Theoretical Biology. 336: 18-35.

Kitada, S., Fujikake, C., Asakura, Y., Yuki, H., Nakajima, K., Vargas, K. M., Kawashima, S., Hamasaki, K., and Kishino, H. (2013). Molecular and morphological evidence of hybridization between native Ruditapes philippinarum and the introduced Ruditapes form in Japan. Conservation Genetics. 14: 717-733.

Bizinoto, M. C., Yabe, S., Leal, É., Kishino, H., de Oliveira Martins, L., de Lima, M., L., Morais, E., R., Diaz, R. S., and Janini, L. M. (2013). Codon pairs of the HIV-1 vif gene correlate with CD4+ T cell count. BMC Infectious Diseases. 13: 173.

Ishibashi, K., Mawatari, N., Miyashita, S., Kishino, H., Meshi, T., and Ishikawa, M. (2012). Coevolution and hierarchical interactions of Tomato mosaic virus and the resistance gene Tm-1. PLoS Pathogen. 8(10): e1002975.

Mollah,M. M. H., Mollah, M. N. H., and Kishino, H. (2012). β-empirical Bayes inference and model diagnosis of microarray data. BMC Bioinformatics. 13: 135.

Nishiyama, T., Kishino, H., Suzuki, S., Ando, R., Niimura, H., Uemura, H., Horita, M., Ohnaka, K., Kuriyama, N., Mastuo, K., Guang, Y., Wakai, K., Hamajima, N., and Tanaka, H. (2012). Detailed analysis of Japanese population substructure with a focus on the Southwest Islands of Japan. PLoS ONE. 7 (4): e35000.

Mariadassou, M., Bar-Hen, A., and Kishino, H. (2012). Taxon Influence Index: assessing taxon-induced incongruities in phylogenetic inference. Systematic Biology. 61: 337E45.

Guo, Y., Shen, Y-H., Sun, W., Kishino, H., Xiang, Z-H., and Zhang, Z. (2011). Nucleotide diversity and selection signature in the domesticated silkworm, Bombyx mori, and wild silkworm, Bombyx mandarina. Journal of Insect Science. 11: 119.

Kitazoe, Y., Kishino, H., Hasegawa, M., Matsui, A., Lane, N., and Tanaka, M. (2011). Stability of mitochondrial membrane proteins in terrestrial vertebrates predicts aerobic capacity and longevity. Genome Biology and Evolution. 3: 1233-1244.

Nishiyama, T., Takahashi, K., Tango, T., Pinto, D., Scherer, S. W., Takami, S., and Kishino, H. (2011). A scan statistic to extract causal gene clusters from case-control genome-wide rare CNV data. BMC Bioinformatics. 12: 205.

Kitada, S., Kishino, H., and Hamasaki, K. (2011). Bias and significance of relative reproductive success estimates based on steelhead data: A Bayesian meta-analysis. Canadian Journal of Fisheries and Aquatic Sciences. 68: 1827-1835.

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Watabe, T. and Kishino, H. (2010). Structural considerations in the fitness landscape of a virus. Molecular Biology and Evolution. 27: 1782-1791.

Koyano, H. and Kishino, H. (2010). Quantifying biodiversity and asymptotics for a sequence of random strings. Physical Review E. 81: 061912.

Tanabe, K., Mita, T., Jombart, T., Eriksson, A., Palacpac, N., Ranford-Cartwright, L., Sawai, H., Sakihama, N., Horibe, S., Ohmae, H., Nakamura, M., Ferreira, M. U., Escalante, A. A., Prugnolle, F., Björkman, A., Färnert, A., Akira Kaneko, A.,  Horii, T., Manica, A., Kishino, H., and Balloux, F.  (2010). Plasmodium falciparum accompanied the human expansion out of Africa. Current Biology. 20: 1283-1289.

Sawai, H.,  Otani, H.,  Arisue, N.,  Palacpac, N., de Oliveira Martins, L., Pathirana, S., Handunnetti, S., Kawai, S., Kishino, H., Horii, T., and Tanabe, K. (2010). Lineage-specific positive selection at the merozoite surface protein 1 (msp1) locus of Plasmodium vivax and related simian malaria parasites. BMC Evolutionary Biology. 10: 52.

