Lisa Sakamoto, Hiromi Kajiya-Kanegae, Koji Noshita, Hideki Takanashi, Masaaki Kobayashi, Toru Kudo, Kentaro Yano, Tsuyoshi Tokunaga, Nobuhiro Tsutsumi and Hiroyoshi Iwata, "Comparison of shape quantification methods for genomic prediction, and genome-wide association study of sorghum seed morphology", PLoS ONE 14 (11): e0224695, 2020. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0224695

Shiryu Kirie, Hideo Iwasaki, Koji Noshita and Hiroyoshi Iwata, "A theoretical morphological model for quantitative description of the three-dimensional floral morphology in water lily (Nymphaea)", PLoS ONE 15(10): e0239781, 2020. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0239781

Yusuke Toda, Hitomi Wakatsuki, Toru Aoike, Hiromi Kajiya-Kanegae, Masanori Yamasaki, Takuma Yoshioka, Kaworu Ebana, Takeshi Hayashi, Hiroshi Nakagawa, Toshihiro Hasegawa and Hiroyoshi Iwata. “Predicting biomass of rice with intermediate traits: modeling method combining crop growth models and genomic prediction models.” PLoS ONE 15(6): e0233951, 2020. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0233951

Kosuke Hamazaki, Hiromi Kajiya-Kanegae, Masanori Yamasaki, Kaworu Ebana, Shiori Yabe, Hiroshi Nakagawa and Hiroyoshi Iwata, “Choosing the optimal population for a genome-wide association study: A simulation using whole-genome sequences from rice”, The Plant Genome, 2020; 13:e20005. [bioRxiv: 10.1101/798850]

Kosuke Hamazaki and Hiroyoshi Iwata, “RAINBOW: Haplotype-based genome-wide association study using a novel SNP-set method”, PLOS Computational Biology, 16(2): e1007663, 2020. [bioRxiv: 10.1101/612028]


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.

Tung Dang and Hirohisa Kishino. (2019). Stochastic variational inference for Bayesian phylogenetics: A case of CAT model. Molecular Biology and Evolution, Volume 36, Issue 4, April 2019, Pages 825–833.


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.

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.

Tanaka, R. and Iwata, H. (2018). Bayesian optimization for genomic selection: a method for discovering the best genotype among a large number of candidates. Theor. Appl. Genet. 131: 93–105.

Togashi, K., Adachi, K., Yasumori, T., Kurogi, K., Nozaki, T., Onogi, A., Atagi, Y., and Takahashi, T. (2018). Effects of selection index coefficients that ignore reliability on economic weights and selection responses during practical selection. Asian-Australasian J. Anim. Sci. 31: 19–25.

Yabe, S., Hara, T., Ueno, M., Enoki, H., Kimura, T., Nishimura, S., Yasui, Y., Ohsawa, R., and Iwata, H. (2018). Potential of Genomic Selection in Mass Selection Breeding of an Allogamous Crop: An Empirical Study to Increase Yield of Common Buckwheat. Front. Plant Sci. 9: 276.

Yabe S, Iwata H, Jannink JL (2018) Impact of mislabeling on genomic selection in cassava breeding. doi: 10.2135/cropsci2017.07.0442


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

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.

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.

Onogi, A., Sasaki, S., Kobayashi, M., Ogino, A., Nozaki, T., Kurogi, K., Yasumori, T., Togashi, K., and Iwata, H. (2017). A genetic analysis of meat compositions in Japanese Black cattle: Genetic parameters and sex influence. J. Anim. Breed. Genet. 134: 373–382.

Yabe, S., Iwata, H., and Jannink, J.-L. (2017). A Simple Package to Script and Simulate Breeding Schemes: The Breeding Scheme Language. Crop Sci. 57: 1347.

Moriya S, Kunihisa M, Okada K, Shimizu T, Honda C, Yamamoto T, Muranty H, Denanc C, Katayose Y, Iwata H, Abe K(2017). Allelic composition of MdMYB1 drives red skin color intensity in apple (Malus 3 domestica Borkh.) and its application to breeding. Euphytica 213.

