Kishino, H., Nakamichi, R.,
and Kitada, S. (2023). Genetic adaptations in the population history of Arabidopsis
thaliana. G3: Genes|Genomes|Genetics. 13:
jkad218.
Yang, Y., Xu, T., Conant, G.,
Kishino, H., Thorne, J. L., Ji, X. (2023). Interlocus
gene conversion, natural selection, and paralog homogenization. Molecular
Biology and Evolution. 40: msad198.
Zhao, X-W., Wu, J., Kishino,
H., and Chen, L. (2022). Massive loss of transcription factors promotes initial
diversification of placental mammals. International Journal of Molecular
Sciences. 23:9720.
Wu, J., Yonezawa, T., and
Kishino, H. (2022). Molecular evolutionary rate predicts intraspecific genetic
polymorphism and species-specific selection. Genes. 13:708.
Nakamichi, R., Kitada, S.,
and Kishino, H. (2022). Exploratory analysis of multi-trait coadaptations
in the light of population history. Ecology and Evolution. 12:
e8755.
Dang, T. T. and Kishino, H.
(2022). Forward
variable selection improves the power of random forest for high-dimensional
microbiome data. Journal of Cancer Science and Clinical Therapeutics. 6: 87-105.
Kitada, S. and Kishino, H.
(2022). An R script for unbiased estimation of stocking effectiveness using a
two-stage sampling strategy based on fishery landings. Fisheries Research.
250: 106266.
Kitada, S. and Kishino, H.
(2021). Population structure of chum salmon and selection on the markers
collected for stock identification. Ecology and Evolution. 11:
13972-13985.
Kitada, S., Nakamichi, R.,
and Kishino, H. (2021). Understanding population structure in an evolutionary
context: population-specific FST and pairwise FST.
G3: Genes|Genomes|Genetics. 11 (11) jkab316.
Wu, J., Yonezawa, T., and
Kishino, H. (2021). Evolution of reproductive life history in mammals and the
associated change of functional constraints. Genes. 12: 740.
Taniguchi, S., Bertl, J., Futschik, A., Kishino,
H., and Okazaki, T. (2021). Waves out of the Korean Peninsula and inter- and
intra-species replacements in freshwater fishes in Japan. Genes. 12:
303.
Zhao, X-W.
and Kishino, H. (2020). Multiple isolated transcription factors act as switches
and contribute to species uniqueness. Genes. 11: 1148.
Kitazoe, Y., Kishino, H., Tanisawa,
T., Udaka, K. and Tanaka, M. (2019). Renormalized
basal metabolic rate describes human aging process and longevity. Aging Cell.
18:e12968.
Dang, T. T. and Kishino, H. (2019).
Stochastic variational inference for Bayesian phylogenetics: A case of CAT
model. Molecular Biology and Evolution.
36: 825-833.
Kitada, S., Nakajima, K., Hamasaki, K., Shishidou, H., Waples, R., and Kishino, H. (2019). Rigorous
monitoring of a large-scale marine stock enhancement program demonstrates the
need for comprehensive management of fisheries and nursery habitat. Scientific Reports. 9: 5290.
Mariadassou, M, Bar-Hen, A. and Kishino, H. (2019).
Tree Evaluation and Robustness Testing. In Encyclopedia
of Bioinformatics and Computational Biology (edited by Ranganathan, S.,
Nakai, K., Schönbach,
C., and Gribskov, M.). Pp. 736-745. Academic Press.
Suwanmontri,P., Kamoshita,A.,
Jongdee, B., Fukai, S., and Kishino, H. (2018).
Comparative analysis of farmers engaged in participatory research to cope with
climate change versus non-participants in Northeast Thailand. Plant Production Science. 21: 287-301.
Li, S., Ajimura,
M., Chen, Z., Liu, J., Chen, E., Guo, H., Tadapatri,
V., Reddy, C. G., Zhang, J., Kishino, H., Abe, H., Xia, Q., Arunkumar, K. P.,
and Mita, K. (2018). A new approach for comprehensively describing
heterogametic sex chromosomes. DNA
Research. 25: 375-382.
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. 17: 1210-1222.
Cheng, T, Wu, J., Wu, Y., Chilukuri, R., Huang, L., Yamamoto, K.,
Feng, L., Li, W., Chen, Z., Guo, H., Liu, J., Li, S., Wang, X., Peng, L., Liu,
D., Guo, Y., Fu, B., Li, Z., Liu, C., Chen, Y., Tomar, A., Hilliou,
F., Montagne, N., Jacquin-Joly, E., d'Alencon, E.,
Seth, R., Bhatnagar, R., Jouraku, A., Shiotsuki, T., Kadono-Okuda, K., Promboon, A., Smagghe, G.,
Arunkumar, K., Kishino, H., Goldsmith, M., Feng, Q., Xia, Q., and Mita, K.
(2017). Genomic adaptation to polyphagy and
insecticides in a major East Asian noctuid pest. Nature Ecology and Evolution. 1:
1747-1756.
Wu, J., Yonezawa, T., and Kishino, H.
(2017). Rates of molecular evolution suggest natural history of life history
traits and a post-K-Pg nocturnal bottleneck of Placentals. Current Biology. 27:
3025-3033.
Kitada, S., Yoshikai,
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.
Guo, H., Cheng, T., Chen, Z., Jiang, L.,
Guo, Y., Liu, J., Li, S., Taniai, K., Asaoka, K., Kadono-Okuda, K.,
Arunkumar, K. P., Wu, J., Kishino, H., Zhang, H., Seth, R. K., Gopinathan, K.
P., Montagne, N., Jacquin-Joly, E., Goldsmith, M. R., Xia, Q., and Mita, K.
(2017). Expression map of a complete set of gustatory receptor genes in
chemosensory organs of Bombyx mori. Insect Biochem.
Mol. Biol. 82: 74-82.
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. (2017). Phylogenomics
and morphology of extinct paleognaths reveal the
origin and evolution of the ratites. Current
Biology. 27: 68-77.
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. 21:
684-697.
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. 91: 209-215.
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.
Chen, H., Shao, K-T., and Kishino, H.
(2016). A
Bayesian hierarchical ANOVA model of stochastic seasonality for Diodon Holocanthus
in northern Taiwan. the Journal of Marine
Science and Technology. 24: 303-310.
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.
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: 337-345.
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.
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.
Thorne, J. L. and
Kishino, H. (2005). Estimation of divergence times from molecular sequence
data. In Statistical Methods in Molecular
Evolution (Nielsen, R. ed.). Springer-Verlag.
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.
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
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
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
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
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.
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
Kishino,
H. (1983). On the separation principle of stochastic control. Journal of the
Faculty of Science. The