Miyashita, S. and Kishino, H. (2010). Estimation of the size of genetic bottlenecks in cell-to-cell movement of Soil-borne wheat mosaic virus (SBWMV) and the possible role of the bottlenecks in speeding up selection on variation in trans-acting genes or elements. Journal of Virology. 84: 1828-1837.

de Oliveira Martins, L. and Kishino, H. (2010). Distribution of distances between topologies and its effect on detection of phylogenetic recombination. Annals of the Institute of Statistical Mathematics. 62: 145-159.

Nishiyama, T., Notohara, M., Sumi, S., Takami, S., and Kishino, H. (2009). Major contribution of dominant inheritance to autism spectrum disorder (ASD) in populationbased families. Journal of Human Genetics. 54: 721-726.

Koyano, H. and Kishino, H. (2009). Observation subarea decision and population density estimation by space scale-invariance. J. Japanese Statistical Society. 39: 77-88.

Li, Z-W., Li, X., Yu, Q-Y., Xiang, Z-H., Kishino, H., and Zhang, Z. (2009). The small heat shock protein (sHSP) genes in the silkworm, Bombyx mori, and comparative analysis with other insect sHSP genes. BMC Evolutionary Biology.  9: 215.

Seo, T.-K. and Kishino, H. (2009). Statistical comparison of nucleotide-, amino-acid-, and codon-substitution models for the evolutionary analysis of protein-coding sequences. Systematic Biology. 58: 199-210.

Choi, S. C., Stone, E. A., Kishino, H., and Thorne, J. L. (2009). Estimates of natural selection due to protein tertiary structure inform the ancestry of biallelic loci. Gene. 441: 45-52.

Kitada, S., Shishidou, H., Sugaya, T., Kitakado, T., Hamasaki, K., and Kishino, H. (2009). Genetic effects of long-term stock enhancement programs. Aquaculture. 290: 69-79.

Kitazoe, Y., Kishino, H., Hasegawa, M., Nakajima, N., Thorne, J. L., and Tanaka, M. (2008). Adaptive threonine increase in transmembrane regions of mitochondrial proteins in higher primates. PLoS ONE. 3 (10): e3343.

O’Loughlin, S. M., Okabayashi, T., Honda, M., Kitazoe, Y., Kishino, H., Somboon, P., Sochantha, T., Nambanya, S., Saikia, P. K., Dev, V., and Walton, C. (2008). Complex population history of two forest-dependent Anopheles dirus mosquito species in Southeast Asia suggests the influence of Pleistocene climate change. Journal of Evolutionary Biology. 21: 1555-1569.

Kawaoka. S., Hayashi, N., Katsuma, S., Kishino, H., Kohara, Y., Mita, K., and Shimada, T. (2008). Bombyx small RNAs: Genomic defense system against transposons in the silkworm, Bombyx mori. Insect Biochem. Mol. Biol. 38: 1058-1065.

de Oliveira Martins, L., Leal, É. and Kishino, H. (2008). Phylogenetic detection of recombination with a Bayesian prior on the distance between trees. PLoS ONE. 3 (7): e2651.

Seo, T.-K. and Kishino, H. (2008). Synonymous substitutions substantially improve evolutionary inference from highly diverged proteins. Systematic Biology. 57: 367-377.

Kitada, S., Kitakado, T., and Kishino, H. (2007). Empirical Bayes inference of pairwise FST and its distribution in the genome. Genetics. 177: 861-873.

Tanabe, K., Escalante, A., Sakihama, N., Honda, M., Arisue, N., Horii, T., Culleton, R., Hayakawa, T., Hashimoto, T., Longacre, S., Pathirana, S., Handunnetti, S., and Kishino, H. (2007). Recent independent evolution of msp1 polymorphism in Plasmodium vivax and related simian malaria parasites. Molecular & Biochemical Parasitology. 156: 74-79.