Ohyama, A., Shirasawa, K., Matsunaga, H., Negoro, S., Miyatake, K., Yamaguchi, H., Nunome, T., Iwata, H., Fukuoka, H., and Hayashi, T. (2017). Bayesian QTL mapping using genome-wide SSR markers and segregating population derived from a cross of two commercial F1 hybrids of tomato. Theor. Appl. Genet. 130: 1601–1616.

Yamamoto, E., Matsunaga, H., Onogi, A., Ohyama, A., Miyatake, K., Yamaguchi, H., Nunome, T., Iwata, H., and Fukuoka, H. (2017). Efficiency of genomic selection for breeding population design and phenotype prediction in tomato. Heredity (Edinb). 118: 202–209.

Atagi, Y., Onogi, A., Kinukawa, M., Ogino, A., Kurogi, K., Uchiyama, K., Yasumori, T., Adachi, K., Togashi, K., and Iwata, H. (2017). Genetic analysis of semen production traits of Japanese Black and Holstein bulls: genome-wide marker-based estimation of genetic parameters and environmental effect trends1. J. Anim. Sci. 95: 1900–1912.

Okada, S., Suehiro, M., Ebana, K., Hori, K., Onogi, A., Iwata, H., and Yamasaki, M. (2017). Genetic dissection of grain traits in Yamadanishiki, an excellent sake-brewing rice cultivar. Theor. Appl. Genet. 130: 2567–2585.

Okada S et al. (2017) Identification of QTLs for rice grain size using a novel set of chromosomal segment substitution lines derived from Yamadanishiki in the genetic background of Koshihikari. Breeding Science

Goto, S., Kajiya-Kanegae, H., Ishizuka, W., Kitamura, K., Ueno, S., Hisamoto, Y., Kudoh, H., Yasugi, M., Nagano, A.J., and Iwata, H. (2017). Genetic mapping of local adaptation along the altitudinal gradient in Abies sachalinensis. Tree Genet. Genomes 13: 104.

Manickavelu, A., Hattori, T., Yamaoka, S., Yoshimura, K., Kondou, Y., Onogi, A., Matsui, M., Iwata, H., and 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 12: e0169416.

Minamikawa MF., Nonaka K., Kaminuma E., Kajiya-Kanegae H., Onogi A., Goto S., Yoshioka T., Imai A., Hamada H., Hayashi T., Matsumoto S., Katayose Y., Toyoda A., Fujiyama A., Nakamura Y., Shimizu T., Iwata H. (2017). Genome-wide association study and genomic prediction in citrus: Potential of genomics-assisted breeding for fruit quality traits. Sci. Rep. 7: 4721.

Kobayashi M., Ohyanagi H., Takanashi H., Asano S., Kudo T., Kajiya-Kanegae H., Nagano AJ., Tainaka H., Tokunaga T., Sazuka T., Iwata H., Tsutsumi N., Yano K. (2017). Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data. DNA Res. 24: 397–405.

Moriya S, Kunihisa M, Okada K, Iwanami H, Iwata H, Minamikawa M, Katayose Y, Matsumoto T, Mori S, Sasaki H, Matsumoto T, Nishitani C, Terakami S, Yamamoto T, Abe K (2017). Identification of QTLs for Flesh Mealiness in Apple (Malus × domestica Borkh.). Hortic. J. 86: 159–170.

Onogi, A., Shirai, K., and Amano, T. (2017). Investigation of genetic diversity and inbreeding in a Japanese native horse breed for suggestions on its conservation. Anim. Sci. J. 88: 1902–1910.


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. http://dx.doi.org/10.1371/journal.pone.0153945

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 ONE, 11(2), e0148609 http://dx.doi.org/10.1371/journal.pone.0148609

Onogi, A and Iwata, H 2016 VIGoR: Variational Bayesian Inference for Genome-Wide Regression. Journal of Open Research Software, 4: e11, DOI: http://dx.doi.org/10.5334/jors.80

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 reports, 6, 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 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.

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.