Atagi Y., Onogi A., Kinukawa, M., Ogino A., Kurogi K., Uchiyama K., Yasumori, T., Adachi K., Togashi K., Iwata H. (2017). Genetic analysis of semen production traits of Japanese Black and Holstein bulls: genome-wide markers-based estimation of genetic parameters and environmental effect trends. Journal of Animal Science. doi:10.2527/jas2016.1186.

Manickavelu A., Hattori T., Yamaoka S., Yoshimura K., Kondou Y., Onogi A., Matsui M., Iwata H., Ban T. (2017). Genetic nature of elemental contents in wheat grains and Its genomic prediction: toward the effective use of wheat landraces from Afghanistan.  PLoS ONE. doi:10.1371/journal.pone.0169416.

Watanabe K., Guo W., Arai K., Takanashi H., Kajiya-Kanegae H., Kobayashi M., Yano K., Tokunaga T., Fujiwara T., Tsutsumi N. and Iwata H. (2017). High-throughput phenotyping of sorghum plant height using an unmanned aerial vehicle and its application to genomic prediction modeling. Front. Plant. Sci. 8:421. doi: 10.3389/fpls.2017.00421


Yabe, S., Yamasaki, M., Ebana, K., Hayashi, T., and Iwata, H. (2016) Island-model genomic selection for long-term genetic improvement of autogamous crops. PLoS ONE 11(4) : e0153945.

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. accepted.

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. accepted.

Onogi, A., Ideta, O., Yoshioka, T., Ebana, K., Yamasaki, M., & Iwata, H. (2016). Uncovering a Nuisance Influence of a Phenological Trait of Plants Using a Nonlinear Structural Equation: Application to Days to Heading and Culm Length in Asian Cultivated Rice (Oryza Sativa L.). PloS ONE11(2), e0148609

Onogi, A and Iwata, H 2016 VIGoR: Variational Bayesian Inference for Genome-Wide Regression. Journal of Open Research Software, 4: e11, DOI:

Onogi, A., Watanabe, M., Mochizuki, T., Hayashi, T., Nakagawa, H., Hasegawa, T., & Iwata, H. (2016). Toward integration of genomic selection with crop modelling: the development of an integrated approach to predicting rice heading dates. Theoretical and Applied Genetics, doi:10.​1007/​s00122-016-2667-5

Yamamoto, E., Matsunaga, H., Onogi, A., Kajiya-Kanegae, H., Minamikawa, M., Suzuki, A., Shirasawa, K., Hirakawa, H., Nunome, T., Yamaguchi, H., Miyatake, K., Ohyama, A., Iwata, H., & Fukuoka, H. (2016). A simulation-based breeding design that uses whole-genome prediction in tomato. Scientific reports6, 19454 doi:10.1038/srep19454

Hori, T., Montcho, D., Agbangla, C., Ebana, K., Futakuchi, K., & Iwata, H. (2016). Multi-task Gaussian process for imputing missing data in multi-trait and multi-environment trials. Theoretical and Applied Genetics, 1-15.


Bondel, M., Onogi, A., Iwata, H., Ueda, N. (2015) A Ranking Approach to Genomic Selection. PLoS ONE 10(6): e0128570. doi:10.1371/journal.pone.0128570.

Chen, H. and Kishino, H. (2015). Hypothesis testing of inclusion of the tolerance interval for the assessment of food safety. PLoS ONE10(10): e0141117.

Chen, H. and Kishino, H. (2015). Global pattern of phylogenetic species composition of shark and its conservation priority. Ecology and Evolution5(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.

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

Iwata H, Ebana K, Uga Y, Hayashi T (2015) Genomic prediction of biological shape: elliptic Fourier analysis and kernel partial least squares (PLS) regression applied to grain shape prediction in rice (Oryza sativa L.). PLoS ONE 10(3): e0120610

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. 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.

Onogi A, Ideta O, Inoshita Y, Ebana K, Yoshioka T, Yamasaki M, Iwata H (2015) Exploring the areas of applicability of whole-genome prediction methods for Asian rice (Oryza sativa L.). Theoretical and Applied Genetics 128(1): 41-53.

Onogi, A., Ogino, A., Komatsu, T., Shoji, N., Shimizu, K., Kurogi, K., Yasumori, T., Togashi, K., and Iwata, H.  (2015) Whole-genome prediction of fatty acid composition in meat of Japanese Black cattle. Animal Genetics, DOI: 10. 1111/age. 12300.


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.

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.

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.

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.

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.

Onogi A, Ogino A, Komatsu T, Shoji N, Simizu K, Kurogi K, Yasumori T, Togashi K, Iwata H (2014) Genomic prediction in Japanese Black cattle: Application of a single-step approach to beef cattle. Journal of Animal Science 92: 1931-1938.

Yabe S, Hara T, Ueno M, Enoki H, Kimura T, Nishimura S, Yasui Y, Ohsawa R, Iwata H (2014) Rapid genotyping with DNA micro- arrays for high-density linkage mapping and QTL mapping in common buckwheat (Fagophyrum esculentum Moench), Breeding Science 64: 291-299.

Yabe S, Ohsawa R, Iwata H (2014) Genomic selection for the traits expressed after pollination in allogamous plants. Crop Science 54:1-10.

Yamamoto E, Iwata H, Tanabata T, Mozobuchi R, Yonemaru J, Yamamoto T, Yano M (2014) Effect of advanced intercrossing on genome structure and on the power to detect linked quantitative trait loci in a multi-parent population: a simulation study in rice. BMC Genetics 15: 50


Babil P, Kondo S, Iwata H, Kushikawa S, Shiwachi H (2013) Intra-Specific Ploidy Variations in Cultivated Chinese Yam (Dioscorea polystachya Turcz.). Trop. Agr. Develop. 57: 101-107

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.

Hayashi T, Iwata H (2013) A Bayesian method and its variational approximation for prediction of genomic breeding values in multiple traits. BMC Bioinformatics 14: 31

Ishii K, Yamanari M, Iwata H, Yasuno Y, Oshika T (2013) Relationship between changes in crystalline lens shape and axial elongation in young children. Invest Ophthalmol Vis Sci. 54: 771-777

Iwata H, Hayashi T, Terakami S, Takada N, Saito T, Yamamoto T (2013) Genomic prediction of trait segregation in a progeny population: a case study of Japanese pear (Pyrus pyrifolia). BMC Genet. 14: 81

Iwata H, Hayashi T, Terakami S, Takada N, Sawamura Y, Yamamoto T (2013) Potential assessment of genome-wide association study and genomic selection in Japanese pear Pyrus pyrifolia. Breed Sci. 63: 125-140

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.

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.

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.

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E36.

Uchiyama K, Iwata H, Moriguchi Y, Ujino-Ihara T, Ueno S, Taguchi Y, Tsubomura M, Mishima K, Iki T, Watanabe A, Ftamura N, Shinohara K, Tsumura Y (2013) Genome wide association mapping for wood property and amounts of male strobili in Cryptomeria japonica. PLoS ONE 8: e79866

Yabe S, Ohsawa R, Iwata H (2013) Potential of genomic selection for mass selection breeding in annual allogamous crops . Crop Sci. 53: 95-105

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.