Choi, S. C., Hobolth, A., Robinson, D. M., Kishino, H., and Thorne, J. L. (2007). Quantifying the impact of protein tertiary structure on molecular evolution. Molecular Biology and Evolution. 24: 1769-1782.

Thorne, J. L., Choi, S. C., Yu, J., Higgs, P. G., and Kishino, H. (2007). Population genetics without intraspecific data. Molecular Biology and Evolution. 24: 1667-1677.

Watabe,T., Kishino, H., Martins, L. O., and Kitazoe, Y. (2007). A likelihood-based index of protein-protein binding affinities with application to influenza HA escape from antibodies. Molecular Biology and Evolution. 24: 1627-1638.

Kitazoe, Y., Kishino, H., Waddell, P. J., Nakajima, N., Okabayashi, T., Watabe, T., and Okuhara, Y. (2007). Robust time estimation reconciles views of the antiquity of placental mammals. PLoS ONE. 1 (4): e384.

Waddell, P. J., Kishino, H., and Ota, R. (2007). Phylogenetic methodology for detecting protein interactions. Molecular Biology and Evolution. 24: 650-659.

Kitakado, T., Kitada, S., Obata, Y., and Kishino, H. (2006). Simultaneous estimation of mixing rates and genetic drift under successive sampling of genetic markers with application to the mud crab (Scylla paramamosain) in Japan. Genetics. 173: 2063-2072.

Kitakado, T., Kitada, S., Kishino, H., and Skaug, H. J. (2006). An integrated likelihood method for estimating genetic differentiation between populations. Genetics. 173: 2073-2082.

Kitada, S. and Kishino, H. (2006). Lessons learned from Japanese marine finfish stock enhancement programmes. Fisheries Research. 80: 101-112.

Okabayashi, T., Kitazoe, Y., Kishino, H., Watabe, T., Nakajima, N., Okuhara, Y., O'Loughlin, S., and Walton, C. (2006). Core set approach to reduce uncertainty of gene trees. BMC Evolutionary Biology. 6: 41.

Watabe, T., Kishino, H., Okuhara,Y. and Kitazoe, Y. (2006). Fold recognition of the HIV-1 V3 loop and flexibility of its crown structure during the course of adaptation to a host. Genetics. 172: 1385-1396.

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Seo, T.-K., Kishino, H., and Thorne, J. L. (2005). Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data. Proceedings of National Academy of Sciences, USA. 102: 4436-4441.

Kitazoe, Y., Kishino, H., Okabayashi, T., Watabe, T., Nakajima, N., Okuhara, Y., and Kurihara, Y. (2005). Multidimensional vector space representation for correlated evolution and molecular phylogeny. Molecular Biology and Evolution. 22: 704-715.

Zhang, Z., Luo, Z., Kishino, H., and Kearsey, M. J. (2005). Divergence pattern of duplicate genes in protein-protein interactions follows the power law. Molecular Biology and Evolution. 22: 501-505.

Saldamando C. I., Miyaguchi, S., Tatsuta, H., Kishino, H., Bridle, J. R., and R. K. Butlin. (2005). Inheritance of song and stridulatory peg number divergence between Chorthippus brunneus and C. jacobsi, two naturally hybridising grasshopper species (Orthoptera: Acrididae). Journal of Evolutionary Biology. 18: 703-712.

Kitada, S. and Kishino, H. (2004). Simultaneous detection of linkage disequilibrium and genetic differentiation of subdivided populations. Genetics. 167: 2003-2013.

Zhang, Z. and Kishino, H. (2004). Genomic background predicts the fate of duplicated genes:evidence from the yeast genome. Genetics. 166: 1995-1999.

Seo, T.-K., Kishino, H., and Thorne, J. L. (2004). Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences. Molecular Biology and Evolution. 21: 1201-1213.

Zhang, Z. and Kishino, H. (2004). Genomic background drives the divergence at synonymous sites of duplicate amylase genes in Drosophila. Molecular Biology and Evolution. 21 222-227.

Wiegmann, B. M., Yeates, D. K., Thorne, J. L., and Kishino, H. (2003). Time flies, a new molecular time-scale for brachyceran fly evolution without a clock. Systematic Biology. 52: 745-756.

Chujo, A., Zhang, Z., Kishino, H., Shimamoto, K., and Kyozuka, J. (2003). Partial conservation of LFY function between rice and Arabidopsis. Plant Cell Physiology. 44: 1311-1319.

Hasegawa, M., Thorne, J. L., and Kishino, H. (2003). Time scale of eutherian evolution estimated without assuming a constant rate of molecular evolution. Genes & Genetic Systems. 78: 267-283.

Zhang, Z., Inomata, N., Yamazaki, Y., and Kishino, H. (2003). Evolutionary history and mode of the amylase multigene family in Drosophila. Journal of Molecular Evolution. 57: 702-709.

Robinson, D. M., Jones, D. T., Kishino, H., Goldman, N., and Thorne, J. L. (2003). Protein evolution with dependence among codons due to tertiary structure. Molecular Biology and Evolution. 20: 1692-1704.

Waddell, P. J., Kishino, H., and Ota, R. (2002). Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees. Genome Informatics Series. 13: 82-92.

Thorne, J. L. and Kishino, H. (2002). Divergence time and evolutionary rate estimation with multilocus data. Systematic Biology. 51: 689-702.

Seo, T.-K., Thorne, J. L., Hasegawa, M., and Kishino, H. (2002). Estimation of effective population size of HIV-1 within a host: A pseudo-maximum likelihood approach. Genetics. 160: 1283-1293.

Seo, T.-K., Thorne, J. L., Hasegawa, M., and Kishino, H. (2002). A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times. Bioinformatics. 18: 115-123.

Ohizumi, H., Matsuishi, T., and Kishino, H. (2002). Winter sightings of humpback and Bryde's whales in tropical waters of western and central North Pacific. Aquatic Mammals. 28: 73-77.

Waddell, P. J. and Kishino, H., and Ota, R. (2001). A phylogenetic foundation for comparative mammalian genomics. Genome Informatics Series. 12: 141-155.

Nakamichi, R., Ukai, Y., and Kishino, H. (2001). Resolving of closely linked quantitative trait loci with a genetic algorithm. Genetics. 158: 463-475.

Kishino, H., Thorne, J. L., and Bruno, W. J. (2001). Performance of a divergence time estimation method under a probabilistic model of rate evolution. Molecular Biology and Evolution. 18: 352-361.

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Kishino, H. and Waddell, P. J. (2000). Correspondence analysis of genes and tissue types and finding genetic links from microarray data. Genome Informatics Series. 11: 83-95.

Waddell, P. J. and Kishino, H. (2000). Cluster inference methods and graphical models evaluated on NCI60 microarray gene expression data. Genome Informatics Series. 11: 129-140.

Waddell, P. J., Kishino, H., and Ota, R. (2000). Rapid evaluation of the phylogenetic congruence of sequence data using likelihood ratio tests. Molecular Biology and Evolution. 17: 1988-1992.

Kitada, S., Hayashi, T. and Kishino, H. (2000). Empirical Bayes procedure for estimating genetic distance between populations and effective population size. Genetics. 156: 2063-2079.

Bar-Hen, A. and Kishino, H. (2000). Comparing the likelihood functions of phylogenetic trees. Annals of the Institute of Statistical Mathematics. 52: 43-56.

Ota, R., Waddell, P. J., Hasegawa, M., Shimodaira, H. and Kishino, H. (2000). Appropriate likelihood ratio tests and marginal distributions for evolutionary tree models with constraints on parameters. Molecular Biology and Evolution. 17: 798-803.

Yamashita,H., Kishino, H., Hanyu, K., Hayashi, C. and Abe, K. (2000). Circulation indices: New tools for analyzing the structure of material cascades. Resources, Conservation and Recycling. 28: 85-104.

Hanyu, K., Kishino, H., Yamashita, H. and Hayashi, C. (2000). Paper recycling and purchasing: a case of toilet paper in Japan Resources, Conservation and Recycling. 30: 177-199.

Kishino, H., Thorne, J. L. and Bar-Hen, A. (1999). Statistical models of molecular evolution and their comparison. 1998 Proceedings of the Business and Economic Statistical Section, American Statistical Association.: 21-30.

Kishino, H., Hanyu, K., Yamashita, M. and Hayashi, C. (1999). Recycling and consumption in Germany and Japan: A case of toilet paper. Resources, Conservation and Recycling. 26: 189-215.

Pastene, L. A., Gotoh, M. and Kishino, H. (1999). An estimate of mixing proportion of `J' and `O' stocks minke whales in sub-area 11 based on mitochondrial DNA haplotype data. Report of the International Whaling Commission, 48: 471-474.

Kishino, H. and Bar-Hen, A. (1998). Maximum likelihood procedure adapted to sampling schemes. Journal of Statistical Planning and Inference. 70: 277-286.

Kishino, H., Hanyu, K., Yamashita, H. and Hayashi, C. (1998). Correspondence analysis of paper recycling society: Consumers and paper makers in Japan. Resources, Conservation and Recycling. 23: 193-208.

Thorne, J. L., Kishino, H. and Painter, I. S. (1998). Estimating the rate of evolution of the rate of molecular evolution. Molecular Biology and Evolution. 15: 1647-1657.

Best, P. and Kishino, H. (1998). Estimating natural mortality rate in female southern right whales Eubalaena australis. Marine Mammal Science. 14: 738-749.

Yoshida, H., Shirakihara, K., Kishino, H. and Takemura, A. (1998). Finless porpoise abundance in Omura Bay, Japan: estimation from aerial sighting surveys. Journal of Wildlife Management, 62: 286-291.

Yoshida, H., Shirakihara, K., Kishino, H. and Shirakihara, M. (1997). A population size estimate of the finless porpoise, Neophocaena phocaenoides, from aerial sighting surveys in Ariake Sound and Tachibana Bay, Japan. Researches in Population Ecology, 39: 239-247.

Chow, S. and Kishino, H. (1996). Phylogenetic relationships between tuna species of genus Thunnus (Scombridae: Teleostei): Inconsistent implications from morphology, nuclear and mitochondrial genomes. Journal of Molecular Evolution, 41: 741-748.

Punt, A. E., Butterworth, D. S., Wada, S. and Kishino, H. (1995). On the use of allele frequency data to provide estimates of the mixing between the various North Pacific minke whale stocks. Report of the International Whaling Commission, 45: 293-302.

Hasegawa, M and Kishino, H. (1994). Acuracies of the simple methods for estimating the bootstrap probability of a maximum-likelihood tree. Molecular Biology and Evolution, 11: 142-145.

Kitada, S. Hiramatsu, K. and Kishino, H. (1994). Estimating mortality rates from tag recoveries: incorporating overdispersion, correlation and change-points. ICES J. Marine Science, 51: 241-251.

Felsenstein, J. and Kishino, H. (1993). Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull. Systematic Biology, 42(2): 193-200.

Matsuishi, T., Wada, T., Matsumiya, Y. and Kishino, H. (1993). Optimal school selection and abundance index in purse seine fishery. Nippon Suisan Gakkaishi, 59: 273-278.

Thorne, J. L. and Kishino, H. (1992). Freeing phylogenies from artifacts of alignment. Molecular Biology and Evolution, 9: 1148-1162.

Thorne, J. L., Kishino, H. and Felsenstein, J. (1992). Inching toward reality: an improved likelihood model of sequence evolution. Journal of Molecular Evolution, 34: 3-16.

Kitada, S., Taga, Y. and Kishino, H. (1992). Effectiveness of a stock enhancement program evaluated by a two-stage sampling survey of commercial landings. Canadian Journal of Fisheries and Aquatic Sciences, 49: 1573-1582.

Kishino, H., Kato, H., Kasamatsu, F. and Fujise, Y. (1991). Detection of heterogeneity and estimation of population characteristics from the field survey data: 1987/88 Japanese feasibility study of southern hemisphere minke whales. Annals of the Institute of Statistical Mathematics, 43: 435-453.

Thorne, J. L., Kishino, H. and Felsenstein, J. (1991). An evolutionary model for maximum likelihood alignment of DNA sequences. Journal of Molecular Evolution, 33: 114-124.

Hasegawa, M., Kishino, H. and Saitou, N. (1991). On the maximum likelihood method in molecular phylogenetics. Journal of Molecular Evolution, 32: 443-445.

Iwabe, N., Kishino, H., Hasegawa, M. and Miyata, T. (1991). Evolution of RNA polymerases and branching patterns of the three major groups of archaebacteria. Journal of Molecular Evolution, 32: 70-78.

Kato, H., Fujise, Y. and Kishino, H. (1991). Age structure and segregation of southern minke whales by the data obtained during Japanese research take in 1988/89. Report of the International Whaling Commission, 41: 287-292.

Kasamatsu, F., Kishino, H. and Taga, Y. (1991). Estimation of southern minke whale abundance and school size composition based on 1988/89 Japanese feasibility study data. Report of the International Whaling Commission, 41: 293-302.

Iwabe, N., Kuma, K.-I., Kishino, H., Hasegawa, M. and Miyata, T. (1990). Compartmentalized isozyme genes and the origin of introns. Journal of Molecular Evolution, 31: 205-210.

Kishino, H., Miyata, T. and Hasegawa, M. (1990). Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. Journal of Molecular Evolution, 31: 151-160.

Hasegawa, M., Kishino, H., Hayasaka, K. and Horai, S. (1990). Mitochondrial DNA evolution in primates: Transition rate has been extremely low in the Lemur. Journal of Molecular Evolution, 31: 113-121.

Kishino, H. and Hasegawa, M. (1990). Converting distance to time: Application to human evolution. In Methods in Enzymology 183 (Doolittle R. F. ed.): 550-570.

Kasamatsu, F., Kishino, H. and Hiroyama, H. (1990). Estimation of the number of minke whale (Balaenoptera acutorostrata) schools and individuals based on the 1987/88 Japanese feasibility study data. Report of the International Whaling Commission, 40: 239-247.

Kato, H., Kishino, H. and Fujise, Y. (1990). Some analyses on age composition and segregation of southern minke whales using samples obtained from the Japanese feasibility study in 1987/88. Report of the International Whaling Commission, 40: 249-256.

Kishino, H. and Hasegawa, M. (1989). Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data. Journal of Molecular Evolution, 29: 170-179.

Hasegawa, M. and Kishino, H. (1989). Confidence limits on the maximum likelihood estimate of the hominoid tree from mitochondrial DNA sequences. Evolution, 43: 672-677.

Kishino, H., Kasamatsu, F. and Toda, T. (1988). On double line transect method. Report of the International Whaling Commission, 38: 273-279.

Kishino, H. and Kasamatsu, F. (1987). Comparison of the closing and passing mode procedures used in sighting surveys. Report of the International Whaling Commission, 37: 253-258.

Hasegawa, M. Kishino, H. and Yano, T. (1987). Man's place in Hominoidea as inferred from molecular clocks of DNA. Journal of Molecular Evolution, 26: 132-147.

Kishino, H. (1987). Variance of sightings in the survey of patchily distributed objects. Annals of the Institute of Statistical Mathematics, 39: 275-287.

Kishino, H. (1986). On parallel ship experiments and the line transect method. Report of the International Whaling Commission, 36: 491-495.

Hasegawa, M., Kishino, H. and Yano, T. (1985). Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution, 22: 160-174.

Hasegawa, M., Kishino, H. and Yano, T. (1984). A new molecular clock of mitochondrial DNA and the evolution of Hominoids. Proceedings of the Japan Academy, 60B(4): 95-98.

Kishino, H. (1983). The least square estimation of the transition probabilities of binary processes on the basis of sample paths. Annals of the Institute of Statistical Mathematics, 35: 425-438.

Kishino, H. (1983). On the separation principle of stochastic control. Journal of the Faculty of Science. The University of Tokyo, 30: 111-137.

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